• DNA is Not Like a Computer

    A pro-ID poster (I assume he’s pro-ID, he’s never actually said anything that supports ID), has made the following claim (here):

    Void, since computer science was one of my undergraduate degrees, I’m gonna do you a solid and answer your question. Genetic information is stored, retrieved, processed and translated by the cell just like a computer would treat digital information.

    Consider the following digital code:
    01001000011000010010000001001000
    01100001001000000100110101100001
    01100100011001010010000001111001
    01101111011101010010000001101100
    01101111011011110110101100100001

    If you take the time to translate the above binary code, you will have used the same intelligently designed information processing that cells have used for billions of years to turn a sequence of A,C,T & G into a protein. Here are the parallels and you’ll see that they are certainly not dissimilar.

    hard drive = DNA
    bits = nucleotides
    bytes = codons
    ASCII table = codon table
    letters = amino acids
    words = proteins

    One of these information processing systems was intelligently designed and the other one we use every day. Which one is which? It should be easy to see why some infer ID from biochemistry.

    This post talks about the old ID canard that DNA is like a computer or DNA is like computer code or DNA is like data on a hard drive. Whatever. Let’s dispense with this right now.

    First of all, argument by analogy always fails. Analogies are a teaching tool. They are for describing a difficult concept to someone who has no experience with that concept. By relating that concept to something that they already understand, then they can begin to see how that concept works.

    To a 5th grade student, I would make the analogy that DNA is like a blueprint. It tells the cells how to make proteins. I would never use that “DNA is like a blueprint” analogy in a discussion with anyone who had the least idea about what DNA actually is. That’s like (pun intended) going up to an automotive engineer and saying that cars are like horses and buggies, and that’s why your latest model is crap.

    It’s arguable that DNA is digital information. True, DNA is made of nucleotides (which are the important bit) attached to a common sugar backbone. Those four nucleotides could be described digitally using two bits[1]. Because of binary notation (like decimal notation, except with two possible values instead of ten), two bits can represent 4 things. In this case, the four DNA nucleotides: A, T, C, and G.

    So, if you see someone using this argument and describing DNA using 4 bits, then you are free to call them out on having zero knowledge of DNA or biochemistry. Here’s why.

    Yes, 4 bits covers the 4 nucleotides for DNA. But you need another bit to get include RNA, which, as we all know can act as a enzyme to change DNA. So, that’s pretty important.

    But DNA is a hella lot more detailed than that. We need to another bit to cover methylation. Basically, the molecule for the nucleotide gets changed and has a methyl group attached to it. That can have a variety of effects, including stopping other things from happening. So we have to consider that. In fact, there are over 100 known chemical changes that can occur to various nucleotides. Each one being either present or not, so we need 100 bits (minimum) to deal with those.

    The real trick in dealing with DNA as digital information is that DNA pieces aren’t taken in isolation. The entire gargantuan molecule that is a DNA chromatid interacts with itself and with other DNA strands. It folds around a histone molecule (most of the time) and certain portions of DNA are more likely to be in certain locations on those histone molecules. That can have an effect on how the DNA is copied, translated, and mutated. So, our digital model has to account for that. Oh, and there are multiple types of histone too.

    Then even the histones can have molecular attachments (at least ten or so) and that has an effect on the DNA as well. For example, acetylation (which is like methylation, but with an acetyl group) of certain histones can change the transcriptional competence. So, we have to consider that.

    Then there’s all kinds of other effects that can’t be taken in isolation. There are alleles that cause mutation in other alleles (and I just learned that today, how freaking awesome!). So, taken by itself, the nucleotides of an allele may be relatively simple to model digitally, but when combined, two stretches of DNA can have marked effects on each other.

    Then of course, we need to talk about the relative effects of various mutational effects on pieces of DNA. Some areas of DNA are much more prone to mutation than others. This is affected by everything I’ve mentioned about and much, much more.

    Any model of DNA that attempts to talk about the whole of DNA, but doesn’t include even a couple of these affects is just not going to work. Honestly, I wish that ID proponents would step up. Information technology is a growing field in biochemistry. It’s being used by several scientists to explore DNA. Not by ID proponents, which is odd, but other scientists.

    At this point, we’re into hundreds of bits just to describe a single nucleotide and possibly trillions or way more to describe their interactions. Honestly, I’m not even sure how to approach it. I’m not a programmer. I don’t even know if it could be hard coded like that. So much of the interaction depends on so many other things. A cell is not an isolated thing, even a single-celled organism has inputs and outputs into the environment.

    As far as I know. We can’t even model protein folding very well and DNA is orders of magnitude more complex.

    But the reason that I said DNA is arguably digital is that it responds to analog inputs. The amount of a hormone in the blood stream determines the DNA response. This is what causes everything from limbs to mouths to form. We have a head end and a butt end. Not because the head end is a digital 1 and the butt end is a digital 0, but because there is a gradient of hormone levels with is higher at the head end and slowly reduces until we get to the butt end.

    I’m going to borrow liberally from Doc Bill’s (most of what follows is an edited version of that) response on this subject too.

    Genetic information is in no way stored, retrieved, processed or translated by the cell like a computer would treat digital information. There’s no CPU, for example. The CPU stores basic operating instructions that tells what it can do, logically speaking. Things like AND, XOR, and other logic and calculation functions are inherit in the CPU. Not so much with the cell, which must create the things that work on the things to make the things. Similarly, there is no “data” vs. “instructions” in the cell. It can all be both.

    Cells and DNA don’t work in discrete steps (further removing the digital aspect). At any one time in a cell, hundreds (if not thousands) of alleles may be being read, copied, repaired, or changed. Dozens of mRNA strands are produced and being read simultaneously. Not the pseudo-simultaneous of a computer, which works so fast, we can’t perceive the steps, but actually at the same time (also so fast that we can’t perceive the steps). At two base pairs per second, it would take you 95 years to copy your DNA. Every cell in your body can do it in 8 hours.

    It gets worse. Computers run off of code. If someone argues that DNA is that computer code, then they don’t understand how DNA works.

    Make a change in a computer code and the whole thing likely crashes. Make a change in a DNA code and you might make it run better. The change probably won’t have any effect at all (what with non-coding regions and the resilient nature of our protein construction system). DNA can repair it’s code (sometimes). DNA can have code from completely different systems (viruses) inserted and will be perfectly fine, unless the virus kills the organism, but the DNA will work until the rest of the cell runs out of fuel.

    DNA can be massively rearranged and it can have no effect on the system. Chromosomes can combine (as they did in our ancestors after the chimpanzee line split off)  with no ill effects. Genes can be moved to different places on other chromosomes with no ill effects (as long as the whole thing got moved).

    Thanks Doc.

    I’ve been trying (via several iterations) to describe what a computer that acted like a cell would be like and I just can’t. It makes no sense in computer language. This is my best attempt.

    There is a hard drive. There’s no CPU. There’s no files. No images, no apps, no data, no executables. There’s just bits on the drive. Now some of those bits can cause the computer to do something. But they only react to certain inputs. If the computer gets too hot, then some bits of the drive will be read by other bits of the drive and produce bits that do other things to other bits of the drive. This isn’t random, because every bit is affected (or not) by it’s position on the drive, what other bits are around it and how the drive is built (occasionally it changes shape). Sometimes, entire chunks of bits are moved around for no apparent reason. Sometimes, the drive copies itself into another drive (which it makes the new drive itself).

    See how weird this is?!!

    So, while information technology tools can be useful in dealing with DNA… DNA is not like a computer.

    _____________________________________
    [1] A bit is the basic unit of information in computing and digital communications. A bit can have only one of two values, usually “on” or “off” or “1” or “0”.

     

    Category: CreationismScienceSkepticism

    Tags:

    Article by: Smilodon's Retreat

    • Void Walker

      Smilodon: 34. Rex Jerkgood: -239.

      Very illuminating piece, Smilodon. Thanks.

      • RexTugwell

        That’s it, Void. Stay on the sidelines where you belong as cheerleader in your short skirt and pompoms, jumping up and down, squealing in delight as you shriek “SMILEY, SMILEY, HE’S OUR MAN*. IF HE CAN’T DO IT NO ONE CAN!!!

        YAAAAAAAAAAAH!!!

        * I use that term loosely as I’ve see the podcast and wonder if he got an extra dose of estrogen in utero.

        • SmilodonsRetreat

          Reduced to insults now. Whatever. Keep squawking.

        • Void Walker

          Sidelines? You mean like requesting a debate and being denied? Or like pointing out that you’re a Christian who’s sole reason for subscribing to ID is to hold together the degrading structure of your faith, only for you to ignore such truths and march ever forward, willfully ignorant?

          I’m in the front of it, Rex. You, on the other hand, are sitting up in the nosebleed section with your thumb up your ass, shouting out your half-assed, baseless, anti-scientific assertions without one iota of credence to back them. Hmm…

          I do enjoy dressing as a cheerleader, though. That may be the first time you’re actually correct about something! Mark this day on your calenders, ladies and gents!

          • Doc Bill

            I sort of like the idea of Void in a cheerleader outfit!

            • Void Walker

              I rock those pompoms, too.

            • Doc Bill

              Meanwhile, Rex is at Academy looking for a jockstrap in XXXS.

            • Void Walker

              I’m pretty sure they don’t have a size small enough for him. Poor fellow will have to have one custom built. How awkward would that request be?

              …then again how awkward, in general, would it be to wake up in the morning, get dressed, and exist as Rex? I can’t even begin to imagine…

          • RexTugwell

            “willfully ignorant?”
            In the unlikely event that we debate free will, I’ll be sure to quote you often. No doubt you’ll accuse me of quote mining. LMAO!!!

            • SmilodonsRetreat

              I guess you don’t read IncrEDulous.

            • RexTugwell

              I guess not

            • Void Walker

              THAT’S your response?! Jayzus, man!

              Actually, we should debate free will. I’ve been engaging one particularly intelligent theist regarding DW/LFW for some time now, and I’d love to sharpen my fangs on a far less intelligent jesus freak such as you. 😀

    • Doc Bill

      A person who doesn’t understand computer technology, biology, chemistry and physics should not try to BS his way through with people who do. Oh, I should add ID creationism to the list because Tuggy doesn’t even rate a Luskin of competence in that either. That’s sad!

      • Void Walker

        Sad is the best word for Rex…

      • RexTugwell

        Doc Bill, the might slayer of strawman arguments, as usual has not grasped what I was saying. Try again.

        I think we’re at the point where you imitate me masturbating. Fire up that imagination, Billy.

        • Void Walker

          “Doc Bill, the might slayer”

          I think you meant “mighty”, Rex. Poor little guy. I can just imagine you, sweaty as fuck, mashing away on your keyboard in a rage. Check your posts before you hit “Post as Rex Jerkgood” in the future, eh?

          • SmilodonsRetreat

            heh, I certainly can’t complain about that.

            Me and proof-reading… blech. That’s what I have copy editors for.

            • Void Walker

              Would you concur with me that his primary reason for espousing ID is that it acts as glue for his faith claims? He always denies as much, but denial is a Christians best friend.

            • SmilodonsRetreat

              Honestly, I have no idea. He’s much too scared to put his actual beliefs on the table. I know of a few Muslim ID proponents. I don’t think I know of any atheist or FSM ID proponents. Though I think Cthulhu would be a good bet for ID.

              What I do know is that he doesn’t seem to know anything about biology that’s not from the mouth of Meyer.

              I do know that he’s perfectly happy supporting Meyer’s lies, misinformation, and quotemining.

              So, if he is a Christian, he’s a pretty good argument for atheism. The classic “Anything is OK as long as it supports my religion.” Of course, I guess the crusaders said the same thing as they raped, looted, and burned most of an entire civilization to the ground.

              Science isn’t easy. And it takes a great deal of mental processing to understand all of it. I sure don’t and I’ve been studying this stuff for decades. But when people ignore actual science to create their own version of they want science to say. Or demand that science explain every miniscule step, while ignoring that their preferred ideas can’t explain anything… those people are just IDiots.

            • Void Walker

              Rex is kinda easy, actually.

              On a few occasions I’ve cornered him, and he’s admitted (without realizing it!) that he’s a Christian. Of course, if directly confronted about his faith, he retorts to “The designer could be anyone!” which is a lie. He’s already made up his mind about who the designer is (Yahweh).

              I was a creationist for 11 years, and I can be very honest about why: it vindicated my faith. It acted as evidence in favor of my beliefs regarding the after life, the purpose of my existence, the all-too comforting notion that a loving, all powerful entity was watching my back through the worst that life could toss my way. I believe it’s the same for Rex, but good luck getting him to concede that. Apparently, the wedge document doesn’t exist in his little world.

            • Doc Bill

              Rexy-wexy isn’t so much a creationist as he is a prick. He gets more joy out of being a prick than he does from creationism. Notice how he can’t sustain a conversation without becoming a petulant baby about it.

            • Void Walker

              I’ve noticed that, especially when he’s exchanging with you or Smilodon (but also with me, clearly). He reminds me of a butt-hurt child on a playground, tossing about insults and nonsense in order to make himself feel just a bit better about his wasted intellectual life.

              Kinda sad.

              By the way, I still get to keep him. I know I’d give him a better home than you….I have a huge back yard that he could run about in, and lots of treats to give him!

            • Doc Bill

              Very, very few creationists and no IDiots will lay out their beliefs, “theories,” such as they are, or convictions. Hambo, at least, proclaims that he “has this book” and that evidence doesn’t matter. ID mechanism? Not a single one of the so-called theorists will touch that one. Dembski called it a “pathetic level of detail” and Behe said it was done by “poof.”

              What about the others, you ask? There are no others. There are only two people responsible for the few bits of dross that comprise “ID theory” which isn’t a theory at all, but an unconnected collection of assertions: Dembski and Behe.

              What about Meyer, you ask? Meyer has done nothing. He hasn’t contributed a single jot to the ID dunghill. All Meyer does is gripe about evolution. You can’t point to a single term or concept that is Meyer’s contribution. Wells? Nothing. Nelson? Nothing. Berlinski? Nothing. Luskin et al, don’t make me laugh! NOTHING!

              And finally, the amount Rexy-wexy has donated to the Disco Tute to keep them in grits – NOTHING!

              Watching these pricks flap around uselessly? Priceless!

            • SmilodonsRetreat

              I love asking ID people if ID is a mechanistic theory. If they say “No”, then I point them to where Behe states that it is (while he was testifying under oath to a court).

              If they say “yes”, then I point them to where Behe says that it doesn’t specify a mechanism (in the same testimony, same court, same oath).

              Repeat as needed.

            • Void Walker

              Damn, I’m gonna have to use that in future debates.

            • SmilodonsRetreat

              Need a link to the comments?

            • Void Walker

              Sure, that would be greatly appreciated.

            • Void Walker

              It’s difficult to wrap ones head around the animosity that these people have towards evolution. It’s really a beautiful theory, and it has incredible explanatory power. It’s simple, yet incredibly complex. It unifies every organism on the planet, gracefully accounts for the diversity of life, and it never ceases to blow my mind how broad in scope it actually is.

              It’s actually quite sad that IDiots cannot see all of the above. Their dogmatic approach to reality has clouded their minds.

              Yeah, watching them flutter about aimlessly is immensely satisfying.

            • Doc Bill

              Also, note how ID cheerleaders like the prick named Rex are incapable of explaining their own theory in their own words. Seriously, if some stranger came up to on the street and asked, “Can you tell me the theory of evolution?” don’t you think you could just rattle off a general outline, off the cuff?

              ID cheerleaders, not. They always say, “Well, read Behe” or Dembski or this or that, but they can never articulate what the theory is. And that goes for the Disco Tute, too. How many times has Luskin whined that scientists have “mischaracterized” ID theory and at the same time crowing about the articulate and concise Meyer and Behe at explaining theory. Can’t have it both ways, dude.

              You know the one person who has NO FREAKING CLUE about ID? Our Rexy-wexy, and he knows it. It adds to his prickiness, being a total doofus. Pitiful.

            • Void Walker

              “but they can never articulate what the theory is.”

              Yep. All they *ever* do is assert that, since certain features of life are very complex, they must have been designed. No mention of the process, mechanisms, designer, experiments done to confirm/disprove their claims, etc.

              It’s really sad that even in todays day and age, with all that we’ve accomplished scientifically, there are still people like Rex who are frightened of science; they are always hiding behind ambiguity and ignorance instead of rationally examining the available evidence.

            • Void Walker said:

              “It unifies every organism on the planet…”

              That is one of the main reasons, and in many cases THE reason, why religious people don’t accept ‘natural’ evolution and scientific evolutionary theory.

              Religious people who believe that they are special, exceptional, superior, and in at least the case of christians, ‘specially created in the image of God’, do not want to be unified with every other organism on Earth or any other planet. They don’t even want to be unified with apes, let alone slugs, fish, worms, snakes, plants, fungi, swine, and slime mold.

              If evolutionary theory were to completely separate humans (or at least self-righteous god pushers) from any connections with the evolution of so-called ‘lower life forms’ and place humans (or at least self-righteous god pushers) in a ‘special creation’ category, I doubt that there would be as much (if any) resistance to evolution and evolutionary theory from religious people.

    • Nicholas J. Matzke

      yep good stuff! Although: “cromatid” –> chromatid

      • SmilodonsRetreat

        One day I will learn to proof read and edit… but probably not anytime soon.

    • Cazimir

      The title is very misleading. Where did the respective say that DNA is like a computer?

      I don’t get your argument. You say the DNA code is not like a computer code because is much more sophisticated. Or a cell is not like a computer because is not exactly like a computer????? Because the code is much more sophisticated that supposed to prove that it was built by random events and random errors??? I don’t get it.

      Do biological systems store digital information that specifies how the system should be built and function?, do they interpret the information stored to execute, build and function? What causes do you know for a system like that? With evidence please.

      the cell is not exactly like a computer is more like a veritable micro-miniaturized factory containing thousands of exquisitely designed pieces of molecular machinery

      “the genetic system is a pre-existing operating system;the specific genetic program (genome) is an application;the native language has a codon-based encryption system;the codes are read by enzyme computers with their own operating system;each enzyme’s output is to another operating system in a ribosome;codes are decrypted and output to tRNA computers;each codon-specified amino acid is transported to a protein construction site; andin each cell, there are multiple operating systems, multiple programming languages, encoding/decoding hardware and software, specialized communications systems, error detection/correction systems, specialized input/output for organelle control and feedback, and a variety of specialized “devices” to accomplish the tasks of life.

      To sum up: the use of the word “program” to describe the workings of the cell is scientifically respectable. It is not just a figure of speech. It is literal.”

      http://www.uncommondescent.com/intelligent-design/what-kind-of-universe-cant-god-make-a-response-to-dr-james-f-mcgrath/

      “Biological information is the most important information we can discover, because over the next several decades it will revolutionize medicine. Human DNA is like a computer program but far, far more advanced than any software ever created.|

      (The Road Ahead, Penguin: London, Revised, 1996 p. 228

      • SmilodonsRetreat

        You know the cell is more like?

        The cell.

        You cannot make arguments using analogies. If you want to talk about cellular work, then talk about cellular work in terms of cellular work.

        What causes for a cell? That’s abiogenesis and it’s a huge field. I’ve talked about it on this blog several times. I’ll provide you with hundreds of papers… or you can look them up yourself.

        Linking to uncommondescent does you no favors here. There are no practicing scientists there. There is no one who does research into ID. I’ve shown that the claims of DNA being like a computer are wrong.

        The Road Ahead was written by Bill Gates… not a biologist.

    • RexTugwell

      Well, it wasn’t easy but I was able to refrain from commenting for 36 hours. I was curious to see just how much traffic this article would generate without my input. I wasn’t disappointed: only 3 unique, pro-Smiley contributors, 1 FB like and zero FB shares. Quite unlike past blog posts. I must say, Smiley, I think your “science” blog is dying a slow death.

      I have to thank you for re-posting word-for-word my original comment. No doubt you were hoping to embarass me with this piece because I caught you in a lie re: Behe. I’ve got bad news for you. It’s the other way around. Of course, Cazimir is exactly right. I didn’t say that DNA is like a computer. You continue to be a liar. So your long-winded yet largely irrelevant article, although very interesting, is worthless.

      Your dismissal of the code in DNA as digital information is either pathological denial or just plain idiocy. I’m betting on the former. As usual, what you didn’t say was more telling than what you did say. I found it extremely informative that any treatment of the codon and codon table (tRNAs) was conspicuously absent from the piece. The discovery of the genetic code along with the codons essential for relating nucleotide triplets with their corresponding amino acids was worthy of a Nobel Prize.

      • SmilodonsRetreat

        “I found it extremely informative that any treatment of the codon and codon table (tRNAs) was conspicuously absent from the piece.”

        Which shows you have no knowlege of biology. I didn’t explicitly state it, but it’s there.

        “The change probably won’t have any effect at all (what with non-coding regions and the resilient nature of our protein construction system). – See more at: http://www.skepticink.com/smilodonsretreat/2014/09/10/dna-is-not-like-a-computer/#comment-1585701048

        You must not read too good.

        In fact, the process for reading DNA into proteins is an essential part of something that no computer science person would ever do. That is doubling the amount of code to provide redundancy IN THE CODE.

        Honestly, I don’t really care what you think. It’s obvious that you don’t know much about biology, like Meyer and the rest of the ID crowd.

        DNA is arguably digital. While the basic core is, there is so much else going on that it very well may be analog, at least in part. DNA is not like a computer system. That much is clear.

      • Doc Bill

        So, Rexy-wexy, you’re saying my house is composed of digital information because it’s made of bricks, each one being discrete, but my neighbor’s stucco house is information free? Do I have the concept correct?

        How does PCR work? You know about PCR I’m sure. Does that use digital information? How so? How about catalytic polymerization of ethylene? Does that use digital information? Is that like a computer?

        • SmilodonsRetreat

          That’s something I had wanted to ask last night.

          Just because something can be described in a digital format, does that mean it’s automatically digital?

          Music being a prime example. It is obviously not digital, yet can be (imperfectly) encoded into a digital format. Still, there is loss and the bitrate of the recording measures that loss.

          Video is another example. Just because the digital imformation is at a high enough rate that we can’t tell it’s digital, doesn’t mean that it is.

          For analog data, it seems that there is an infinite range of digital information that would (to one degree or another) emulate that data. 4K TVs spring to mind here and 35 megapixel cameras.

          hmmm… implications for DNA as digital?

          • Sarah Fix

            This reminds me of the Turing test. A robot will never be a human, but an AI robot is arguably a sentient being, which is pretty similar.

            • Doc Bill

              “Never” is a house bet. You’ll always lose in the long run! I don’t know the latest on the Turing Test but I suspect it’s either already toast or nearly cooked. Siri is pretty good. I know people who are less informative and articulate than Siri. I know, sad.

              There are many examples of devices that do quite well judging and not just following step-by-step. Rice cookers and bread machines use “fuzzy logic” to make adjustments as would a cook or baker. Self-driving cars are almost a reality and flying drones can already adjust for atmospheric conditions. Those are very Turing-like things.

              I have no doubt that soon Amazon will send me a box with a tag that reads, “You will need this soon.” And they will be right.

            • Sarah Fix

              By human I meant homo Sapien. Suppose it depends on your definition of human. Which was my point. What’s your definition of digital? At some point in the future it might be difficult to distinguish between digital and biological. Is someone with a mechanical heart a cyborg? Is a cyborg digital or biological?

              Edit: if there’s a hypothetical future where genes and DNA are analyzed by computers to reduce genetic diseases and improve health (before the embryo is born, using IVF, etc. ), is the result biological humans or are they something different?

            • Doc Bill

              True enough, a robot will most likely never be human, although Blade Runner is one of my favorite movies. My definition of “digital” is the standard definition: data represented by 0’s and 1’s (although one could broaden that to “discrete symbols” as opposed to a continuum.

              People are not digital. We are analog, composed of chemical gradients and driven by equilibrium.

              I think that digital organisms will be quite different from us. Perhaps we’ll eventually become the Eloi. The machines will get bored with us and leave the planet to explore the universe as we bags of water will never do. (oops, I said never!)

              Since a cyborg is a mixture of manufactured and “natural” organic parts, I guess a person with a mechanical heart would be a cyborg. Usually the term is used in science fiction to mean a biological organism that is considerably enhanced by mechanics. Some of the new prosthetic devices are along those lines.

            • antiquatedtory

              I wonder if an analog computer would be a better analogy.

        • Void Walker

          Doc Bill, too many big words for Rex to process. You’re going to hurt him!

          • Doc Bill

            Rexy-wexy will have to Wikipedia “analog computer.” Some math problems can be solved simply and exactly with an analog computer that are only approximated in digital code. Creationists and other science ignoramuses praise computers like chimps at a monolith, and with about as much understanding. But it’s really Rexy-wexy’s abject, complete and total ignorance about chemistry that will forever confine him to a world of simplistic, childish and wrong analogies. However, ignorance is curable unless you’re a prick and that’s Rexy’s real problem.

        • RexTugwell

          Smiley states that he has a problem with analogies and what does The Smilodonian Sage offer as argument?

          … an analogy!

          Did you do that on purpose, you rascal?
          Think, Doc. THINK!!!

          • SmilodonsRetreat

            Again, you don’t read too good.

            I explained what I use analogies for. I offered it for explanation, not as the argument.

            I guess you missed the 18 paragraphs between those to things. Typical creationist quotemine.

            • RexTugwell

              You’re making my point, Mr. Retreat. How is Doc’s analogy an explanation and not an argument?

              You don’t write too well.

            • SmilodonsRetreat

              And you are making my point any thing to attack. Except the actual points made in the article.

            • Void Walker

              Rex, you don’t think, learn, or comprehend *anything* too well. It’s getting really sad at this point. You haven’t even addressed Smilodons points….

              Take a nap, little guy. You seem tired. Maybe the wife will let you get a little boob for the first time in 4 years? 😉

            • RexTugwell

              My wife died 3 years ago.

            • Void Walker

              If that’s the truth, I feel like an absolute fucking ass hole and apologize.

            • RexTugwell

              I forgive you

            • Void Walker

              Seriously, I apologize. I’ve lost loved ones too, and I was in full-on “super prick” mode.

          • Doc Bill

            Tuggy, I would have thought with your pointed head you’d be able to get points.

            Here’s the point you missed: I just destroyed your “DNA is a komputer” rant.

            You got nothing, boy, and I don’t mean just “down there!”

    • Cazimir

      Do biological systems store digital information that specifies how the system should be built and function?, do they interpret the information stored to execute, build and function? What causes do you know for a system like that? With evidence please.

      “I’ll provide you with hundreds of papers… or you can look them up yourself.”

      Translated “We have no evidence”. Evolutionists always resort to that line when have no evidence. hundreds of papers peer reviewed by evolutionists payed buy us to tell stories about evolution, but of course no evidence.

      • SmilodonsRetreat

        Are you reading the rest of the comments before jumping? Are you reading the information I presented above?

        Do biological systems store digital information? Partially.
        … that specifies how the system should be built and function? No. That is not digital. It is analog. I would suggest you read Sean Carroll’s “Endless Forms Most Beautiful”

        do they interpret the informaion stored to execute, build, and function? No. They do not interpret. Portions are translated and transcribed and these have specific biological meanings.

        Why can’t you actually talk about the cell using biology terms? Oh that’s right, you desperately need this to be digital so then you can try your complex systems equal designer bit.

        What causes do you know for a system like that? Natural causes as there are no supernatural causes. Unless you can provide evidence of supernatural causes, then everything in the universe (including the universe) has a natural cause… that is a cause that is based in the laws of chemistry, physics, and biology.

        I said I can provide them. You know what. I’ve never had a creationist actually ask me for the list. But it exists. It’s not MY problem if you aren’t interested in evidence.

        If you reject peer-reviewed papers, then you need to turn off the computer, put down the cell phone, turn off the AC, and quit eating anything grown or processed in North America. That’s all based on science.

        It’s really a joke. You aren’t the first person to do this. You aren’t even the thousandth person to do this.

        Do you honestly think that a few loaded questions will cause evolution to stop working? Do you think that a grade school knowledge of biology will somehow find the fatal flaw in a theory that’s well over 100 years old with thousands of predictions that have been confirmed?

        Really?

        Let me ask this. What evidence do you require to accept that evolution is true.

        • Doc Bill

          cazimir is what we call a “dumb fuck” who requires no reply at all.

          • SmilodonsRetreat

            The nuts are coming out of the woodwork this week. Even Joe is back on his thread at AtBC

            • Void Walker

              Wait…Joe is back?!

              OMG.

              Link, please? I love shredding him!

            • SmilodonsRetreat

              http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=ST;f=14;t=6647;st=7650#entry237410

              It started Thursday, just in time for a minor Friday meltdown, though I don’t know what he’s written on his blog.

              Joe is kind of like Rex. If you just choose the accept the opposite of what they say about any science, then you are much more likely to be correct than wrong.

            • Void Walker

              You should see Joe’s “knowledge” of theology at work. Deny the problem of evil exists, shove your head up your bum, and hum really loud. Classic YEC fundie moron.

    • RexTugwell

      So as Smiley’s best and brightest contributors, Doc and Void, battle it out to see who can write the most infantile comments, our host sits there scratching his ass wondering why his blog is circling the drain.
      Meanwhile, Rex and his coworkers prepare the popcorn and enjoy the show.

      What a bunch of
      011000100110100101101110011000010111001001111001
      01100011011011110110010001100101 !!!

      • SmilodonsRetreat

        Actually, that’s one of the most accurate things you’ve said in a long time.

        Scientists do things (and yeah, I’m doing some other projects right now), while creationists sit on their asses and do nothing except plan on how to make whatever things others do work for them instead.

        I couldn’t have said it better myself.

        BTW: Regarding the infantile comments. There’s no point in anything but ridicule. You have yet to do anything to support your position. In spite of dozens of attempts, you have not discredited anything I’ve written. You focus on cheap shots and ignore the entire argument.

        Again, perfectly typical of a creationist. While you might be a little nicer than most, you still are just another typical creationist who has no idea what’s going on.

        Meyer’s lies are perfectly OK with you, because he supports your ideas with them.

        • Doc Bill

          In all my years playing Creationist Whack-a-Mole I have only come across one person, a “young” lady (I’m assuming) who wandered into the lion’s den, Panda’s Thumb, and asked if someone could explain briefly the problems with Noah’s Flood without just mocking her. Fair request. We always give a new poster the benefit of a doubt (yes, Rex, very generous of us) unless and until they reveal themselves to be a Rex-prick. So, we laid it out in a couple of paragraphs: where’d the water come from, how much was needed, where did it go, Baumgardner’s racing continents theory, heat, vapor pressure, geology, biodiversity and so forth. Probably four or five blog postings worth, about 2000 words.

          Didn’t hear from her for a couple of weeks but she came back and said something like, “Holy shit, have I ever been given a bunch of crap! And I believed it. Just never thought about it. Thanks!” She hung around for about a year asking better and better questions. Anyway, that’s the only one who showed up without and axe to grind, and I don’t mean Doug. Ba dump ching!

          • Void Walker

            That woman gives me hope for Rex.

            ….or not. :-/

            Still, that’s fucking awesome. I hadn’t realized you commented over at Panda’s Thumb, btw.

        • RexTugwell

          By all means, continue the ridicule. Ratchet it up a notch even. It’s fun to watch you and your 2 minions cannibalize your blog to the point of it becoming a ghost town.

          • SmilodonsRetreat

            So you absolutely refuse to support your claims. You accept then that Doc Bill and my comments regarding DNA are correct. And you accept that you have not (and apparently have no intentions to) support any form of ID.

            OK, That’s fair enough. I just misunderstood your purpose. I thought you were interested in learning and my explanations of why Meyer is a liar and a terrible researcher would be worthy of your discussion. But you don’t care. You accept his lies without question because he supports your ideas.

            Everything else is just trolling.

      • Doc Bill

        Oh, this is rich! You just copied that string right off the Internet! Ha, ha, ha you’re so stupid I don’t care.

        I see you gave up on your “analogy.” Pity that you didn’t spend that time learning a little chemistry then you would be less of an idiot. Alas, lead a horse to water syndrome.

      • Void Walker

        Finally you aren’t hidden! Disqus must have cast quite a spell on you…

        This way I can track your activity like a creepy stalker.

    • cryptoguru

      DNA is exactly like a computer program, the cell is like a computer … let me explain why.

      A strand of DNA is transcribed into RNA in the same way that a computer reads a hard drive and loads it into RAM as a loaded program. The code is then interpreted when it is translated or run (as a computer OS interprets the program from RAM and produces output dependent on input). DNA is not just a guide for a 3D protein-printer! The ENCODE project has proved that, what was thought of as “junk DNA” has now been shown to be functional and non-linear (we only have about 20K different protein expressing genes … yet we produce over 100K different proteins i.e. non-linear) https://medium.com/the-physics-arxiv-blog/human-genome-shrinks-to-only-19-000-genes-21e2d4d5017e. Multiple parts of the code reference other parts, switching modules off and on and expressing other parts of the code in different ways, all to produce a specific output (just like a computer program) … and to be able to reproduce whilst maintaining functionality in the face of mutations.

      DNA has functional operands, logic, input and output, therefore is nothing like a blueprint. A blueprint is a diagram of an object that needs to be built, it includes no information about how to build the object, what materials to use, how to build the materials, the skills required to construct the parts, how to assemble the parts in what order etc.

      An intelligence needs to take a blueprint, understand what it represents and then use skill to implement it. A cell (like a computer) has no intelligence, it is simply following instructions. Those instructions must be exhaustive, i.e. they can’t just explain how to make something, they are the steps for making every component part and material and assembling them in the correct order. And all that in an 800MB program for an entire human. (iOS 8 on an iPad is 1.03GB)

      It doesn’t just describe how to build a human as a finished 3D object, it contains time-dependent morphological information; how you will grow (e.g. stages of life, puberty etc). And somewhere in there is the instruction set to build the brain, which comes loaded with a tonne of reflex programs so we can breathe, pump blood, eat, root for milk, not drown at birth etc.

      Saying DNA is like computer code is not just analogous, it is functionally equivalent.

      It’s more like saying that a car is like a go-cart, only with a bigger engine and a stereo and other stuff … but they are functionally the same.

      Let me explain which parts of the cell map to counterparts in a computer

      Mitochondria = power supply

      DNA = hard drive containing compressed progam code stored with error correcting codes

      RNA = RAM (programs loaded into memory)

      cellular transport mechanisms = motherboard BUS

      RNA Polymerase & Ribosome = CPU (runs the code)

      Your comment “Make a change in a computer code and the whole thing likely crashes. Make a change in a DNA code and you might make it run better” .. is completely ill-informed. Mutations to DNA are also deleterious, we have never observed a genetic mutation that has a purely advantageous effect (getting malarial resistance through Anaemia is not advantageous … having your feet amputated would also prevent Athletes Foot). We see thousands of damaging and harmful mutations though, that ironically DNA is trying to fix with its error correction routines. If DNA is optimised to mutate, why does it try its best to stop any mutations? If you randomly mutate a large operating system small amounts you will often see no discernible difference for a while as rarely used or negligible functionality is changed or deleted, but eventually the computer will crash … in biology we call that death. That’s exactly how our bodies stop working as mutations enter our cells every cell division and cause ageing, eventually this affects critical processes in our body, this is what cancer is … a deleterious mutation that propagates

      It seems to me that your issue with comparing DNA to computer code derives from the fact that you don’t like the conclusions that could be arrived at from that approach … that is a very fallacious argument.

      How do you explain an entire subject in genetics and active field of research that is using the human cell as a computer to run our own codes???
      http://med.stanford.edu/news/all-news/2013/03/biological-transistor-enables-computing-within-living-cells-study-says.html

      If DNA can be used as a replacement control for CPU functions, and a Turing Machine can explain CPU functions; DNA is a Turing Machine.

      • SmilodonsRetreat

        Please describe the logical functions in DNA.

        The ENCODE project defined “functional” so loosely as to be almost useless. http://pandasthumb.org/archives/2012/09/the-encode-delu.html

        You said:
        “Mutations to DNA are also deleterious, we have never observed a genetic
        mutation that has a purely advantageous effect (getting malarial
        resistance through Anaemia is not advantageous … having your feet
        amputated would also prevent Athletes Foot). We see thousands of
        damaging and harmful mutations though, that ironically DNA is trying to
        fix with its error correction routines. If DNA is optimised to mutate,
        why does it try its best to stop any mutations? If you randomly mutate a
        large operating system small amounts you will often see no discernible
        difference for a while as rarely used or negligible functionality is
        changed or deleted, but eventually the computer will crash … in
        biology we call that death. That’s exactly how our bodies stop working
        as mutations enter our cells every cell division and cause ageing,
        eventually this affects critical processes in our body, this is what
        cancer is … a deleterious mutation that propagates”

        There is so much in here that is wrong, half wrong, partially wrong, and partially correct that it’s almost impossible to pick apart totally. I’ll say this, since your premises are all completely or partially wrong, then your conclusions, no matter how logically correct, are also wrong.

        There are many positive mutations. I’ve noted many in this blog. For example, Lenski’s E. coli Your example of the sickle cell mutation is a positive mutation IN THAT ENVIRONMENT. And that’s a critical fault in your DNA is a computer program explanation. Computer output is not changed by environment. Biological output is dependent on environment.

        The VAST majority of mutations have zero effect. I’ve written about this several times as well.

        If you randomly mutate actual computer code, then compile it, There is a huge chance that it will not work… unless you just happen to hit data in an object or some such. In other words, computers are completely opposite of biology. In biology, the vast majority of mutations do nothing… one reason is that the vast majority of DNA doesn’t actually do anything (again, see the reviews of ENCODE by actual scientists). However, the vast majority of random mutations in computer code NOT DATA, but the code itself will be purely detrimental.

        DNA is not optimized to mutate, except in specific places, for example, the immune response parts of human white blood cells.

        You really know what causes aging? Wow, you should publish and get a nobel prize. That’s pretty awesome.

        Cancer patients die not from the fact that the tumors exist, but because the tumors cause blockages in normal components or consume too many resources.

        I need to remind you that DNA is not the ONLY thing that influences proteins. There are epigenetic effects. There are changes to the proteins made after the protein is built by the ribosomes. You aren’t taking those things into effect.

        So, I’m sorry, but I still don’t buy this analogy. And it is still just an analogy. We can talk about DNA and the processes without comparing to other systems and process with various values of analogousness.

        The only purpose for trying to compare DNA to a computer program is to try to compare DNA to a system that does require an intelligence to make and therefore try to show that god created DNA. But that’s a waste of time. If you want to talk about god, then talk about god and provide evidence. If you want to talk about DNA, then talk about DNA.

      • Doc Bill

        I don’t know where to start other than writing the word “wrong” about fifty times.

        NotGuru wrote: DNA is a hard drive.
        NotGuru wrote: DNA is a Turing Machine.

        What’s next, NotGuru, DNA is a peanut butter sandwich?

        This is the most embarrassing bunch of meaningless word salad I’ve read this year! But, it’s early days.

        • cryptoguru

          is that a response?
          Your response is not a response … it’s absurd
          Your response is a peanut butter sandwich. 🙂

          There were plenty of meaningful words formed into sentences in my post that are backed up with research … I assumed you guys would be pretty au fait with all the current stuff, so didn’t feel the need to reference and back-up every sentence I said.

          Which part of it are you struggling with? … please be specific.
          (saying all of it is a cop out)

          BTW: what’s a NotGuru? Is that a mutated copy-paste or an attempt at ad hominem?

          • Doc Bill

            No, nitwit, NotGuru is a cheap, playground insult – a taunt.

            Please, IDiot creationist, look up ad hominem and use it correctly in a sentence. I did not say that your argument is wrong because you are NotGuru the Nitwit, I said your argument was wrong. Wrong. Period. It would be just as wrong if it had my name attached to it but the chance of that is about 1 in 10^bazillion.

            • cryptoguru

              you obviously have nothing to contribute here … So I can only assume you don’t know anything about the subject, or how to have a discussion with other human beings.

              You’re correct though, children say the kinds of things you did in the playground … I’ve heard similar from other EVILutionists … Haha see what I did? That was so clever of me wasn’t it? I bet you’re convinced of my argument now because I created a lame pun to use as an insult.

              You’re just plain wrong … I’m going to so write it a kazillion times and all the way to the moon and back

            • Doc Bill

              Sorry, NotGuru, but it is you who is stupid, not me. Your analogy is flawed and I’m terribly sorry (not really) you’re too stupid to see why. You fricking creationists are all alike, so stupidly arrogant it makes my head spin.

              Tell you what, NotGuru, take some time off, say 5 years and study biochemistry at a good school like UT or Purdue, then come back and we’ll have a discussion about pH and concentration gradients and stochastic processes, reaction rates and my favorite, equilibrium.

              Meanwhile, have fun with your Legos because that’s your intellectual level. You’e not fooling anybody. You’re just another boring creationist.

            • cryptoguru

              I didn’t say you were stupid … I said you must know nothing about the subject as you seem unable to have an intellectual and rational discussion about it, after I have raised many points backed with actual, real research …. why are you unable to have a discussion about facts which other evolutionists are happy to agree on? You just keep going straight to insult, which makes me think you either don’t know/understand the answers or don’t like them.

              Why on earth would I want to study in the USA, when we have the best Universities over here in the UK? 😉
              I’m finishing off a PhD in Mathematical Biology (modeling biological processes), I came to it later in life after being a Computer Scientist and applied mathematician in industry.

              “you’re not fooling anybody”
              I’m not trying to fool anyone, you’re the one who goes off-topic, avoids answering simple questions and seems to be getting angry about it. I don’t really care what your religious evolutionism agenda is, but I’m trying to have a straight-forward discussion about the nature of the genome based on research I’ve seen according to how I understand it. If you disagree explain, why this view is wrong, backed up with some evidence …. otherwise you’re just pushing a faith-based position, and no-one likes a religious wing-nut just ranting at anyone who challenges their worldview.

            • Doc Bill

              Oh, you’re in the UK! So you understand that you are nothing but an ignorant wanking twit! Wonderful. Turns out I got my PhD at Imperial College, not the podunk, regional poly where you are “studying.” You’re still an ignorant wanker with a stupid analogy. At Imperial we would have thrown you into the Thames.

              Oh, you said “worldview.” Well, boy-o, that makes you one of those simple-minded, Bible thumping, wanking twits we knew, and discarded, so well. Hate being called out for an IDiot, don’t you? Well, no accommodation here! You want to have a rational discussion then propose something rational to discuss instead of that chunder you barf out your gob hole. You’re intellectually disgusting, you know. Oh, wait, you don’t know it. You’re probably a lager drinker, too. Pisses me off, it does.

            • cryptoguru

              I’m picturing a 70 year old alcoholic who did a PhD once in the UK, but has been sitting unemployed for the last 40 years in a trailer park shouting obscenities at pigeons, and calling them stupid creationists. Am I right?

              Yeah unlikely that not knowing you at all I’d be able to guess your background, current situation and skill-set just from a few of your anti-creationist rants.

              No I didn’t go to a Poly. I went to a real Uni … Like that matters at all in the context of this discussion anyway. I actually did a presentation once at Imperial.

              You’re just embarrassing yourself now, I don’t see how I provoked this kind of emotionalism, do you ever hear creationists screaming at Evolutionists for being irrational and wilfully ignorant and then make all sorts of dumb personal insults up instead of discussing science. I really hope you’re a 16 year old who’s just pretending they’re a PhD microbiologist … Because the alternative is frightening.

            • Doc Bill

              Your characterization is spot on, except for the rats with feathers you call pigeons. I shout at real rats. Big ones.

              So, here’s where you went wrong, NotGuru. You plunked down an analogy (like we haven’t heard the cell “is like a computer” before, then when challenged you got your back up and your knickers in a twist.

              If you want to play in a sandbox with your fellow creationists then go over to the AIG website, or the Disco Tute website, or Uncommon Descent and have yourself a good old time. They’ll welcome you as a fricking genius, they will! Oh, except for the Disco Tute that doesn’t allow comments or AIG that doesn’t allow comments, either, or Uncommon Descent who will ban you if you dissent.

              You want to talk science, eh? I don’t believe it but I’ve got nothing better to do on a rainy afternoon. All the rats are sheltering under the trailer.

              William Paley’s watchmaker argument. You know how it goes. One is strolling on the heath and one comes across a pocket watch lying on the ground. Etc, etc, etc.

              Why a pocket watch? Why not an iPhone?

              Now it’s your turn. Take the argument from here.

              p.s. you haven’t praised me for my “cell is like a kitchen” analogy. I’m hurt.

            • cryptoguru

              Firstly I should apologise for not praising your “cell is like a kitchen” analogy. It’s possible that it was so good that I felt threatened by its potential impetus .. and was concerned that endorsing an idea that amazing may result in you having a platform to preach your evilutionist religion thingy, with all the eugenics racism and what-not. (which I don’t really like that much)

              [BTW: I’m going to call you Bilbo from now on, like the Hobbit … he’s pretty cool you know … even though he was really old, and had big feet]

              Secondly, I’m very glad I still have the ability to guess exactly what a person is like, their emotional history and what they are doing now, simply from the way they structure insults. I will be sure to use it again in the future, should the opportunity present itself.

              I didn’t “plonk down an analogy” … the problem with MicroBiology is that you just think about chemicals and reactions and think everything is just a physical/chemical/mechanical entity. We mathematicians and computer geeks know that’s not true … we deal with information every day and know how it works. A pile of stones may just be a pile of stones, but if I arrange them into the shape of a map with directions on to show where I hid my treasure (a rare recording of The Beatles on vinyl) it becomes information. The information isn’t IN the stones or their material properties, it’s in the arrangement of the stones. DNA holds information in the arrangement of the chemicals, which is interpreted and expressed through the process pipeline of the cell.

              So my “analogy” wasn’t an analogy it was a definition … the living cell IS a computer. The cell ISN’T a blueprint … and Love ISN’T An Open Door (see Frozen – Disney)

              The Oxford dictionary (slightly wrongly) gives this definition of a computer

              “An electronic device which is capable of receiving information (data) in a particular form and of performing a sequence of operations in accordance with a predetermined but variable set of procedural instructions (program) to produce a result in the form of information or signals.”

              It’s ALMOST right, but a computer doesn’t have to be electronic … a computer can be clockwork if you like, or made out of qubits (Quantum Computer), or made out of chocolate if you manage not to eat it before making it. (that’s not an exhaustive list of computers)

              DNA is a set of procedural instructions which is processed via transcription and translation to result in other information e.g. reprogrammed DNA & RNA (at times) and physical output e.g. proteins/other stuff (at other times).

              Even taking the simplest (incorrect) understanding of the cell as a simple 3d printer that just runs a sequential tape of codons which are instructions on how to build a protein through a copy process and then a building process START CODON CODON CODON ETC STOP … that would still be considered a computer.

              So NO it’s not an analogy. However I’m explaining it’s much more complex than that … and we do know this stuff from research done by people who have eyes and brains and such.

              DNA is processed in multi-dimensions:
              DNA is transcribed in a non-linear fashion to create RNA, it is not a simple linear zipper like we are taught at school. DNA can read forwards, backwards and can be folded to create 3D structures which are read across intersections … this is highly non-linear functionality.
              (have a read of this … it’s properly mind-blowing)
              https://img.jgi.doe.gov/er/doc/multidimensional-genome-annotation.pdf

              DNA handles time-dependence:
              there are a possible 64 codons that can be coded with 3 base pairs. (don’t worry I checked using my fingers that I had my sums right). However they only code for 20 amino acids plus START/STOP (I know you know that). Why?? Well, 2 reasons. First is that they are used as an error correcting code, introducing redundancy (but not ambiguity) allows simple read errors to be corrected through the maths. Also recent research suggests the different forms of amino acid could create time differences in expression, so allow some proteins to be delayed in order to be built at exactly the correct time so they can be assembled in the right order. They are obviously not the only thing controlling timing … as that wouldn’t account for other complex assembly timings and also the fact that through your life different programs are used at different stages. (I suppose a Caterpillar -> Butterfly demonstrates that quite well)

              The cell doesn’t just chuck out a pile of proteins and hope for the best. There are chaperones that guide the assembly process into complex structures and each step has to be done at the right time. (Maybe a bit of time with lego would help right now Bilbo)

              So Bilbo, It’s like building a robot assembly kit … gears have to be put together and housed correctly, and wiring assembled and joined to the right places etc etc (or for someone of your generation, think about an Airfix Spitfire kit, which is a bit crap because it doesn’t move like a cool robot does). DNA has to control this process … the cellular molecular machines aren’t intelligent, they just follow patterned behaviour. So DNA has functional information.

              I don’t want to go to AiG and post on their forum or whatever … they already know a lot of this, so that would be boring. You’re much more fun.

              If you’re still struggling with my logic, maybe you should go back to a reputable school (not just a College) 🙂 and learn some mathematics, information theory and computer science (and who knows … maybe learn some manners too)

            • SmilodonsRetreat

              “DNA is processed in multi-dimensions:”

              Thank you, you’ve just agreed that DNA is not like a computer. Well done. Now, if you want to learn about some biology, then I’ll be happy to help you.

              You can start by answering this question. Which has more information, a 30-minute political speech or 30 minutes of white-noise?

            • Doc Bill

              Your analogy, NotGuru, is childish and shite to boot. It’s not worth taking apart any more than my peanut butter sandwich comment.

              Face it, NotGuru, you’re not a guru and not even a grasshopper.

              So, fuck off, OK?

            • cryptoguru

              > “Thank you, you’ve just agreed that DNA is not like a computer”
              I agreed that?? Really? Where? Computer programs process in multi-dimensions. The multidimensionality of the genome and the way it is read forwards, backwards and jumping through the DNA (due to 3D folding)
              http://newsoffice.mit.edu/2013/reading-dna-backward-and-forward-0623
              is exactly the same as what is done in nearly every computer program (only DNA is much more advanced). Even algorithms such as 3D video compression and signal processing utilise convolution and this kind of multidimensional indexing. IT IS A COMPUTER! (even if you don’t like it … it won’t stop being a computer)

              Thank you, you’ve just agreed that DNA is designed! (yeah I know you didn’t … but I wanted to join the fallacious argument bandwagon at least once, I was feeling left out)

              I made a mistake in my last post, I have just learned something new myself. The redundancy in codons isn’t functional redundancy. They may code for the same amino acids, but apparently according to new research the different versions of the same amino acid promote different kinds of binding, so they’re not equivalent. i.e. even more complex and polymorphic.
              http://www.sciencemag.org/content/342/6164/1367.abstract

              You guys aren’t keeping up with the research … other evolutionists are at least panicking about some of these recent findings and having to invent new stories to try to explain the science we see. Here’s one that tries to show how dual-protein coding (polymorphism: multi-functional control and re-use of the same code for different purposes) could happen by chance even though it seems impossible. Have fun …
              http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0030091

              So instead of putting your fingers in your ears and shouting loudly “go away! We don’t like you! It’s lies! All lies I tell ya! No-one agrees with that creationist nonesense!” … maybe you should take a look around at your evolutionist contemporaries and realise that they know what I’m saying is true, and they’re scrabbling around trying to find new magical fairy-dust stories to explain how these things could’ve happened by accident. I’m not giving you creationist arguments, I’m simply showing you the science and asking you to validate your claim that DNA is not like a computer, when it clearly is … and the majority of current genetics research is agreeing with me.

              Whilst an amusing jab at politicians, the (reluctantly) correct answer is that white-noise has no information, the speech is information-rich. If information is embedded in white-noise (e.g. spread spectrum encoding below the noise floor), it is no longer white-noise even if it sounds like it. Random noise is NOT information. A 30-minute political speech contains speech and an intended message .. even if they are lying and avoiding facts in order to push an ideology on those who are not well informed enough to call them out on it (like you guys are doing) their language has intended purpose for a recipient, they are not random words. My stones analogy was a better one … the same material is used in both scenarios. 1) randomly distributed and meaningless stones 2) purposely distributed into a message that has a meaning for an intended recipient. The stones have not changed in any way except their position. The information is not an inherent characteristic of the stones themselves, nor could it be. The only reason you can’t accept it, is because it creates a problem with your voodoo-science “something out of nothing all by itself” story. We have never observed that ever happening with information. Observable science continues to back up a creation explanation for origins, evolutionism relies on fairytales that have to keep changing their TRUE FACT story to account for the contradictions, whilst avoiding putting the new versions of the stories in the popular press in case the general public get wind of the fact that the goal posts keep moving to account for a scientifically indefensible ideological position being presented as SCIENCE FACT.

              Bilbo: you’re right I’m not a grasshopper … I’m glad we cleared that one up at least. I still haven’t seen one scientific or rational argument from you … can you remember any of the stuff you learned back at The Imperial College (cue Star Wars Imperial March), or was that before the days of Watson & Crick when the entire cellular biology course was “here’s a blob of protoplasm”?

              No idea what your watch/iPhone comment is about … care to elaborate? Yes, I’m aware of Paley’s argument … I don’t see what that has to do with this discussion about the cell operating as a computer.

              But here let’s get to the bottom of this “DNA is not like a computer” nonsense … it’s pretty obvious I’ve made my case clearly now with lots of non-creationist references. And your defence has been “no it’s not! you’re wrong, because I say so … and because you’re stupid! (because you’re a creationist)”. Either put up a decent argument why my analysis is scientifically wrong or admit defeat on this point.

            • SmilodonsRetreat

              “Whilst an amusing jab at politicians, the (reluctantly) correct answer is that white-noise has no information, the speech is information-rich. ”

              So, you have zero knowledge of information as well. Note that I said information, not “meaning”. White noise may be meaningless to us, but it is non-compressible, which means that it contains more INFORMATION (in the Shannon sense) than a politician’s speech. The speech is filled with many words that are the same, many pauses, etc. all of which are compressible.

              You have done what every creationist I’ve ever met does. You confuse information with meaning. Let me give you another example. Which has more information? 30 minutes of random white noise or 30 minutes of encrypted data? Answer, it’s the same. Even though both are meaningless to you. The meaning can be extracted from the randomness by someone with the proper key.

              Now, to continue with your analogy (and make no mistake, that’s all that it is, an analogy).

              How do you calculate the information in a strand of DNA?

            • cryptoguru

              yeah I do sort of understand this stuff (you picked the wrong guy to argue this with) … I worked in Cryptography for 7 years (hence the name … invented security cryptosystems and wrote patents for them), Signal processing (audio/image), Compression Algorithms (image/video) etc. in the real world writing algorithms that get used to do stuff, not making up wacky esoteric definitions of things on a blog to try and pull the wool over people’s eyes.

              The dictionary defines “information” as:
              “what is conveyed or represented by a particular arrangement or sequence of things.”
              it defines “represent” as
              “To have as a meaning, suggestion, or association; stand for or symbolize”
              Information can therefore be equivalently defined as “Information is that which is meant by a particular arrangement or sequence of things”. Information communicates meaning.

              “White noise may be meaningless to us, but it is non-compressible, which means that it contains more INFORMATION (in the Shannon sense)”

              Come on … really??!! You didn’t just write that?! White noise is maximally entropic, you’re getting yourself very confused there (or trying to be deliberately deceptive). There is no information in white noise, it has a random distribution. The definition of information is that which has a particular arrangement … i.e. a non-random distribution.
              http://c2.com/cgi/wiki?WhatIsEntropy
              White noise has entropy of 1!
              http://soundanalysispro.com/manual-1/chapter-4-the-song-features-of-sap2/wiener-entropy

              Dude (I’m assuming you’re a dude), if every creationist on here before me has said that white noise has no information then you’ve been served well by a long line of scientifically accurate creationists.

              “Which has more information? 30 minutes of random white noise or 30 minutes of encrypted data? Answer, it’s the same”
              WRONG AGAIN!! The random white noise has no information in it, the encrypted data has information in it, but it is potentially undetectable by analysing the frequency content of the cipher.

              Encryption is about hiding the information … if you handed me a signal of what seemed to be white noise (as I described before), the information could be hidden in the noise floor and I may think it isn’t information, when information is in actual fact hidden there. The white noise itself is not information … it is hiding the information and making it look maximally entropic.

              Consider the code

              TURN 90 DEGREES
              TURN 70 DEGREES
              TURN 50 DEGREES
              TURN 30 DEGREES
              TURN 10 DEGREES

              It contains entropy through repetition. It would be more efficient to write

              ANGLE = 90
              DO WHILE ANGLE > 0
              TURN ANGLE DEGREES
              ANGLE = ANGLE – 20
              END WHILE

              But, if you’re writing a computer program entropy is sometimes necessary, because it is more efficient computationally (i.e. faster) to execute the 5 things in succession rather than the overhead involved to implement the WHILE loop, which needs to store variables, perform boolean tests, do arithmetic and control the flow. So measuring entropy in a computer program is not going to tell you how clever the program is.

              We can calculate the information in a strand of DNA when we understand what it all means to the translation mechanism. Currently we can see it doing things, understand some of it … but there’s vast amounts we don’t know and can’t quantify, that doesn’t mean we don’t know it’s functional, we just can’t comprehend it all yet … and may never get clever enough or powerful enough computers to analyse exactly how the information stored in DNA is used. This itself is a testament to the superiority of the designer. We can see it has function and form, we can analyse some of the functional codependencies, but we can’t see the full big picture, because it’s just too complex for us to currently fathom.

              How do you accurately calculate the exact number of water molecules in the world’s oceans? You just can’t, it’s too difficult. Does that mean that there aren’t any water molecules in the ocean? NO … we can count some of them and we observe the rest, we just can’t quantify it all.

              You keep saying “your analogy” … but I’ve demonstrated to any logical and scientifically minded person beyond any doubt that the living cell behaves as a computer and satisfies the definition of a computer, and Turing machine.

              This Nature journal article from a respected evolutionary geneticist says that the living cell is a Turing machine …
              http://www.readcube.com/articles/10.1038%2F482461a

              I’m hoping that you’re eventually starting to see sense. Please do read the things I’ve linked to … they’re not random noise, I chose them as information to convey the meaning that comports with my argument.

              You ready to back down yet? You haven’t posted ANY research to support your view at all!

            • SmilodonsRetreat

              While you can say whatever you like. You are STILL conflating information and meaning. That’s why I said “Shannon information”.

              information is not meaning. Meaning is not information.

              I really don’t know why this is hard. It’s basic information science. Stuff that an expert like you should be very familiar with.

              So, let’s see what we have here. We have an “cryptology expert” who doesn’t understand Shannon information. He’s also a computer expert. And has very limited knowledge of biology.

            • cryptoguru

              no I defined the difference between them, contrasted against your ridiculous “white noise is information” claim … information is the communication of meaning. They are both related to meaning.

              Did you read about maximal entropy? That is Shannon’s theorem. http://en.wikipedia.org/wiki/Shannon%27s_source_coding_theorem White noise is the definition of maximal entropy, which is why Shannon’s theorem is called “the noiseless coding theorem”. You can’t apply his theorem to noise!!! You can’t compress it because it contains no information to compress. That doesn’t prove it is information. Utter nonsense. Stop lying and saying I don’t understand this stuff … you’re grasping at straws. Straw-men.

              What about the ACTUAL point I was raising (cell is a Turing machine), instead of this bizarre side-issue of an alleyway you’re taking us down?

            • SmilodonsRetreat

              YOU brought up information. Not me.

              So, when you send white noise across a telephone line.. .purposefully… you are not sending information. There could be no reason to send white noise across a telephone line.

              Says the guy who claims to be a cryptographer.

              Wow.

            • cryptoguru

              if you send white noise across a telephone line in a sequence or pattern … e.g. you tell your friend “when you hear a burst of white noise kill the president”, the noise has meaning … how? … because the context of the noise becomes the information … the signal is carried in the knowledge that the presence or absence of noise means something … the noise still isn’t information.

              so now you’re saying the cell IS a Turing machine???
              And DNA is a computer code that is processed?
              Therefore it contains information???

            • SmilodonsRetreat

              We’re just talking past each other now.

              There’s no point in continuing.

              My OP is that DNA is not a computer. You have changed your mind about that, from it is a computer, to it is not a computer, but the cell is a Turing machine.

              You have agreed with my OP.

              I have never, anywhere, said that the cell is not like a Turing machine. I think it’s not a bad analogy. But the cell is also like a factory. That’s not a bad analogy either.

              They are still analogies.

              I will remind you that information is not meaning. I can send you an epic poem in Swahili and it will have no meaning for you. However, it still contains information.

              When you encrypt data (meaning) and produce an effectively purely random string that is then sent, you are, in effect, sending white noise. That’s the entire point of cryptology, is to hide the meaning. So, please stop conflating meaning and information.

            • Doc Bill

              Hey, don’t forget my Great Kitchen Analogy, praise be to Julia!

            • SmilodonsRetreat

              So, to you, the phrase
              “the living cell is a Turing machine”

              and

              “Turing machines and cells have much in common”

              Are exactly the same.

              I think I begin to see the problem…

              Which is why you are still arguing about an analogy instead of arguing about DNA.

              What does a Turing machine do? It manipulates a set of data according to rules. With careful programming, the Turing machine could be made to emulate any algorithm or anything else.

              However, DNA is not the Turing machine is it? It’s the data. Isn’t it?

            • cryptoguru

              HAHA … I was kind of expecting you to do more than just read the title.

              “Arguably the best examples of Turing’s and von Neumann’s machines are to be found in biology. Nowhere else are there such complicated systems, in which every organism contains an internal description of itself. The concept of the gene as a symbolic representation of the organism — a code script — is a fundamental feature of the living world and must form the kernel of biological theory.”

              “Biologists ask only three questions of a living organism: how does it work? How is it built? And how did it get that way? They are problems embodied in the classical fields of physiology, embryology and evolution. And at the core of everything are the tapes containing the descriptions to build these special Turing machines.”

              He calls the cell “special Turing machines”

              I never said DNA is the Turing machine … I said that DNA is stored computer code, the living cell is a computer. (Turing machine)
              If I did say DNA is a Turing machine anywhere please point it out, I would like to correct myself, that would be an error. But pretty sure I showed how the different parts of a living cell operate the same as the parts of a digital computer (i.e. the whole cell is involved) … and the living cell is a Turing machine.

            • SmilodonsRetreat

              So, we have wasted all this time.

              Because I never said that the cell wasn’t a Turing machine.

              Perhaps you should have read my title.

              So, thank you very much for wasting all of our time. Well done.

              Feel free to go away now.

            • SmilodonsRetreat

              So, we have wasted all this time.

              Because I never said that the cell wasn’t a Turing machine. And a Turing machine is not a digital computer.

              Perhaps you should have read my title.

              So, thank you very much for wasting all of our time. Well done.

              Feel free to go away now.

            • Doc Bill

              I don’t think NotGuru who we can now call Old Cobber even read your original posting where you clearly destroyed his argument by analogy.

              If you recall from Meyer’s book, Ciggie in the Cell, he presents a general discussion of information theory and describes both Shannon information and Kolmogorov complexity as a prelude to defining what IDiots call Complex Specified Information, then proceeds to say that CSI is neither. I kept waiting for the “ta da!” and it never came. At the end of the book you’re left no wiser as to what CSI is, much less how to calculate it. It’s just bafflegab, like what Old Cobber tosses out.

              Since the old git isn’t likely to hang around here much longer I’ll at least address my Paley’s iPhone proposition. Simply put, the reason Paley didn’t find an iPhone on the heath was because it hadn’t been invented yet! Yeah, so obvious. In Paley’s day the pocket watch was the hight of technological engineering much as the iPhone is today. Why is Old Cobber’s cell like a computer and not like the Krell machine of Altair IV? Limited imagination coupled with a total lack of knowledge of chemistry.
              Real biochemistry is very difficult; stupid analogies are a dime a dozen. Just ask Julia.

              Incidentally, I had fun imagining Paley finding a fully charged iPhone and turning it on. Of course, there would be no ATT or wifi but some of the apps would work. The next day, all excited, he’d go out to show his friends and colleagues but the iPhone’s battery would be dead and it would just sit there. Taking it apart they would have no idea what they were looking at. Not a single component would be recognizable.

            • SmilodonsRetreat

              That’s actually a pretty neat idea. Back to the “some level of technology is indistinguishable from magic” concept.

              Of course, some level of biology, chemistry, and physics are also indistinguishable from magic… for people who don’t understand the concepts.

            • Doc Bill

              As you can tell I was quite impressed by the Krell machine and “monsters from the id!” That was a VERY advanced scifi film for its day. Some years later I was both surprised and a little annoyed when the TV show Lost in Space conscripted Robbie the Robot. He was never the same as the show descended into abject absurdity. I had the hots for Angela Cartwright, too, and was sad when she was killed by the Alien.

              I should write a story, Fun with Paley, and come up with time-age appropriate analogies: finding a fully shaped stone tool, finding an inscribed stelae, finding a printing press and so on.

              We still say crazy things in everyday conversation, I guess because technology is moving faster than language. People still say “I taped that” when shooting video on an iPhone, or “watch a film.” Old Cobber rambling on about a “hard disc” is really showing his age. Soon we’ll be back to solid state storage devices, full circle, and hard discs will be as obsolete (but still in the language) as floppy discs. Why isn’t DNA like a deck of punched cards? Teh mind bogglz!

            • SmilodonsRetreat

              Heh, Disqus won’t let me change it.

              I love that movie too. There’s not many that age that well. The Black Hole is still very, very good. The Cat From Outer Space… not so much.

              Back to Forbidden Planet. I like how they had a massive energy system all to create a small monster. They knew it would take lots of power (like the output of a small star) to create the mass. Very cool stuff.

              I know, maybe I should have a DNA analogy contest, just for the LOLs.

            • Doc Bill

              Well, Gollum, all you’ve demonstrated is that you’re an Orc-eating IDiot!

              Answer my question. Why didn’t Paley find an iPhone on the heath?

            • Doc Bill

              P.S. AIG is a young earth creationist organization based on the Bible being literally and factually perfect. Seriously, you think AIG “know a lot of this?”

              That is the most pig ignorant, stupidest, dumbest thing I’ve ever heard. Obviously you have NO IDEA, sorry, NO FUCKING IDEA what AIG is.

              Quit posing, NotGuru, you’re embarrassing!

            • Doc Bill

              I’m going to make one final comment, NotGuru, and I don’t expect you to understand it or to change your mind because clearly you’re as thick as two planks AND a bag of doorknobs.

              You wrote the following astounding pile of shit:

              “the problem with MicroBiology is that you just think about chemicals and reactions and think everything is just a physical/chemical/mechanical entity. We mathematicians…”

              First of all, it’s “microbiology.” I know Creationists are FonD of RanDoM Capitalization and I’m sure you’d use multiple fonts and colors if you could. Microbiology is the study of microscopic organisms. Micro for microscopic and biology for the study of living organisms.

              When you “think about chemicals and reactions” then you are in the realm of biochemistry which is the study of the chemistry of living organisms which would include DNA, RNA, proteins, cyclic reactions, gradients, equilibria, reaction kinetics and so forth.

              So, clearly you have no idea what you are talking about just from that mess. I don’t know why you wrote “physical/chemical/mechanical entity” other than to further demonstrate you have no fucking idea what you are talking about. Well, you certainly succeeded there! Yes, biochemistry is chemistry and it’s useful in that discipline to remain at the level of chemistry, although physics and especially quantum mechanics and orbital dynamics can be useful when modeling enzyme activity, cell membrane permeation, affinities and so forth.

              So, yeah, biochemists look upon what they study as chemistry because that’s exactly what it fucking is: chemistry.

              As for your comment, “We mathematicians…” you owe me a new keyboard because I spewed my coffee on my old one. That is such a narcissistic, pompous, delusion of grandeur that I couldn’t but think you are redefining “mathematicians” to mean a collection of idiots, morons and uneducated opinionated buffoons with large red noses, funny hair and big shoes all stuffed into a tiny car. Mathematician, indeed! Paint me skeptical.

              Perhaps you can add and subtract, NotGuru, but information science is not your friend. I’m not surprised, even the paid IDiots have a difficult time with the concept because, you see, it just doesn’t support their theology. You confuse “information” with “meaning” just like all IDiots. As a “computer geek” surely you know that eight bits,

              01000001

              could represent an ASCII character, or a CPU instruction, or a data value, or the status of valve positions, or a measurement of the cosmic background radiation or nothing at all.

              Which takes us back to Paley. Why didn’t he find an iPhone on the heath? The answer is both simple and profound but I’m giving up hope that you have the mental power to figure it out.

            • SmilodonsRetreat

              ” I don’t see how I provoked this kind of emotionalism, do you ever hear creationists screaming at Evolutionists for being irrational and wilfully ignorant and then make all sorts of dumb personal insults up instead of discussing science. ”

              All the fucking time. In fact, that almost ALL that they do.

              Look, you have spent all this time and effort to argue that an ANALOGY is actually a good one.

              Who cares?

              It’s an ANALOGY. Even if the analogy was 100% accurate (which is, by definition, not possible), then it still wouldn’t mean that DNA was designed.

              I assume that you understand science. You have to provide evidence that DNA is designed. An analogy won’t do it. You simply must have evidence that a designer exists… and you don’t.

      • SmilodonsRetreat

        Please describe the logical functions in DNA.

        The ENCODE project defined “functional” so loosely as to be almost useless. http://pandasthumb.org/archive

        You said:
        “Mutations to DNA are also deleterious, we have never observed a genetic
        mutation that has a purely advantageous effect (getting malarial
        resistance through Anaemia is not advantageous … having your feet
        amputated would also prevent Athletes Foot). We see thousands of
        damaging and harmful mutations though, that ironically DNA is trying to
        fix with its error correction routines. If DNA is optimised to mutate,
        why does it try its best to stop any mutations? If you randomly mutate a
        large operating system small amounts you will often see no discernible
        difference for a while as rarely used or negligible functionality is
        changed or deleted, but eventually the computer will crash … in
        biology we call that death. That’s exactly how our bodies stop working
        as mutations enter our cells every cell division and cause ageing,
        eventually this affects critical processes in our body, this is what
        cancer is … a deleterious mutation that propagates”

        There is so much in here that is wrong, half wrong, partially wrong, and partially correct that it’s almost impossible to pick apart totally. I’ll say this, since your premises are all completely or partially wrong, then your conclusions, no matter how logically correct, are also wrong.

        There are many positive mutations. I’ve noted many in this blog. For example, Lenski’s E. coli Your example of the sickle cell mutation is a positive mutation IN THAT ENVIRONMENT. And that’s a critical fault in your DNA is a computer program explanation. Computer output is not changed by environment. Biological output is dependent on environment.

        The VAST majority of mutations have zero effect. I’ve written about this several times as well.

        If you randomly mutate actual computer code, then compile it, There is a huge chance that it will not work… unless you just happen to hit data in an object or some such. In other words, computers are completely opposite of biology. In biology, the vast majority of mutations do nothing… one reason is that the vast majority of DNA doesn’t actually do anything (again, see the reviews of ENCODE by actual scientists). However, the vast majority of random mutations in computer code NOT
        DATA, but the code itself will be purely detrimental.

        DNA is not optimized to mutate, except in specific places, for example, the immune response parts of human white blood cells.

        You really know what causes aging? Wow, you should publish and get a nobel prize. That’s pretty awesome.

        Cancer patients die not from the fact that the tumors exist, but because the
        tumors cause blockages in normal components or consume too many
        resources.

        I need to remind you that DNA is not the ONLY thing that influences proteins. There are epigenetic effects. There are changes to the proteins made after the protein is built by the ribosomes. You aren’t taking those things into effect.

        So, I’m sorry, but I still don’t buy this analogy. And it is still just an analogy. We can talk about DNA and the processes without comparing to other systems and process with various values of analogousness.

        The only purpose for trying to compare DNA to a computer program is to try to compare DNA to a system that does require an intelligence to make and therefore try to show that god created DNA. But that’s a waste of time. If you want to talk about god, then talk about god and provide evidence. If you want to talk about DNA, then talk about DNA.

        • cryptoguru

          “Please describe the logical functions in DNA.”

          I’m not claiming we can describe and quantify the functions in DNA … only that we know it has them.
          Control genes in nonprotein coding sites that regulate the expression of proteins are functional (in a pure sense). We don’t know exactly how these work yet because most genetics research has had it’s fingers in its ears shouting “lalalala” concerning junk DNA until very recently. But we do know from Information Theory that if a part of DNA which is transcribed and translated (i.e. the code is run) has the end effect of causing another part of the code to sometimes run and sometimes not run, this is flow control, which is a logical operation. Who knows what logical operands the flow is dependent on … it doesn’t matter … it makes sense that they’re the same universal laws of logic that we all know and love.

          I mentioned in my original post that we have 19K protein sites expressing 100K proteins. This is deterministic … i.e. it always produces the same stuff; it’s not a stochastic method creating random proteins. The only way to get 100K different proteins from 19K mechanisms and combine in the correct order at the correct time is using flow control, timing mechanisms and logic. DNA is not magic, there are no fairies involved. So we can infer quite nicely that polymorphism (which is a programming concept) requires functional inheritance.

          Show me how any of this is NOT like a computer code.

          You never addressed my point about the blueprint being vastly insufficient as an analogy.

          Even Wikipedia covers the concept of noncoding DNA performing functional http://en.wikipedia.org/wiki/Noncoding_DNA
          “However, it has been known for decades that many noncoding sequences are functional. These include genes for functional RNA molecules (see above) and sequences such as origins of replication, centromeres, and telomeres.”

          You said:
          “There are many positive mutations. I’ve noted many in this blog. For example, Lenski’s E. coli Your example of the sickle cell mutation is a positive mutation IN THAT ENVIRONMENT. And that’s a critical fault in your DNA is a computer program explanation. Computer output is not changed by environment. Biological output is dependent on environment.”

          OK let me backpedal on my enthusiasm there … I’d like to rephrase my original comment to “I have never seen any purely advantageous mutation” … point me in the direction of some so I can evaluate whether or not they could also be categorised as deleterious. That’s beside the point (even if there are advantageous ones) … we have a tiny few dubious examples of beneficial mutations that I’ve heard of (Apo-AIM, LRP5, HbC … they all also have measurable disadvantages). So how does natural selection select these extremely rare and dubiously advantageous mutations over the 100 germline mutations that creep into every DNA at every generation? Fitness has a NET decrease. Population geneticists know this.

          DNA is not simply a collection of chemicals, it is an arrangement of chemicals that serves a functional purpose. The properties of the arrangement are expressed as it is translated, the fact that RNA generates amino acids and proteins, which are produced in such a way that they fold in a specific manner to perform a specific function and not a set of electrical impulses on a graphical display does not mean this is not a computer.
          DNA -> RNA -> protein is a functional superset of computer code -> instruction set -> 3D printer
          A 3D printer needs a computer program that takes a 3D CAD model (an efficient representation of the target model) and processes that to produce an instruction set that the printer can use to make the model. OK so we could store the entire printer instruction set instead and run that … that would work fine (very inefficient) for a static 3D model, not for one that needed to be assembled though, you’d definitely need a program for that to synchronise and manage the processes … oh and you need to build the printer as well and copy the instruction set, that needs a program. Oh and you need to print millions of parts that are all functional and need to be generated at the correct time and the whole moving model needs to work without interruption while it is being assembled.

          So as you can see you need “programs” that control flow, logic, timing at a very minimum. As you mentioned DNA is much more complex than this and needs to also be able to respond to environmental input, turning modules off and on as it responds to environmental changes.
          Epigenetics is a completely separate subject and not really relevant to what we’re discussing here.

          In contrast to your statement:
          The only purpose for trying to not compare DNA to a computer program is to avoid comparing DNA to a system that requires an intelligence to make it.

          I thought we were discussing science, why are you trying to change the subject?

          • SmilodonsRetreat

            Stop right here: “I’m not claiming we can describe and quantify the functions in DNA … only that we know it has them.”

            1500 years ago, everyone KNEW the Earth was flat.
            700 year ago, everyone KNEW the sun went around the Earth.
            You KNOW that the DNA has logic functions even though you can’t describe them, identify one or even how many there might be?

            When you say things, I’m going to need citations. Your 19k protein sites producing 100k proteins, for example. Really? Are you talking about alleles here? or totally different proteins?

            I couldn’t care less about blueprints. It ALL an analogy. If you want to talk about DNA, then let’s talk about it. What your doing now is trying to convince me that an ANALOGY for a thing is correct. Really?

            Again, you can’t take a mutation in isolation. That just shows you have no idea what’s going on. You have to consider the ENVIRONMENT. The environment also includes other mutations. Darwinian Evolution on a Chip by Gerald Joyce. A mutation that decreases ribozyme efficiency by itself, more than doubles the ribozyme efficiency when combined with another mutation .

            I am discussing science. YOU are discussing analogies.

            • cryptoguru

              Stop right here: “I’m not claiming we can describe and quantify the functions in DNA … only that we know it has them.”

              > 1500 years ago, everyone KNEW the Earth was flat.

              haha, oh dear, you really need to do a bit more reading … people did not believe the earth was flat 1500 years ago

              http://en.wikipedia.org/wiki/Myth_of_the_Flat_Earth

              In fact people have believed in a round earth for at least 2500 years by the ancient Greeks, the Old Testament Bible also says the earth round (in Isaiah), which would have been understood to be a sphere (they had no separate word for sphere in Hebrew) and that it is suspended in space (in Job).

              > 700 year ago, everyone KNEW the sun went around the Earth.

              wrong again …

              according to Lucio Russo, the heliocentric view was expounded in Hipparchus’s work on gravity. (source: Lucio Rosso, The Forgotten Revolution, How Science was Born in 300BC and Why it had to be Reborn, pp 293-296). Hellenistic Jews believed in Heliocentricity.

              It was not until the 16th century that a fully predictive mathematical model of a heliocentric system was presented (by a Catholic cleric)

              So heliocentricity has been accepted for thousands of years … what’s your point exactly? That long-held paradigms of science can be wrong in the light of new discoveries? That’s exactly my argument here.

              > You KNOW that the DNA has logic functions even though you can’t describe them, identify one or even how many there might be?

              this is all standard stuff … I’ll stick to Wiki to avoid being accused of getting obscure and using unconfirmed research to support my view

              http://en.wikipedia.org/wiki/Noncoding_DNA

              (copying from the Wiki article in case you can’t be bothered to read it)

              “many types of noncoding DNA sequences do have important biological functions, including the transcriptional and translational regulation of protein-coding sequences, origins of DNA replication, centromeres, telomeres, scaffold attachment regions (SARs), genes for functional RNAs, and many others”

              regulation of anything is a logical function!

              if (this_is_true) then

              express_this_gene

              else

              express_that_gene

              I don’t see what your scientific problem with this is (other than you don’t like where the conclusions head), look at genetic switches etc.

              http://www.ncbi.nlm.nih.gov/books/NBK26872/

              Entire modules of DNA (like subroutines) are switched off and on … functional regulation.

              > When you say things, I’m going to need citations. Your 19k protein sites producing 100k proteins, for example. Really? Are you talking about alleles here? or totally different proteins?

              http://www.sciencedaily.com/releases/2014/07/140703112830.htm

              TOTALLY DIFFERENT PROTEINS … again, this is all well-known stuff.

              http://publications.nigms.nih.gov/insidelifescience/genetics-numbers.html

              > I couldn’t care less about blueprints. It ALL an analogy. If you want to talk about DNA, then let’s talk about it. What your doing now is trying to convince me that an ANALOGY for a thing is correct. Really?

              I’ve been talking about real DNA with references to literature and VERY basic logical arguments that show how DNA is functional code (widely held nowadays) and therefore because it is non-linear and functional and translated (executed), it fulfills (as part of the living cell) the definition of a Turing machine … so it IS a computer. In fact DNA is more identifiable as a Turing machine (physically it’s closer to Turing’s description) than the electronic computers we have today.

              > Again, you can’t take a mutation in isolation. That just shows you have no idea what’s going on. You have to consider the ENVIRONMENT. The environment also includes other mutations. Darwinian Evolution on a Chip by Gerald Joyce. A mutation that decreases ribozyme efficiency by itself, more than doubles the ribozyme efficiency when combined with another mutation .

              Just because you say I have no idea what’s going on, doesn’t make that true. My argument was about the NET effect of mutations, we see that it is degenerative.

              http://www.nature.com/nrg/journal/v13/n8/pdf/nrg3241.pdf?WT.ec_id=NRG-201208

              http://www.nature.com/nature/journal/v488/n7412/full/nature11396.html?WT.ec_id=NATURE-20120823

              Checkout what the actual science shows the mutations do … proband autism, dwarfism, schizophrenia, epilepsy consititutes the vast majority of mutations. The rest are unclassified … none in population studies have been seen to be advantageous. What you discuss is identifying individuals who have a mutation that could be advantageous … this is not how statistic works. How is even an advantage going to persist and propogate when it is 1 in a million and diluted through reproduction against all these negative de novo mutations? How does natural selection measure an increase in fitness for that one individual when they also carry at least 50 negative mutations as well? You’re talking about voodoo-science, something that is not observed or even logical.

              > I am discussing science. YOU are discussing analogies.

              YOU are doing the equivalent of looking at the effects of gravity and pretending that gravity is just some invisible pixies pulling on objects using invisible strings. I’m demonstrating how it’s more complicated and less absurd than that with actual science to back it up. Your blueprint analogy is vastly deficient, you still haven’t address that. I’m not claiming that DNA is the same as a PC, I’m claiming the cell is a computer in the proper definition of the word. My comparison of the different parts of a cell to a PC is an analogy … my assertion that the living cell is a computer is not.

              Hope this helps clarify the points.

            • SmilodonsRetreat

              Whatever, the point was not WHEN people knew something, but the fact that they KNEW something that wasn’t true. Though I gues that explains why you are arguing than an analogy is true.

              I haven’t addressed my blueprint analogy because it’s an ANALOGY and I don’t care. If you want to talk about DNA then talk about DNA.

              “How is even an advantage going to persist and propogate when it is 1 in a million and diluted through reproduction against all these negative de novo mutations?How does natural selection measure an increase in
              fitness for that one individual when they also carry at least 50
              negative mutations as well?””

              It’s called population genetics. And it’s been a highly regarded field of research for almost 100 years.

              Again, the vast majority of mutations are totally neutral. You will now stop lying about this.

              One positive advantage, however small, will TEND to cause the organism to reproduce. You list dwarfism as a disadvantage. Which is a mistake. It’s an advantage if you are trapped on a small island. Pygmy elephants, rhinos, and people.

              You have to stop looking at mutations and determining if they are beneficial or deleterious based on your own idea of what “good” is. You must compare it to the environment. If you don’t do that, then you are doomed to fail.

              Then NET effect in Joyce’s work was a 94 fold increase in ribozyme efficiency in less than 72 hours of reproduction in a highly mutational environment. You should read the paper before you try to reject it.

              So, now you have identified the logical process yes. I thought you couldn’t do that. What website did you read that from?

              This source : http://www.sciencedaily.com/releases/2014/07/140703112830.htm
              does not support your claim that 17,000 gene code for 100,000 proteins. Please document that claim.

            • cryptoguru

              > One positive advantage, however small, will TEND to cause the organism to reproduce. You list dwarfism as a disadvantage. Which is a mistake. It’s an advantage if you are trapped on a small island. Pygmy elephants, rhinos, and people.

              HAHAAA!! Seriously, that’s amazing … best laugh I’ve had in ages. That was a joke right? Like Ewok Island … but with mini elephants? Or Willow!!

              Seriously though, Dwarfism is a genetic disease, which causes a spectrum of medical issues … it is NOT an advantage. Checkout bone dysplasia, they’re not just shorter, their bones are crooked too. You’re arguing that if the environmental conditions are correct then all the neutral/negative things can be seen as positive. We SEE 50-100 de novo mutations introduced at every generation … we’ve identified only a tiny handful of rare mutations that could be considered advantageous in certain circumstances … even if all the other mutations were “neutral” and not harmful, they would still overwhelm the code. They are copying errors, neutral does not mean good, especially when they accumulate, neutral means bad, but hasn’t had a measurable effect yet. It’s like arguing that eating an LDL rich diet when you’ve got Atherosclerosis isn’t harmful, it’s neutral, because on a day to day observation it’s having no discernible effect … it is accumulating, eventually it will kill you (if something else doesn’t first). You still haven’t explained any selective mechanism that could persist these “advantageous” mutations.

              Anyway we’re going waay off topic here … let’s stick to the stuff about computers, bacause that’s what the initial post was about. Happy to discuss the other stuff somewhere else so we’re not jumping between arguments.

              > Whatever, the point was not WHEN people knew something, but the fact that they KNEW something that wasn’t true. Though I gues that explains why you are arguing than an analogy is true.

              Firstly, you just tried to make a point from something that likely never happened … i.e. that people KNEW the world was flat. If you’re wanting to argue science here, you should really know what you’re talking about.

              Secondly, it’s not possible that they “KNEW something that wasn’t true”.

              The definition of knowledge (in the Oxford dictionary) is “True, justified belief; certain understanding, as opposed to opinion.” So they didn’t KNOW the sun orbited the earth … they were believing a lie. A better understanding of what’s actually happening through observation helps us to learn the truth and acquire knowledge.

              So what’s my point? Well, your comparison of my “we know that DNA is functional” claim and your claim that “ancient civilisations KNEW the sun orbited the earth” are not equivalent. Ancient civilisations believed the sun orbited the earth because they misunderstood what they observed as they could not see outside of the domain that they were trying to analyse. When science started to understand more about what we were observing, they were able to prove that it was the other way around. We OBSERVE DNA performing functional operations, this is not an analogy or a guess, or wishful thinking it is truth and therefore knowledge, and therefore not something that will change. We won’t suddenly find that all the laws of logic can break and the non-linearity, multi-dimensionality (DNA folds and expresses different proteins across the folds you know?) and functional dependencies found in the expression of DNA aren’t there anymore … any more than we will find tomorrow that it was the sun orbiting the earth all along.

              You are the one who is quoting yesterday’s beliefs as fact … we now know that is not true, so you will be the flat earther if you cling to misinformation and refuse to accept that DNA is not a functional non-linear computing entity.

              BTW: you still didn’t address my point about the biological computer … if a cell is able to be hijacked by us and used as an actual computer with our own simpler codes, how is the cell not a computer? When we’re using it as a computer!!

              http://med.stanford.edu/news/all-news/2013/03/biological-transistor-enables-computing-within-living-cells-study-says.html

              With reference to that article it says
              “the Group, updates the number of human genes -those that can generate proteins- to 19,000; 1,700 fewer than the genes in the most recent annotation, and well below the initial estimations of 100,000 genes”

              They guessed it had 100K originally because that’s how many different proteins are expressed. Here read the last bit

              “The sources of human complexity lie more in how genes are used rather than on the number of genes, in the thousands of chemical changes that occur in proteins or in the control of the production of these proteins by non-coding regions of the genome, which comprise 90% of the entire genome and which have been described in the latest findings of the international ENCODE project, a Project in which the Valencia team participates.”

              “HOW GENES ARE USED”, “CONTROL” … i.e. polymorphism, multifunctionality.

              I’ll dig out more papers to support this if this doesn’t do it for you.

            • Doc Bill

              OMG, NotGuru is on the right track, but not with the computer analogy; that’s too new. DNA is very old so there must be an older analogy that also points to a Higher Power (cue choir).

              I know! DNA is like a recipe but not any old recipe. DNA is like a recipe in Julia Child’s book “The Art of French Cooking!” I always looked upon Julia as a god and it makes perfect sense. The cookbook represents all the genes.

              The DNA Recipe (might as well capitalize Recipe like a good little creationist) contains the ingredients, amino acids and other stuff, to make proteins and other stuff. The instructions in the recipe describe the tertiary structure (folding, NotGuru – look it up). Different chapters – soups, appetizers, salads – correspond to different protein families. The kitchen is the cell with all the support structures – pots, pans, utensils, ovens, sinks, etc – to get everything “cooked,” rather, Cooked and there’s even a Pantry for raw materials, and a trash can and garbage disposal for waste.

              Just as every watch has a Watchmaker, and every painting has a Painter, every cookbook has Chef. Do you think that all the words in the Cookbook just appeared randomly as if a tornado had blown an infinite number of pens, typewriters and monkeys through a print shop? NO! The Information, Cooking Specified Information or CSI, had to come from an intelligent agent or at least a cordon bleu Chef.

              I now challenge the brilliant mind, and I use the term loosely, of NotGuru to poke holes in my analogy but good luck with that; it’s perfect!

    • SmilodonsRetreat

      hmmm… my response to ccrytoguru is not showing up.

      Trying this.

      Please describe the logical functions in DNA.

      The ENCODE project defined “functional” so loosely as to be almost useless. http://pandasthumb.org/archive

      You said:
      “Mutations to DNA are also deleterious, we have never observed a genetic
      mutation that has a purely advantageous effect (getting malarial
      resistance through Anaemia is not advantageous … having your feet
      amputated would also prevent Athletes Foot). We see thousands of
      damaging and harmful mutations though, that ironically DNA is trying to
      fix with its error correction routines. If DNA is optimised to mutate,
      why does it try its best to stop any mutations? If you randomly mutate a
      large operating system small amounts you will often see no discernible
      difference for a while as rarely used or negligible functionality is
      changed or deleted, but eventually the computer will crash … in
      biology we call that death. That’s exactly how our bodies stop working
      as mutations enter our cells every cell division and cause ageing,
      eventually this affects critical processes in our body, this is what
      cancer is … a deleterious mutation that propagates”

      There
      is so much in here that is wrong, half wrong, partially wrong, and
      partially correct that it’s almost impossible to pick apart totally.
      I’ll say this, since your premises are all completely or partially
      wrong, then your conclusions, no matter how logically correct, are also
      wrong.

      There are many positive mutations. I’ve noted many in this
      blog. For example, Lenski’s E. coli Your example of the sickle cell
      mutation is a positive mutation IN THAT ENVIRONMENT. And that’s a
      critical fault in your DNA is a computer program explanation. Computer
      output is not changed by environment. Biological output is dependent on
      environment.

      The VAST majority of mutations have zero effect. I’ve written about this several times as well.

      If
      you randomly mutate actual computer code, then compile it, There is a
      huge chance that it will not work… unless you just happen to hit data
      in an object or some such. In other words, computers are completely
      opposite of biology. In biology, the vast majority of mutations do
      nothing… one reason is that the vast majority of DNA doesn’t actually
      do anything (again, see the reviews of ENCODE by actual scientists).
      However, the vast majority of random mutations in computer code NOT
      DATA, but the code itself will be purely detrimental.

      DNA is not optimized to mutate, except in specific places, for example, the immune response parts of human white blood cells.

      You really know what causes aging? Wow, you should publish and get a nobel prize. That’s pretty awesome.

      Cancer
      patients die not from the fact that the tumors exist, but because the
      tumors cause blockages in normal components or consume too many
      resources.

      I need to remind you that DNA is not the ONLY thing
      that influences proteins. There are epigenetic effects. There are
      changes to the proteins made after the protein is built by the
      ribosomes. You aren’t taking those things into effect.

      So, I’m
      sorry, but I still don’t buy this analogy. And it is still just an
      analogy. We can talk about DNA and the processes without comparing to
      other systems and process with various values of analogousness.

      The
      only purpose for trying to compare DNA to a computer program is to try
      to compare DNA to a system that does require an intelligence to make and
      therefore try to show that god created DNA. But that’s a waste of time.
      If you want to talk about god, then talk about god and provide
      evidence. If you want to talk about DNA, then talk about DNA.

    • SmilodonsRetreat

      Once again, Disqus isn’t posting my comments:

      1) So, cryptoguru, you have moved the goal posts. I’m beginning to see a lot of creationist tactics here. Argument by analogy. Argument from authority (I’m a cryptographer). Moving the goal posts.

      Please read the OP again, heck just the title. It says DNA is not like a computer. I never said that the cell wasn’t complex system that manipulates data, produces products, etc. But the claim that the cell is a factory or turing machine or anything else is still just an analogy.

      An analogy is a tool to describe a complex idea to someone who has no references for that concept. I could go into a long discussion of very detailed steps of transcription, translation, etc. But it would probably be meaningless to you (despite containing lots of information). You don’t have the references for it. So I create an analogy that contains ideas you can understand. The DNA is like a blueprint. The ribosome is like a factory production line. The Golgi body is LIKE a packaging plant. etc.

      But it is useless to start arguing that the ribosome is more like a production robot than a factory production line. This is like arguing about who is faster, Superman or the Flash. It could be fun, but it’s a waste of time.

      Instead, you could be learning about the ribosome and what it actually does, how it does it, and what the results are. But no, we’re arguing about whose analogy is more correct.

      2) So, to you, the phrase

      “the living cell is a Turing machine”

      and

      “Turing machines and cells have much in common”

      Are exactly the same.

      I think I begin to see the problem…

      Which is why you are still arguing about an analogy instead of arguing about DNA.

      What does a Turing machine do? It manipulates a set of data according to rules. With careful programming, the Turing machine could be made to emulate any algorithm or anything else.

      However, DNA is not the Turing machine is it? It’s the data. Isn’t it?

      3) While you can say whatever you like. You are STILL conflating information and meaning. That’s why I said “Shannon information”.

      information is not meaning. Meaning is not information.

      I really don’t know why this is hard. It’s basic information science. Stuff that an expert like you should be very familiar with.

      So, let’s see what we have here. We have an “cryptology expert” who doesn’t understand Shannon information. He’s also a computer expert. And has very limited knowledge of biology.

      • cryptoguru

        Oh my word … I’ve countered every point you made with actual science, and yet this is your defence?

        You introduced fallacy after fallacy in a wonderful Gish Gallop style .. all of which I’ve addressed, with scientific research and links to papers and articles and widely understood definitions in dictionaries.
        You twist my words, claim nonsense about Shannon’s theorem, pretend that White Noise is information, are unable to read articles written by evolutionists who discredit your uneducated opinion and make stupid conclusions at every post.

        I never said I was right because I was a cryptographer, I said you picked the wrong person to argue this topic with, I know what I’m talking about. Then I posted independent verification of the facts.

        The only thing you have against what I’m saying is that you think it may rock your evolutionist boat and that is completely unacceptable.

        SO … post some science to show me where I’m wrong! I’m waiting.

        Time for you to Retreat methinks.

        • SmilodonsRetreat

          Why? I’ve already showed you the things you link to do not say the things you think that they do.

          You have changed your argument (as noted above).

          And you know what… WE’RE STILL ARGUING ABOUT AN ANALOGY.

          The cell is a cell. DNA is DNA. Why don’t we talk about that instead of arguing about whether the cell is a turning machine?

          I don’t know why not.

          You’ve posted some interesting articles. But so what if DNA has multiple reading frames. There’s no law that says a exon can’t also be an intron. And that an intron can’t be an intron for two different proteins.

          That sure doesn’t support your claim that 17,000 genes codes for 100,000 proteins.

          • cryptoguru

            the point comes down to the fact that your article hit out at creationists for thinking that DNA is processed like computer code and you used Bilbo’s argument about it not being this and that and the other to show that it’s nothing like that (presumably to avoid the fact that when a computer code mutates; it breaks it … but DNA magically evolves from Bananas to Barack Obama instead of crashing)

            ALL the research I’ve shown you by evolutionists proves the exact opposite of your claim. So you’re changing the story now in a slippery evolutionist way … I’m being straight forward.

            Here is my argument again so you can’t misrepresent it
            1) you said DNA does not work like a computer and is not processed like a computer processes.
            2) I challenged that assumption with LOTS of research, articles etc
            3) you insulted me, tried to sidetrack the argument with other unrelated nonsense about white noise and claiming that I don’t know my Biology and now don’t know that White Noise is magic too.
            4) I’m hitting my head against the wall … this is my first ever interaction with evolutionists on a blog … I’ve been avoiding it for years (but felt like it would be nice to get the other side for once) … you guys really are even more wilfully ignorant than I thought.

            I haven’t changed my mind about the living cell being a computer, and DNA being computer code. I’ve used the Turing machine to show you that. The Turing machine is a computer … you keep trying to argue from equivocation.

            Now you’re on a mission to show that DNA has no meaning … tell you what … go live next to some radioactive waste for a few years … let’s see how all the extra information-rich point mutations make you a better person.

            I proved to you the cell is like a computer … a Turing machine … DNA holds information, which has meaning to the translation process, which makes use of that meaning to make someone who is capable enough to buy a computer and argue on an internet site that their DNA is not a computer.

            P.S I never said 17K … I said 19K … and they reckon it’s more like 200-300K proteins … I was just being generous. I posted an article earlier that mentioned at least 100K proteins when we discussing it.

            • SmilodonsRetreat

              “1) you said DNA does not work like a computer and is not processed like a computer processes.”

              And you agree with me. You have changed your idea to “a cell is a turing machine”. In fact, you claimed (wrongly) that you never said that DNA was a computer. I quoted you saying other wise.

              “2) I challenged that assumption with LOTS of research, articles etc”

              None of which say things that are relevant or correct to the claim “DNA is like a computer”

              “3) you insulted me, tried to sidetrack the argument with other unrelated nonsense about white noise and claiming that I don’t know my Biology and now don’t know that White Noise is magic too.”

              I didn’t insult you. I said what I thought. If you are insulted, then perhaps you should consider why I said what I did.

              YOU brought up information. I didn’t. I just showed that you, like many others, all of whom are creationists, conflate meaning and information. Which you have done and continue to do.

              “4) I’m hitting my head against the wall … this is my first ever interaction with evolutionists on a blog … I’ve been avoiding it for years (but felt like it would be nice to get the other side for once) … you guys really are even more wilfully ignorant than I thought.”

              We’re not the ones making mistakes. You are. Your own cognitive biases are your own problem. Can you not actually see that you claimed one thing several days ago and are now saying that you never said that?

              “I haven’t changed my mind about the living cell being a computer, and DNA being computer code. I’ve used the Turing machine to show you that. The Turing machine is a computer … you keep trying to argue from equivocation.”

              You are trying to argue to support AN ANALOGY!!!!! And you talk to me about arguing from equivocation. You conflate computers and Turing machines. You conflate meaning and information. (Conflate means to combine two or more things into one.) A turing machine is a system for changing data according to rules. At best, a Turing machine is a CPU and memory. It is not the data, the data storage, or the other elements required in a computer.

              “Now you’re on a mission to show that DNA has no meaning”

              That’s a lie. You are now adding “purposeful misrepresentation” to your list of problems here. Why is that?

              “go live next to some radioactive waste for a few years … let’s see how all the extra information-rich point mutations make you a better person.”

              Do you think that’s how it works? Do you think that is how I think it works?

              And you talk about me being willfully ignorant. Wow.

              Evolution is about populations. Not individuals. Mutations occur at the individual level, but unless they happen in the gamete, then they can’t go to the next generation. Please, learn some actual biology before doing this anymore.

              “I proved to you the cell is like a computer … a Turing machine … DNA holds information, which has meaning to the translation process, which makes use of that meaning to make someone who is capable enough to buy a computer and argue on an internet site that their DNA is not a computer.”

              No. You are saying that an analogy is better than I give it credit for. Of course, that’s NOT what the article is about is it?

              And now you’re just getting snippy. What’s the matter, I’m not taking your word for it and showing you that your references are not that useful?

              For example, you posted an article about duons, that is, snippets of genetic code that are used in more than one gene. That’s pretty cool. Thanks. It’s meaningless to our discussion… because computers don’t do that. Unless you are claiming that my spreadsheet show financial data can also be used as my data for a World of Warcraft character.

              “P.S I never said 17K … I said 19K … and they reckon it’s more like 200-300K proteins … I was just being generous. I posted an article earlier that mentioned at least 100K proteins when we discussing it.”

              OK, you never said it. You still haven’t given any support for it. The article you linked to did not list any number of proteins… just genes. That was all. I read it. Perhaps you would care to again?

              I’d like to point out to you, because it doesn’t appear that you are aware of this, that the common biology model of DNA -> mRNA -> protein is not entirely correct.

              There are many methods by which DNA, mRNA, ribosomes, and proteins can be changed without being directly influenced by the nucleotide sequence in the DNA.

              For example,

              “Here we show, using a new four-dimensional separation system, identification of 1,043 gene products from human cells that are dispersed into more than 3,000 protein species created by post-translational modification (PTM), RNA splicing and proteolysis.”http://www.nature.com/nature/journal/v480/n7376/full/nature10575.html

              Most of the proteins are closely related to each other. So while there would appear to be a 3:1 protein:DNA correspondence. That’s not really the case. The mRNA may have come out of the transcription process exactly the same. But post transcription processes have altered the RNA and/or protein.

              You have the right to not change your mind. I couldn’t care less. You came here arguing about an analogy and have continued to do so.

              Yes, information technology tools can be applied to biological systems. Yes, computer programming and other computer processes can be applied to biological systems. These tools can provide insight and some fascinating knowledge that we wouldn’t have otherwise had. It still doesn’t mean that DNA is a computer.

              Evolutionary tools are applied to everything from stock markets to factory scheduling. It doesn’t mean that stock markets and factories are biological systems that can evolve.

              If you want to talk about DNA or the cell or the like. Let’s talk about it. But you (and I) have been arguing for several days now as to whether an analogy is valid or not.

            • cryptoguru

              Oh man … let’s go over this one more time.

              You made an argument “DNA is not like a computer” … you were setting up a straw-man argument. So when I addressed the intention of your article (rather than the actual title) you bait and switch and say that “aha! I never said the cell isn’t like a computer I said DNA is not like a computer” … So ARE you saying the cell is like a computer???

              I don’t know what you’re saying anymore, it changes with every twist and turn … trying to get a straight-forward and logical train of thought from you is frankly impossible.

              I obviously took it one step further, because I’m allowed to … and said “actually the cell IS a computer, it’s not just like one” … i.e. NOT AN ANALOGY (you can underline that and put it in bold in your calendar if that helps)

              I demonstrated that quite well by defining what a computer is … a modern computer is an instance of a Turing machine. If you can prove that something is a Turing machine, it’s a computer … they’re the same thing!! It doesn’t need to run Excel to be called a computer. It’s the nature of the system that determines if it’s a computer or not. We did that already .. and other people are saying the cell works this way, with DNA operating as the computer code (like I said earlier)

              WRT meaning/information … I stand by my assertion that in this application information is an arrangement of things (chemicals) to convey meaning (to the transcription/translation processors). The wider understanding of information/meaning is really a philosophical argument, and seeings as I’m not a philosopher I am willing to be wrong on this. It doesn’t really matter for this specific example, I’m not trying to generically define information and meaning … DNA carries a code (information) that is intended to be run by the cell. This information means something to the processor of the cell. The same way that IKEA instructions mean something to you if they are written for you to understand (and not in Japanese for example) so that you can build a cupboard to put all of Bilbo’s massive shoes in.

              “I’d like to point out to you, because it doesn’t appear that you are aware of this, that the common biology model of DNA -> mRNA -> protein is not entirely correct.”
              Yes I’m fully aware of this … and you are arguing my point for me. Post transcriptional processes are controlled by RNAs interacting with RBPs … to create multi-functionality. Where does that functionality come from? It doesn’t happen randomly … it was original stored in DNA, unpacked and processed in a non-linear fashion to affect the manufacture and assembly pipeline. Regulation can occur at any of the stages (transcription, translation, protein) … RNA isn’t always transported to the cytoplasm either, it can hang around in the nucleus and be used later for differential processing. This is EXACTLY what I have been saying … multiple levels of control, state management, functional expression these are computational processes that are all stored in a compressed state in the DNA.
              Glad we agree on that.

              Some sources are claiming that as many as 2 million different types of protein (finding it difficult to find reliable numbers and sources on this … everyone agrees there’s a lot more than 19K) are generated from the human genome. But there’s only 19K protein genes. Where does all this regulation and control come from? It’s information stored in the noncoding DNA that has been expressed in different ways and affects the generation and assembly of proteins.

              So tell me … how can a DNA code, with multiple levels of functional complexity evolve without breaking? If you change DNA that codes for a specific protein you likely break MANY others. How can selection choose the fittest, when your isolated and rare advantageous mutations are introducing syntax errors into the code?

              BTW:
              This book says 2 million.
              https://books.google.co.uk/books?id=3ZvIAAAAQBAJ&pg=PA304&lpg=PA304#v=onepage&q&f=false

              Also Evolutionary models are great for solving puzzles … I used one to solve the 2048 game last week … no evolutionary models I have seen even attempt to model what evolutionists claim is happening. So are useless for modelling evolution. Mendel’s Accountant is the only one I know of that does a decent job … and that shows that evolution is impossible due to the high entropy in the genome.

            • SmilodonsRetreat

              Well, I guess that takes of that. You have proven that the wiring in my computer, which was built by the CPU, directly affects how the video appears on my screen and can even change the video on my screen… exactly like a cell.

              If you don’t understand evolutionary algorithms, you need to learn more about your chosen field. There are even evolutionary algorithms used in cryptography research.

              But, now we get it. The question that seems to be cause of your issues.

              “So tell me … how can a DNA code, with multiple levels of functional complexity evolve without breaking?”

              The answer is, easily. Trivially. All the time. I’d like to retype all the things about evolution I’ve already written about here several times. But I’m not. This isn’t a super easy concept, but it’s pretty obvious.

              http://www.skepticink.com/smilodonsretreat/2014/02/06/can-mutation-cause-changes-part-2/

              http://www.skepticink.com/smilodonsretreat/2014/02/20/most-mutations-are-harmful/

              http://www.skepticink.com/smilodonsretreat/2014/01/22/mutations-do-create-new-abilties/

              http://www.skepticink.com/smilodonsretreat/2013/02/24/weaknesses-of-evolution-part-10-most-mutations-are-harmful/

              http://www.skepticink.com/smilodonsretreat/2013/02/24/weaknesses-of-evolution-part-9/

              http://www.skepticink.com/smilodonsretreat/2014/02/16/evolution-of-associated-proteins/

            • SmilodonsRetreat
            • Doc Bill

              Dear LyingWankerNotGuru aka Old Cobber,

              You wrote the following in your very first post and I quote so don’t try to lie, you bastard, and say you didn’t write this:

              “DNA is exactly like a computer program, the cell is like a computer … let me explain why.”

              LIKE a computer program and LIKE a computer.

              That is a fucking analogy, not a statement of fact. You didn’t write “DNA is a computer program” and “the cell is a computer.” You fucking wanker!

              A recipe is like a program and a kitchen is like a computer. Nicely put if I do say so myself.

              A city council is like a program and city services is like a computer.

              A forest is like a program and an ecology is like a computer.

              Peanut butter and jelly is like a program and a peanut butter sandwich is like a computer.

              NotGuru, you are one dumb fuck.

    • SmilodonsRetreat

      So, we have wasted all this time.

      Because I never said that the cell wasn’t a Turing machine. And a Turing machine is not a digital computer.

      Perhaps you should have read my title.

      I’ll also note that cryptoguru started arguing that the DNA was like a computer (” I’m simply showing you the science and asking you to validate your claim that DNA is not like a computer, when it clearly is” ) . and how has changed his argument to “the cell is a turing machine”.

      Oh, by the way, you did say that DNA was a computer so, this statement “I never said DNA is the Turing machine”, is a lie.

      So, thank you very much for wasting all of our time. Well done.

      Feel free to go away now.

      • Beth Hambridge

        Although a year has past since you have written the above, you have not wasted your time,,,TY for the info 🙂

    • SmilodonsRetreat

      I’ll probably shut down this discussion. Disqus is not behaving correctly. In this thread, I’ve posted maybe 8 comments that haven’t gone through.

      Here’s the last one. The quotes are guru’s.

      “1) you said DNA does not work like a computer and is not processed like a computer processes.”

      And you agree with me. You have changed your idea to “a cell is a turing machine”. In fact, you claimed (wrongly) that you never said that DNA was a computer. I quoted you saying other wise.

      “2) I challenged that assumption with LOTS of research, articles etc”

      None of which say things that are relevant or correct to the claim “DNA is like a computer”

      “3) you insulted me, tried to sidetrack the argument with other unrelated nonsense about white noise and claiming that I don’t know my Biology and now don’t know that White Noise is magic too.”

      I didn’t insult you. I said what I thought. If you are insulted, then perhaps you should consider why I said what I did.

      YOU brought up information. I didn’t. I just showed that you, like many others, all of whom are creationists, conflate meaning and information. Which you have done and continue to do.

      “4) I’m hitting my head against the wall … this is my first ever interaction with evolutionists on a blog … I’ve been avoiding it for years (but felt like it would be nice to get the other side for once) … you guys really are even more wilfully ignorant than I thought.”

      We’re not the ones making mistakes. You are. Your own cognitive biases are your own problem. Can you not actually see that you claimed one thing several days ago and are now saying that you never said that?

      “I haven’t changed my mind about the living cell being a computer, and DNA being computer code. I’ve used the Turing machine to show you that. The Turing machine is a computer … you keep trying to argue from equivocation.”

      You are trying to argue to support AN ANALOGY!!!!! And you talk to me about arguing from equivocation. You conflate computers and Turing machines. You conflate meaning and information. (Conflate means to combine two or more things into one.) A turing machine is a system for changing data according to rules. At best, a Turing machine is a CPU and memory. It is not the data, the data storage, or the other elements required in a computer.

      “Now you’re on a mission to show that DNA has no meaning”

      That’s a lie. You are now adding “purposeful misrepresentation” to your list of problems here. Why is that?

      “go live next to some radioactive waste for a few years … let’s see how all the extra information-rich point mutations make you a better person.”

      Do you think that’s how it works? Do you think that is how I think it works?

      And you talk about me being willfully ignorant. Wow.

      Evolution is about populations. Not individuals. Mutations occur at the individual level, but unless they happen in the gamete, then they can’t go to the next generation. Please, learn some actual biology before doing this anymore.

      “I proved to you the cell is like a computer … a Turing machine … DNA holds information, which has meaning to the translation process, which makes use of that meaning to make someone who is capable enough to buy a computer and argue on an internet site that their DNA is not a computer.”

      No. You are saying that an analogy is better than I give it credit for. Of course, that’s NOT what the article is about is it?

      And now you’re just getting snippy. What’s the matter, I’m not taking your word for it and showing you that your references are not that useful?

      For example, you posted an article about duons, that is, snippets of genetic code that are used in more than one gene. That’s pretty cool. Thanks. It’s meaningless to our discussion… because computers don’t do that. Unless you are claiming that my spreadsheet show financial data can also be used as my data for a World of Warcraft character.

      “P.S I never said 17K … I said 19K … and they reckon it’s more like 200-300K proteins … I was just being generous. I posted an article earlier that mentioned at least 100K proteins when we discussing it.”

      OK, you never said it. You still haven’t given any support for it. The article you linked to did not list any number of proteins… just genes. That was all. I read it. Perhaps you would care to again?

      I’d like to point out to you, because it doesn’t appear that you are aware of this, that the common biology model of DNA -> mRNA -> protein is not entirely correct.

      There are many methods by which DNA, mRNA, ribosomes, and proteins can be changed without being directly influenced by the nucleotide sequence in the DNA.

      For example,

      “Here we show, using a new four-dimensional separation system, identification of 1,043 gene products from human cells that are dispersed into more than 3,000 protein species created by post-translational modification (PTM), RNA splicing and proteolysis.”http://www.nature.com/nature/j…

      Most of the proteins are closely related to each other. So while there would appear to be a 3:1 protein:DNA correspondence. That’s not really the case. The mRNA may have come out of the transcription process exactly the same. But post transcription processes have altered the RNA and/or protein.

      You have the right to not change your mind. I couldn’t care less. You came here arguing about an analogy and have continued to do so.

      Yes, information technology tools can be applied to biological systems. Yes, computer programming and other computer processes can be applied to biological systems. These tools can provide insight and some fascinating knowledge that we wouldn’t have otherwise had. It still doesn’t mean that DNA is a computer.

      Evolutionary tools are applied to everything from stock markets to factory scheduling. It doesn’t mean that stock markets and factories are biological systems that can evolve.

      If you want to talk about DNA or the cell or the like. Let’s talk about it. But you (and I) have been arguing for several days now as to whether an analogy is valid or not.

    • SmilodonsRetreat
    • SmilodonsRetreat

      You know, I think I understand the problem.

      Computer scientists think that everything in the universe is deterministic. While some can see beyond their keyboard and into the real world, others can’t. Perhaps that’s why a large percentage of creationists are engineers and computer scientists.

      They study, work, and live thinking abut a deterministic paradigm. Not realizing that things that aren’t computers or engineered (i.e. biology) is not deterministic.

      Of course, a simple experiment shows this to be untrue. Identical twins, despite having the same genes, can have some differing traits. Identical Twins aren’t: http://www.sciencedirect.com/science/article/pii/S000292970800102X

      The mere fact that environment can change genes, pushes away from a Turing machine type of idea about the cell or DNA.

      • Doc Bill

        Well, except that NotGuru is not a computer scientist, he’s just a typical creationist wanker with an opinion. He should be getting a check from the Disco Tute for his “insight.”

        • cryptoguru

          the problem with biologists is they don’t understand that just because something looks random, doen’t mean it is … chaos is deterministic.

          Take your twins … the changes between the twins is accounted for by functional changes in the epigenome. The epigenome is responding to input, it could be random input, but it responds deterministically. You’re constantly conflating input with functionality. There are no random computer programs that work … but, we have computer programs that implement randomness. Your twins can’t evolve new traits, that’s impossible, the time-frame is too short, you have a population of 1 and no selection.

          Variations in a genome happen too quickly to be evolution, they are variation caused by regulation of genes responding to many different things, some of it hard-coded variables in the DNA, some of it responding to environmental input. This is no more random than a thermostat turning the heating on when Bilbo’s hobbit-house temparature drops below 16 degrees. Heat may vary randomly, but the temperature control function is deterministic and monitors thresholds.

          Alternatively I may want to pick a random variation of a colour when making an eye’s iris, I could do the following

          iris_colour = dads_colour*0.6 + mums_colour*0.3 + random_colour*0.1

          Yes the new colour has a degree of randomness to it, but the function is not random … let’s mutate the function

          iSis_colour = dads_colour*0.6 + mums_colour*0.3 + random_colour*0.1

          Now we’re setting the colour of the Islamic State, but the genome doesn’t know what to do with that.

          These variations and adaptations are built in to the functionality of the genome, they can’t be described by random mutation plus selection … you CAN’T honestly believe that … DO YOU??? There is no population, there are no offspring, there is no selection, just an individual genome responding to input. This can’t be evolution … even if evolution were possible. So the variation between twins has NOTHING at all to do with evolution or random mutations, it’s to do with the variability of the epigenome, which responds to input.

          You haven’t done the basic maths on evolution have you.

          So let me do a little example for you. You believe that random mutation plus natural selection can introduce a new advantage. That means that somebody has to get an advantageous mutation. Therefore some of the 100 de novo random mutations must create an advantage. Lets look at how likely it is for ANY new codon to be inserted, but I’m trying to make it easy for evolution. How likely is it for someone to get a codon change in their DNA through random mutation. So the first base-pair can change anywhere (P=1), the second must be next to it (P=3.125e-10), and the third next to that (P=9.77e-20). Oh! But we get 100 chances to get it right, that’s P=9.77e-18 (pretending nothing bad ever happens). Still not looking great is it … I’ve got better probability winning the lottery twice in a row. So if it’s that hard to get ONE single codon ignoring negative effects and pretending that ANY codon will do (sing Joseph & Technicolor Dreamcoat: Any Dream Will Do), how on earth does randomness get us anywhere at all? Remember you MUST have an advantage at each generation, and it must be preserved somehow magically by natural selection. This is wishful thinking at a Disney level. So don’t accuse me of not understanding “not deterministic” (i.e. probabilistic). A child who’s done a week of basic probabilties at school could poke holes in your argument. (oh I also assumed that any kind of mutation would do point/deletion/insertion).

          You’ll now exclaim that I KNOW NOTHING ABOUT POPULATION GENETICS, because I looked at the individual. I did that because it’s practically impossible to define the “population” in this case. Who is the population that is awaiting the advantageous mutation? Not the whole human race … because it’s too widely dispersed, improvements in Alaska won’t make it anywhere else (nor would we want them to). And what about the selection process? Cumulative selection is supposed to take the winner from the last generation and use it as the basis for the next improvement. So EVERYONE else dies luckily preserving the person with the advantage??? What if you magically developed resistance to Swine flu and there was a Tsunami in your village?? Who gets preserved? Fatter people who float better? You’ve lost the advantage. Natural selection is not intelligent, it’s not setting challenges that only the elite most benefically mutated will endure. But let’s pretend that we’re dealing with a population of 1Million people who we will eventually replace with a more highly evolved race. Our stats are still improbable. The probability of any person in our population getting ANY codon is still 9.8e-12 … a lot less likely than me winning the lottery. How do you explain this? This is unlikely to happen once … you want it to happen repeatedly for every single organism world-wide. HAHA! I do really admire the faith you hold in this process against all odds, against intuition and against observation.

          And NO … again, the environment is used by the genes in the conext of the program as input, like a Turing machine. If the environment changes the code we get undefined behaviour and eventually a crash. It’s still a computer, amazingly, even with input (like every other computer).

          • Doc Bill

            “You’ll now exclaim that I KNOW NOTHING ABOUT POPULATION GENETICS, ”

            Let me condense this.

            You know nothing.

            Now, sober up and piss off.

            • cryptoguru

              hehe … you’re like a hairy little guard dog trying to scare off creationists, from a blog in the Creationism topic. #irony

              Come on Bilbo, engage with me … you know you want to. Entertain the questions, just because it contradicts your religion doesn’t mean you shouldn’t consider the implications of the questions I’m asking, and present qualified counter-arguments.

              Your behaviour is indicative of the sort of evolutionist fundamentalist censorship nonsense that goes on around this subject “OH DON’T TOUCH THE SACRED COW!!!”
              I’m asking you to justify your beliefs that fly in the face of most people’s common sense and fail to show nothing but overly protracted stories with as much terminology in as possible to confound the layperson.

              I bet you were raised in a Christian home weren’t you … you only get this kind of emotional reaction when asking evolution-challenging science questions to people who turned their back on God because of some scientific epiphany. When you use voodoo-science as a crutch to justify your rejection of God it makes you MAD when people question it. Look at Dawkins … complete psycho-nutter, raised in a Christian home. Just rips into creationists with a venom and zeal that is completely illogical if he is correct.

              Logically, though, if you are an objective follower of rational and proven science … why should you get upset with someone like me? The majority of the westernised scientific community agrees with you, they’re on your side … I’m the underdog here. When I ask a question that challenges your science you should be able to present a clear irrefutable and concise explanation backed with observation that anyone could confirm that I’m waaay off base. You’ve done none of those things … and neither has Kevin. But at least he’s having the discussion, even if he does keep wandering all over the place, and has to keep pretending I’m agreeing with him on things.

              Lighten up … get some 2nd breakfast, and look on the bright side … you’re just a bag of chemicals and none of this matters at all. Everything you’re feeling right now isn’t anger, it’s just some random chemical reactions caused by lots of point mutations on some soup.

            • SmilodonsRetreat

              And we have. Every single time. Yes, you seem to present a lot of interesting information. But you don’t get it. The stuff you are giving us, discredits your own ideas.

              You ignore the material I give you and promote the likes of creationists.

              Positive mutations happen. You can’t get past that. Once you do, then you’ll see that everything is OK and evolution actually works. It’s trivial to see it work. Lenski, Joyce, and hundreds of thousands of papers show that it does. Mutations produce new proteins that are better, give different functions, etc. And I’ve linked you to the articles.

              Your entire complaint on all of those articles was that I didn’t talk about translational pausing. That’s it. You think you have dismissed all of the evidence because I didn’t talk about one tiny part. Typical.

            • cryptoguru

              yeah you’re right … I’m not getting how it discredits my ideas.

              I didn’t ignore your material, I explained how it is based on faulty assumptions. Which you keep denying. Randomness can not create order unless it is used intelligently, it’s not possible. It doesn’t matter how many papers you link to that tell stories of an isolated protein that got mutated and now it’s slightly different, this does not explain how your theory violates the laws of nature. Order does not come out of disorder unless there is a prescribed law that determines the order. This is something a child can understand … your room won’t tidy itself, your smashed car won’t repair itself and a book that’s ripped up into tiny letters won’t arrange itself on the floor as a new book. You know this, so you appeal to magic unobservable and untestable processes of natural selection, which are supposed to select from things that don’t exist yet over an observable amount of time. Matter plus energy, plus time does not equal ordered information … ever. You can come up with another edge-case that requires hand-waving and say “pay no attention to the man behind the curtain” … but some of us aren’t stupid enough to accept what we’re told at face value … we’re sceptical of wild and unnatural claims. Ironic that the sceptics now are the ones trying to preserve the status-quo and fend off sceptical creationists.

              You don’t know how the mutations that you consider advantageous got there … it would be more reasonable to assume that some deterministic process controlled by the DNA code has allowed regulation, because we observe those processes. Any manual intervention with DNA that produces an advantageous output is intelligent design and can’t possibly be used to prove that it happens naturally in the wild.

              The fact that codons don’t have redundancy like your blog post attests they do and uses it as a central argument for evolution is NOT a “tiny part”. Specificity of codon mapping means that the genome is even more tightly coupled in its functionality and can’t endure random mutation. Which is why it doesn’t want anyone to change the DNA.

            • SmilodonsRetreat

              Damn it’s getting annoying to try to talk to you. You have no idea what’s going on.

              “yeah you’re right … I’m not getting how it discredits my ideas.”

              Because you aren’t interested in discussion. Just preaching. It is a fact that mutations can create new function and improve existing function. It’s been shown in the lab and in the wild. You have not even attempted to deal with those I posted and the thousands of additional articles that support this.

              Which means that your entire idea that all mutations are bad and only degenerate is WRONG.

              “I didn’t ignore your material, I explained how it is based on faulty assumptions. ”

              No, you did ignore. You pointed out ONE case where an unknown amount of synonymous really aren’t. OK, fine. This is not an unknown process and I’ve already mentioned to you several times that other processes can affect proteins.

              “Which you keep denying. Randomness can not create order unless it is used intelligently, it’s not possible.”

              You may be right, though I could do some research and maybe disagree with you. But the main point is that EVOLUTION IS NOT RANDOM!!!

              You (and other creationists) keep forgetting the idea of SELECTION. Which is decidedly not random.

              “It doesn’t matter how many papers you link to that tell stories of an isolated protein that got mutated and now it’s slightly different, this does not explain how your theory violates the laws of nature.”

              I find this kind of claim fascinating. You think that actual observations of reality are wrong because they disagree with what you believe to be true. Wow.

              “Order does not come out of disorder unless there is a prescribed law that determines the order. This is something a child can understand … your room won’t tidy itself, your smashed car won’t repair itself and a book that’s ripped up into tiny letters won’t arrange itself on the floor as a new book.”

              Is this somehow related to the Second Law of Thermodynamics?

              That’s the only time I see the words “order”, “disorder”, etc thrown about like this with no understanding. What does order mean?

              If it means that complex molecules can’t arise from simply atoms, then it’s fundamentally wrong. Fe + O = Fe2O3. More complex (but lower energy) from simpler.

              If you want a lower complex to higher, with the input of energy, then look at all the various hydrocarbons. C, O, and H, combined by the addition of energy to create more complex (and higher energy) compounds.

              This is very, very basic stuff and shows a fundamental misunderstanding of biology and chemistry.

              “You know this, so you appeal to magic unobservable and untestable processes of natural selection, which are supposed to select from things that don’t exist yet over an observable amount of time.”

              “things that don’t exist yet”, what does that mean? Selection can only work on things that exist, even if only for the lifetime of a single cell.

              You have created (or more likely borrowed) a strawman of truly epi cproportions here.

              “Matter plus energy, plus time does not equal ordered information … ever”

              Define “information” in this case. Are you still conflating meaning and information?

              “You can come up with another edge-case that requires hand-waving and say “pay no attention to the man behind the curtain” … but some of us aren’t stupid enough to accept what we’re told at face value … we’re sceptical of wild and unnatural claims.”

              Your not skeptical. You are a denier. You reject it and have freely admitted that no amount of evidence would convince you.

              I am a skeptic. You provided me with some new information. I’ve already downloaded a few dozen papers and will review them as I get time. I can and will be convinced by evidence.

              “Ironic that the sceptics now are the ones trying to preserve the status-quo and fend off sceptical creationists.”

              Nope. No one ever said creationists can’t have good ideas and be correct about some things. However, as a skeptic, it takes extra effort ton convince me because creationists have a lot of issues dealing with reality (as you have shown).

              Again, you aren’t a skeptic. You are a denier. Big difference.

              “You don’t know how the mutations that you consider advantageous got there … it would be more reasonable to assume that some deterministic process controlled by the DNA code has allowed regulation, because we observe those processes.”

              You yourself mentioned several process and I know of a dozen more… all of which can be examined. Copying errors, radiation of various kinds, other epigenetic factors, DNA methylation and related factors, All of these cause mutations and can be observed and controlled for.

              That paper that you refuse to read by Joyce is an excellent example. He used a RNA polymerase that is known to be low fidelity, thereby increasing the number of mutations per cycle. And still the RNA ribozyme increased in efficiency. By 92-fold in less than 72 hours.

              “Any manual intervention with DNA that produces an advantageous output is intelligent design and can’t possibly be used to prove that it happens naturally in the wild.”

              “Manual” is the key word there. What about DNA changes that are not manual. You are really going to tell me that you don’t know of a single DNA change that has resulted in improved surviability? Wow again!

              “The fact that codons don’t have redundancy like your blog post attests they do and uses it as a central argument for evolution is NOT a “tiny part”.”

              It’s not a “central argument” for evolution and no one ever said it was. Another strawman argument. Well done, your creationist cred is through the roof.

              It’s an explanation for why the vast majority of mutations are neutral. Scientists actually looked at mutations and discovered that the vast, vast majority are neutral long before this discussion took place.

              “Specificity of codon mapping means that the genome is even more tightly coupled in its functionality and can’t endure random mutation.

              And yet, random mutation and selection still have produced all the life around us and no one has been able to show otherwise.

              I know you THINK you’ve shown otherwise, but you have shown, in this post, that you have no idea what’s really going on. You have strawman belief after strawman belief.

              You have stated that you refuse to accept evidence that you are wrong.

              You latched onto ONE minor thing that I didn’t talk about, and ignored all the actual evidence of mutations increasing fitness that I posted.

              “Which is why it doesn’t want anyone to change the DNA.”

              I don’t even understand what you are trying to say. Every human being has about three mutations in their genome. And yet, we still exist just fine.

              You’re wrong. It’s that simple.

            • cryptoguru

              decided to rename you from Bilbo to “Ad Hominem Erectus”

              As you argue ad hominem 95% of the time. At least Kevin uses other fallacies.

            • SmilodonsRetreat

              I have asked you a question. When do you plan on answering it?

              Tell you what, why don’t you visit After the Bar Closes. I’m sure you could handle it. http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=54b43a0d24c5a7bb;act=SF;f=14

    • SmilodonsRetreat

      “So let me do a little example for you. You believe that random mutation plus natural selection can introduce a new advantage. ”

      NO!

      I don’t believe that. I have mountains of evidence to show that it DOES happen.

      If you actually looked at that evidence, you would see it. But it conflicts with your worldview and thus, you ignore the evidence.

      Come back when you have reviewed all the evidence.

      • cryptoguru

        I need a nickname for you Smilodon … I’m going to call you Kevin (the extinct bird from the movie Up).

        Well, Kevin, firstly … your post on harmful mutations is WRONG

        http://www.skepticink.com/smilodonsretreat/2014/02/20/most-mutations-are-harmful/

        You do 2 things wrong here. (on top of assuming that I don’t know what you guys believe happens)

        1) You assume that the codes are redundant … they code for the same amino acid, but the different codes allow different timings in translation. So although GGU, GGC, GGA and GGG all code for glycine they are not functionally equivalent and will end up creating differently folded proteins http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00140/abstract

        A mutation from GGU to GGC will likely create a non-functioning protein

        2) you’re not accounting for multiple reading frames. A mutation in one frame will have an effect on all the other frames. How is that NOT harmful?

        So just looking at one of your articles there’s fundamental flaws that make evolution impossible.

        http://www.skepticink.com/smilodonsretreat/2014/02/06/can-mutation-cause-changes-part-2/

        I’m not claiming that random mutations can’t create new features, but I’m claiming those features are either known to be harmful or have a temporarily neutral effect but will accumulate to have a degenerative one. Don’t mix up variation that is programmed into the Genome to allow epigentic variations by responding to the environment with random de novo mutation … they are NOT the same. The mutation of a control gene that ends up creating an extra mutant leg is not preserved and has never been an observed advantage to an organism.

        You never commented on my sums … how can you justify a probabilistically impossible solution?

        • Doc Bill

          There is no point in engaging you, NotGuru, because what you write is simply wrong, stupid and ignorant. What is there to engage. For example, if a solution is probabilistic it can’t be impossible, can it?

          There is no point in engaging you, NotGuru, because you are a disingenuous liar. You presented an analogy in your very first statement, then denied doing so.

          However, as a creationist chew toy you have provided some positive entertainment value on a grey, wet day. As far as creationists go, NotGuru, unfortunately you’re quite average. Not as excitable and patently moronic as JoeG (denier of ice) or as cognitively challenged as the religious fanatic FL or as boringly repetitive as one-trick-pony Quest or an abject sociopath like BatShit77. No, NotGuru, you’re more like a 4-year old who is not yet potty trained and quite possibly never will be.

          Now it’s time for you to run along and play with your little cell computer.

          OMG, what am I thinking? I forgot about Gary Gaulin. He’s already modeled a cell as a computer – years ago! You’ve been scooped, NotGuru! Gary’s got his very own thread over at After the Bar Closes on the Panda’s Thumb. Silly me!

          Here’s the link:

          http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=54b542ef645992ff;act=ST;f=14;t=7420;st=12780

          • cryptoguru

            “For example, if a solution is probabilistic it can’t be impossible, can it?”

            Of course, you are correct in theory … but in practise, we deem things impossible where the probability is low enough to be so unlikely we should expect it never to happen.
            In cryptography codes are deemed “unbreakable” when the probability of recovering the key is low enough that with a specified amount of resources and effort we would never expect to find the key.

            Also, I don’t believe the genome is probabilistic, which is my whole point. But even when I humour your assumptions, the probabilities don’t work.

            I am not a liar … you just don’t like the facts I’m describing and seem unable to put up a nice straightforward argument for how evolution could even be theoretically possible.

            Anyone can say “there’s mountains of evidence”, “everyone knows it’s true”, “this has been proved a million times over” … then quote a just-so story and then quickly jump to ad hominem.
            A sort of argumentative hit-and-run

            You raise a question … I give an answer .. then you jump straight to insult instead of discussing.

            In proper academia, Bilbo (Ad Homimem Erectus was too long to write), we have to present arguments like that.
            We don’t have the luxury of evolution-based research which can make up a story, put a pretty picture to it, measure something that sounds related … and publish to cheers, rapturous applause and shouts of “praise be to randomness and natural selection, the masterful builder of everything”.

            This is the depth of madness you have to go to when you limit science to exclude any non-material causation.

            I’m well aware of the field of DNA computing, which obviously shows that the living cell is a form of computer, which we are adopting so that we can develop our own languages and use for our own problem solving. (my original point in this discussion topic)

            Again, if DNA specifies all the functionality of an organism, from how it grows, to how to build each material part, to how to assemble them as well as programs behaviour into the organism (brain, reflexes etc) … how can this program develop by pure chance? THAT IS NOT POSSIBLE.

            you can keep saying that’s how it works because we see function and know that random mutation + selection is how we got here, but all you’re doing is begging the question.
            You’re not demonstrating the mechanism.

            Please show me a computer model/ maths algorithm, which models the evolutionary mechanism, that doesn’t cheat by either setting a future target (i.e. isn’t blind .. it’s a search algorithm) or by prescribing functionality (i.e. it’s an AI optimisation algorithm).

            If you can’t do this then your theory is doomed … remember the burden of proof is on you, not me. Mine isn’t the widely held, government approved, media backed theory that is being force-fed to every child and college student and preached on every TV channel to mock and deride the stupid religious people who would dare to question such a water-tight FACT.

    • SmilodonsRetreat

      Guru,

      Once again, I have to question your contact with reality. What you are saying is that

      arginine =/= arginine

      Wow. Your logic is truly stunning.

      Linking to an article by David Abel. Well, I guess that’s just confirmation bias. He says what you want to hear, so you link to him. I find it interesting that you ignore the actual research on the subject and instead forward a link by a guy who works from his house and another guy who works a General Dynamics.

      http://scienceblogs.com/pharyngula/2012/02/04/zooming-in-on-the-origin-of-li/

      http://www.skeptical-science.com/science/claims-peer-review-intelligent-design-examined/

      http://freethoughtblogs.com/pharyngula/2012/02/02/more-bad-science-in-the-literature/

      Now we can add linking to other creationists as if they are actual scientists to your list of creationist credentials.

      But, let’s talk about translational pausing. It’s an interesting concept. Of course, it neatly defeats your idea that the DNA is responsible for everything. Because, I have mentioned multiple times to you, things outside of the control of the DNA can affect the final proteins.

      Let me ask you this. If I provide a peer-reviewed paper that says that a mutation resulting in a translational pause improved the function of a protein, will you stop with your silly assertions that all mutations are bad?

      First, I’ve clearly shown that all mutations are not “bad”. Unlike your claim.

      Second, even those that are “bad”, may end up being “good”, in a particular environment or when combined with other mutations.

      At least we’re not talking about analogies anymore.

      • cryptoguru

        “arginine =/= arginine”

        Eh? I showed that codon mapping isn’t redundant … that’s been proved through translational pausing. So legobrick 1 may be exactly the same as legobrick 2, but 2 has a note attached which says to never put on the bottom of the model … THAT changes everything. If you end up with the brick without the note on it, when you should have a note on it, you’ll build the wrong model.

        Doesn’t really matter who did the research does it if it’s correct. If you think any of the papers/research I posted links to were incorrect in anything they represented I’d be very interested to know.

        I never said the DNA is responsible for everything … but it is the computer code that defines everything (not an analogy). It sets other things up that are responsible for some stuff, and don’t forget it needs its operating system to run in (all the little cellular machines) that understand the code. It deterministically creates the system, which controls exactly how the organism is to be built and grown, including how it should respond to external environmental factors.

        “Let me ask you this. If I provide a peer-reviewed paper that says that a mutation resulting in a translational pause improved the function of a protein, will you stop with your silly assertions that all mutations are bad?”

        Nope! I’m not denying you can create a protein which does something that you think is an advantage .. problem is, how do you know that every other protein or RNA expression affected by that mutation is unchanged? You can’t know that. And also how do you know that what you think is an advantage in one function of the protein isn’t a disadvantage in another functional way? Also probabilistically a mutation is likely to inhibit function somewhere even if it’s not where you’re looking. That’s my point. You can’t isolate an expression and say “look” that’s a bit better. Natural selection doesn’t work on the atomic level anyway, it knows nothing about DNA … it acts on the whole organism. How can natural selection differentiate the good mutation from the bad ones? (and we know of lots of bad ones for sure)

        It’s hardly surprising that creationists have to work from their garage … neo-Darwinian censorship makes sure that a professing creationist can’t get a job in any application of science, publish papers or anything.

        • SmilodonsRetreat

          Codon redundancy isn’t ALWAYS correct and the amount of synonymous changes are unknown at this time.

          That’s a far cry from “Isn’t redundant”

          I thought you said that DNA wasn’t a computer code? You keep changing.

          For your last… in other words, no amount of evidence will convince you. And you say I’m the one with “beliefs”. Wow.

          • cryptoguru

            No I said DNA isn’t a computer … the cell is a computer … DNA is computer code. The cell satisfies the definition of a Turing machine.
            I clarified this when you were trying to catch me out on semantics.
            Your post was that DNA is not like a computer, I explained it is processed like a computer, in fact the living cell is a computer.

            You’re dead right … you can’t break a fundamental law of nature “life from non-life”, “order from disorder without intervention”. It’s not evidence, it’s just-so stories.

            Like with Junk DNA, which was a main argument against creationists for years, which was paraded as “evidence” of evolution. It’s not, never was true. There’s no warehouse of genetic material waiting for the magic evolution squirrel to pick from and fashion into an amazingly perfected yet random design. At least 98% of it is functional, they reckon 100% of it is functional. So your arguments aren’t convincing, especially when it comes to claiming that mutations are beneficial and can be preserved. It’s unintuitive, unobserved and cleverly unobservable.

            • SmilodonsRetreat

              “No I said DNA isn’t a computer … the cell is a computer … DNA is computer code. The cell satisfies the definition of a Turing machine.
              I clarified this when you were trying to catch me out on semantics.
              Your post was that DNA is not like a computer, I explained it is processed like a computer, in fact the living cell is a computer.”

              Which, you and agree with. DNA is not like a computer. I never said anything about the cell…

              “You’re dead right … you can’t break a fundamental law of nature “life from non-life”, “order from disorder without intervention”. It’s not evidence, it’s just-so stories.”

              And yet, every single abiogenesis experiment has resulted in more complex systems coming from less complex systems. Every single biochemical pathway has been shown to be possible, without a designer, without previous life. In fact, most of them have multiple pathways.

              It’s not just so stories. It’s basic chemistry.

              “Like with Junk DNA, which was a main argument against creationists for years, which was paraded as “evidence” of evolution. It’s not, never was true. There’s no warehouse of genetic material waiting for the magic evolution squirrel to pick from and fashion into an amazingly perfected yet random design. At least 98% of it is functional, they reckon 100% of it is functional.”

              Oh good, the ENCODE thing comes back. Well, I guess if your definition of functional is “some detectable chemical activity”, then I guess that’s fair enough. Of course, random DNA, RNA, and amino acids sequences also exhibit “some detectable chemical activity” too. Which neatly blows your ideas on randomness out of the water.

              “So your arguments aren’t convincing,”

              Of course they aren’t. You would never be convinced. You admitted already that no amount of evidence would convince you.

              You have made up your mind and that’s the way it is.

              “especially when it comes to claiming that mutations are beneficial and can be preserved.”

              Which is trivial to show and I have. You ignored all of those posts to focus on one area that I didn’t include everything on.

              “It’s unintuitive,”

              Much of science it that way. When will you stop using your intuition and actually look at the data?

              “unobserved and cleverly unobservable.”

              Clearly untrue as I have posted several observed instances of mutation improving function. There are people on this planet right now who are immune to HIV due to a mutation. There are people who are immune to heart disease due to a mutation. There are dozens of plants and animals that you eat on a weekly basis that exist because of mutations.

              Just stick your head in the sand.

    • SmilodonsRetreat

      I should add here Cryptoguru, that if you have actual evidence for an intelligent designer, then I have an open invitation for anyone with such evidence to have a guest post here.

      • Doc Bill

        NotGuru is clearly turning into Quest – denying evidence, repeating the same creationist tropes over and over, and just making up shit. My kingdom for some fresh meat!

      • cryptoguru

        well there’s mountains of evidence for a designer, but we’re not talking about abiogenesis are we? Unless you want to somewhere else of course.
        Obviously everything I present as evidence you will dismiss out of hand as not evidence.

        BTW: I watched the blind watchmaker video you posted … very cool indeed … but not evolution. I’ve gone through the code.
        It’s just a souped-up version of Dawkin’s Weasel, which is NOT blind. Comparing to a known target (the correct time and a bunch of other constraints) is breaking the rules. There’s also all the correct components present in sensible quantities (30 gears, 7 hands, 1 ratchet, 1 spring, 1 base). The algorithm is a stochastic optimisation algorithm, which predetermines function and the value of the function as the target. It’s trying different combinations of a very few things that we know provide a function when combined in the correct order.

        He also traps a lot of places where the algorithm would go down a potentially infinite blind alley, these are all part of the test cycle
        – Gears cannot be connected to more gears than teeth they have
        – Hands can only be connected to max 4 objects
        – Ratchet can only be connected to 1 object via its teeth and 2 objects via its center
        – Spring has 2 ends, each end can connect to two objects
        – Pendulum must connect through ratchet to a gear
        – having a hand on a gear is beneficial
        This is the very thing I have been talking about, natural selection works on a whole population either on fitness (old stylee evolution – which people don’t really believe anymore) or via differential reproduction. This model is old stylee, but how does he measure fitness? He measures a bunch of stuff and throws out things that won’t get where he needs to be. Natural selection could never know how to do this. Even if it could, the constraints of this model make it easy enough to randomly combine stuff and get something that’s functional (2% of his first iteration produces functioning clocks … this is obviously not analogous to any kind of DNA use-case)
        Algorithms like this are excellent for helping us to optimise designs, they do not design things.
        BTW: this example actually demonstrates irreducible complexity very well, the clock only needs about 4 parts to function simplistically, the rest of the adaptation is about non-regression and improving the timing by combining gears the correct way. You would expect to get the correct arrangement of the 4 parts in 16 variations, then it’s a game of optimising the gear arrangement. Pretty vanilla stuff really. Now let’s look at biology, the smallest functional protein TRP-Cage is 20 amino acids long (4^80 nucleotide combinations assuming only point mutations on existing “junk” material), that’s 1461501637330902918203684832716283019655932542976 nucleotide combinations compared to 16 clock combinations in a computer model that can run millions of operations per second. We’re not even talking about the simplest organism there, just the simplest protein. Computer models like this clock one get evolutionists all excited and make the uninformed convinced that random mutation plus a selective pressure is designing something .. it’s a delusion … the algorithm is DESIGNED to converge at the solution, it’s not creating functioning clocks through random mutation and natural selection.

        I developed an algorithm similar to the clock one last week that solved the game 2048 http://gabrielecirulli.github.io/2048/ … my solution used this approach, clone the board a bunch of times times, try a random move (out of 4 moves) for each board, score the board according to how much space is left on it (this is a heuristic, I figured that the highest score is achieved by the game not ending, and it ends when the board is full), pick the move that created the variants with the biggest accumlative space. I quickly realised that to get it to work, I needed to do one of two things 1) improve the specificity of the test 2) look into the future. It turns out I need to look about 50 moves into the future to figure out the best move out ofthe 4 and I need about 100 offspring at each stage. Or I can improve the resolution of the test so that the test is more intelligent. This is very tricky and the best solution out there https://github.com/nneonneo/2048-ai uses a number of heuristics and still needs to look into the future. So as you can see something as simple as combining adjacent identical numbers by swiping to make a high number can only be solved with either lots of intelligence and looking into the future, or less intelligence and looking far into the future

        We’re discussing the deterministic nature of the function of the living cell as prescribed by DNA and how that makes evolution of new traits impossible.

        • SmilodonsRetreat

          No, there’s not. What is the designer?

          Argument by big numbers.

          Misunderstanding what evolution is.

          Assuming anything built by a person can’t replicate evolution (of course, if you don’t know what evolution is…)

          Assuming results of an intelligently designed process are, themselves intelligently designed.

          blah blah blah

          • cryptoguru

            God is the designer … but I’m not going to let you draw us into a faith discussion … anymore than you are willing to be drawn into a faith discussion about naturalistic abiogenesis, which is the foundation of your faith.

            We are discussing whether evolution happens and if your evidence for it is compelling … I have shown it is not.

            Nope I’m arguing from the facts, you’re avoiding numbers of any kind, rationale of any kind. Evolution itself is an argument by randomly selected big numbers ….

            “4.7 or 8 or something BILLIONS of years of small changes have led to the diversity we see today.”
            “oh but I don’t see the changes”
            “yes, Billions is a lot and therefore things happen either too slowly or too quickly for you to see it … here’s some big numbers for you to look at”

            My big numbers relate directly to the problem and are repeatable, by you. That’s called science Kevin … it’s what we do in science. We hypothesise, predict, test and analyse. You need to use numbers to do that and sometimes a calculator and then engage your brain in understanding what it means.

            You don’t just draw a picture, say “it works like this” and then invent a computer model that supports it and say QED!. Or I could just write a program that prints out “KEVIN, THIS IS GOD!!! HERE IS THE PROOF YOU’VE BEEN WAITING FOR [this message will self-destruct in 5 seconds]” and expect you to be satisfied.

            “of course, if you don’t know what evolution is..”
            Fallacious! Hedging! Go on … enlighten me Kevin, what IS evolution? (or alternatively keep the ambiguity game going)

            Nope, I assert that an intelligently designed process that is designed to select a favourable outcome is intelligent design. WAKE UP KEVIN!!! LOOK AT THE CODE!!! THE STATS ARE FIXED!!!

            Same with Dawkin’s Weasel … the use of the knowledge of the target string enforces a stochastic based locking mechanism, which means you’re more likely to improve than regress or stay neutral. That is how all these tricks work!

            go with me on this thought process if you will
            1) choose a complex functioning device to build
            2) have all necessary parts available (and no others) to build your device
            3) randomly assemble some parts
            4) randomly change parts (do lots of attempts)
            5) score the device based on your knowledge of how the final device functions
            6) choose the one with the highest score
            7) now fine tune it by using this as the starting point and repeat steps 4 -> 6 until you get to your device.

            Yes there is probabilistic variability in the algorithm, but the restriction of which parts are used and limiting the accepted functionality makes this a search for a solution that we are guaranteed to get.

            Roll a die 1000 times if you ever get 2 6s in a row, that’s the power of evolution.

            • SmilodonsRetreat

              Unlike you, I have evidence to support that abiogenesis is possible… it’s a rich field of study and every published report since the 50s supports that everything that needs to happen can, chemically.

              You have no evidence for god.

              It’s that simple. Unless you have a designer, then the entire ID movement is meaningless… and you don’t.

            • cryptoguru

              Answer the question I asked … I analysed the algorithm you posed as an evidence for evolution.
              Each “evidence” you have given me is fundamentally flawed, and I have explained why using science. Tell me why I’m wrong … using science.

              HEHE …REALLY? I expect you’re attempting an ambiguous reference to the Miller-Urey experiment, which proved the exact opposite. I can explain if you like, but I expect you already know why that experiment was flawed.
              (left and right-handed amino acids, oxygen-reducing environment needed, chemical traps used, amino acids can’t self-replicate, etc)

              You just assert I’m wrong, without explanation or proof.
              Your science is shambolic.

              (I have plenty of evidence for God … use a capital G, God is a proper noun … like Santa … atheism is no excuse for poor grammar)

            • SmilodonsRetreat

              OK. You are wrong. You analysed it and determined that it wasn’t evolution. You are wrong.

              How’s that?

              It doesn’t matter, you won’t listen to anything I’ve said.

              You haven’t used science. You have used big scary numbers. This is one of the things that got Behe into trouble in the Dover trial.

              If you assume that every gene must have appeared as it exists right now, then yes, it’s a really scary big number. Sadly, only creationists believe that, biologists don’t.

              Look at the video again. It’s a changing population. That’s what evolution is. Not your mythical strawman.

              That which is claimed without evidence can be dismissed without evidence.

            • cryptoguru

              *breathes deep sigh*

              SO … how am I wrong Kevin?

              I analysed the clock code http://www.mediafire.com/?1umdtnwayyp … it cheats. I told you how it cheats. Dawkins’ Weasel cheats, I told you how he cheats. Look at the MATLAB code and tell me how I’m wrong.

              Ignore the big scary numbers if you don’t like them, they may just go away.

              “it’s a changing population”
              Oh dear, you just hear a buzzword and think that’s an explanation???
              “it’s a bird … it’s a plane … it’s a magic armadillo”
              LOOK AT THE CODE!!!

              You can prove non-material causation by the impossibility of the contrary … you’re breaking the laws of logic, the laws of nature and every “evidence” you’ve given me is fundamentally flawed.
              If you can’t address the flaws, you have no evidence.

              How can you be scientific if you just take everyone’s claims at face value who supports your view and reject the rest, without understanding the details?

            • SmilodonsRetreat

              “You can prove non-material causation by the impossibility of the contrary … you’re breaking the laws of logic, ”

              Except that you aren’t. This is common stuff. I’ve talked about it dozens of times.

              Wow, I’m the one who regularly reads the literature and writes about it. And I take everything at face value.

              Of course, I’m expected to take your word for what you say.

              Again, we’re just talking past each other. I’ve written about all of this before… feel free to click the abiogensis link on the right.

              Evolution works. Inescapable fact. Sorry.

            • cryptoguru

              you haven’t addressed one single point … well done!

              you just repeat the mantra … “evolution is fact, it works, it works.” … and the magical kingdom will be safe.

              Do you know how insane it is that I’ve raised countless valid points (which you just out of hand dismiss as invalid without explaining why) and you haven’t seriously addressed ONE of them, you just keep bringing it back to generalities and ambiguous statements.
              Does that not make you feel weird? Like deep in the gut? To, in the context of a scientific discussion, just brush over huge anomalies and declare them as fact?

              I think this conversation has run its course … can’t wait to find an actual real evolutionist who can scientifically defend their assumptions enough to make me have to go and learn some new stuff.

              I’m going to miss you … and Bilbo with his big feet and small brain … but I will be back, when you talk about something interesting.

            • SmilodonsRetreat

              Once again, you have been shown, multiple times, that the things you say are not correct.

              Until you address your misunderstanding of the processes of evolution (and chemistry), then there’s not point in going on.

              Addressing 1 thing missing from 1 post out of the handful I gave you does not mean you dismiss an entire body of work.

            • cryptoguru

              OK one last attempt:

              YOU gave me “evidence” to support your view … I looked at some of it and gave reasons why it fails as evidence.

              You ignore the analysis and state I don’t understand evolution.

              When I challenge you for an explanation of why my analysis is wrong or what I have specifically misunderstood about evolution in your opinion, you say nothing except “you’re wrong” or “you misunderstand”.

              So one last time … THE BLIND WATCHMAKER and WEASEL are the only two models that I’ve seen, both are fundamentally flawed models. So either
              1) where have I misunderstood what they are modelling and I thought they weren’t?
              2) where, then, is the model which shows the VERY simple and universally repeatable algorithm of evolution?

              There should be one … if evolution happens … it happens everywhere right? to all organisms? where is the law of evolution? the repeatable scientific law that we can write as an equation that we can model with a computer? (without cheating)

              Tell you what … how about I write a program based on what I think evolution is and you tell me what it’s doing wrong until we demonstrate evolution?
              You up for that as an exercise?

            • SmilodonsRetreat

              WEASEL was never intended to model evolution.

              WEASEL IS a target search. It’s function is to demonstrate the difference between pure random and target search heuristics

              “Although the monkey/Shakespeare model is useful for explaining the distinction between single-step selection and cumulative selection, it is misleading in important ways. One of these is that, in each generation of selective ‘breeding’, the mutant ‘progeny’ phrases were judged according to the criterion of resemblance to a distant ideal target, the phrase METHINKS IT IS LIKE A WEASEL. Life isn’t like that. Evolution has no long-term goal. There is no long-distance target, no final perfection to serve as a criterion for selection, although human vanity cherishes the absurd notion that our species is the final goal of evolution. In real life, the criterion for selection is always short-term, either simple survival or, more generally, reproductive success..” Dawkins

              So, your examination is flawed, because you aren’t looking at evolution or even evolutionary algorithms.

              As far as the rest, there are many documented examples of evolutionary algorithms that work very well. Here’s a list:

              “Adaptive Learning: Fly the Brainy Skies.” Wired, vol.10, no.3 (March 2002). Available online at http://www.wired.com/wired/archive/10.03/everywhere.html?pg=2.

              Altshuler, Edward and Derek Linden. “Design of a wire antenna using a genetic algorithm.” Journal of Electronic Defense, vol.20, no.7, p.50-52 (July 1997).

              Andre, David and Astro Teller. “Evolving team Darwin United.” In RoboCup-98: Robot Soccer World Cup II, Minoru Asada and Hiroaki Kitano (eds). Lecture Notes in Computer Science, vol.1604, p.346-352. Springer-Verlag, 1999.

              See also: Willihnganz, Alexis. “Software that writes software.” Salon, August 10, 1998. Available online at http://www.salon.com/tech/feature/1999/08/10/genetic_programming/.

              Andreou, Andreas, Efstratios Georgopoulos and Spiridon Likothanassis. “Exchange-rates forecasting: A hybrid algorithm based on genetically optimized adaptive neural networks.” Computational Economics, vol.20, no.3, p.191-210 (December 2002).

              Ashley, Steven. “Engineous explores the design space.” Mechanical Engineering, February 1992, p.49-52.

              Assion, A., T. Baumert, M. Bergt, T. Brixner, B. Kiefer, V. Seyfried, M. Strehle and G. Gerber. “Control of chemical reactions by feedback-optimized phase-shaped femtosecond laser pulses.” Science, vol.282, p.919-922 (30 October 1998).

              Au, Wai-Ho, Keith Chan, and Xin Yao. “A novel evolutionary data mining algorithm with applications to churn prediction.” IEEE Transactions on Evolutionary Computation, vol.7, no.6, p.532-545 (December 2003).

              Beasley, J.E., J. Sonander and P. Havelock. “Scheduling aircraft landings at London Heathrow using a population heuristic.” Journal of the Operational Research Society, vol.52, no.5, p.483-493 (May 2001).

              Begley, Sharon and Gregory Beals. “Software au naturel.” Newsweek, May 8, 1995, p.70.

              Benini, Ernesto and Andrea Toffolo. “Optimal design of horizontal-axis wind turbines using blade-element theory and evolutionary computation.” Journal of Solar Energy Engineering, vol.124, no.4, p.357-363 (November 2002).

              Burke, E.K. and J.P. Newall. “A multistage evolutionary algorithm for the timetable problem.” IEEE Transactions on Evolutionary Computation, vol.3, no.1, p.63-74 (April 1999).

              Charbonneau, Paul. “Genetic algorithms in astronomy and astrophysics.” The Astrophysical Journal Supplement Series, vol.101, p.309-334 (December 1995).

              Chellapilla, Kumar and David Fogel. “Evolving an expert checkers playing program without using human expertise.” IEEE Transactions on Evolutionary Computation, vol.5, no.4, p.422-428 (August 2001). Available online athttp://www.natural-selection.com/NSIPublicationsOnline.htm.

              Chellapilla, Kumar and David Fogel. “Anaconda defeats Hoyle 6-0: a case study competing an evolved checkers program against commercially available software.” In Proceedings of the 2000 Congress on Evolutionary Computation, p.857-863. IEEE Press, 2000. Available online at http://www.natural-selection.com/NSIPublicationsOnline.htm.

              Chellapilla, Kumar and David Fogel. “Verifying Anaconda’s expert rating by competing against Chinook: experiments in co-evolving a neural checkers player.” Neurocomputing, vol.42, no.1-4, p.69-86 (January 2002).

              Chryssolouris, George and Velusamy Subramaniam. “Dynamic scheduling of manufacturing job shops using genetic algorithms.” Journal of Intelligent Manufacturing, vol.12, no.3, p.281-293 (June 2001).

              Coale, Kristi. “Darwin in a box.” Wired News, July 14, 1997. Available online at http://www.wired.com/news/technology/0,1282,5152,00.html.

              Coello, Carlos. “An updated survey of GA-based multiobjective optimization techniques.” ACM Computing Surveys, vol.32, no.2, p.109-143 (June 2000).

              Davidson, Clive. “Creatures from primordial silicon.” New Scientist, vol.156, no.2108, p.30-35 (November 15, 1997). Available online at http://www.newscientist.com/hottopics/ai/primordial.jsp.

              Dawkins, Richard. The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design. W.W. Norton, 1996.

              Dembski, William. No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence. Rowman & Littlefield, 2002.

              Fleming, Peter and R.C. Purshouse. “Evolutionary algorithms in control systems engineering: a survey.” Control Engineering Practice, vol.10, p.1223-1241 (2002).

              Fonseca, Carlos and Peter Fleming. “An overview of evolutionary algorithms in multiobjective optimization.” Evolutionary Computation, vol.3, no.1, p.1-16 (1995).

              Forrest, Stephanie. “Genetic algorithms: principles of natural selection applied to computation.” Science, vol.261, p.872-878 (1993).

              Gibbs, W. Wayt. “Programming with primordial ooze.” Scientific American, October 1996, p.48-50.

              Gillet, Valerie. “Reactant- and product-based approaches to the design of combinatorial libraries.” Journal of Computer-Aided Molecular Design, vol.16, p.371-380 (2002).

              Giro, R., M. Cyrillo and D.S. Galvão. “Designing conducting polymers using genetic algorithms.” Chemical Physics Letters, vol.366, no.1-2, p.170-175 (November 25, 2002).

              Glen, R.C. and A.W.R. Payne. “A genetic algorithm for the automated generation of molecules within constraints.” Journal of Computer-Aided Molecular Design, vol.9, p.181-202 (1995).

              Goldberg, David. Genetic Algorithms in Search, Optimization, and Machine Learning. Addison-Wesley, 1989.

              Graham-Rowe, Duncan. “Radio emerges from the electronic soup.” New Scientist, vol.175, no.2358, p.19 (August 31, 2002). Available online at http://www.newscientist.com/news/news.jsp?id=ns99992732.

              See also: Bird, Jon and Paul Layzell. “The evolved radio and its implications for modelling the evolution of novel sensors.” In Proceedings of the 2002 Congress on Evolutionary Computation, p.1836-1841.

              Graham-Rowe, Duncan. “Electronic circuit ‘evolves’ from liquid crystals.” New Scientist, vol.181, no.2440, p.21 (March 27, 2004).

              Haas, O.C.L., K.J. Burnham and J.A. Mills. “On improving physical selectivity in the treatment of cancer: A systems modelling and optimisation approach.” Control Engineering Practice, vol.5, no.12, p.1739-1745 (December 1997).

              Hanne, Thomas. “Global multiobjective optimization using evolutionary algorithms.” Journal of Heuristics, vol.6, no.3, p.347-360 (August 2000).

              Haupt, Randy and Sue Ellen Haupt. Practical Genetic Algorithms. John Wiley & Sons, 1998.

              He, L. and N. Mort. “Hybrid genetic algorithms for telecommunications network back-up routeing.” BT Technology Journal, vol.18, no.4, p. 42-50 (Oct 2000).

              Holland, John. “Genetic algorithms.” Scientific American, July 1992, p. 66-72.

              Hughes, Evan and Maurice Leyland. “Using multiple genetic algorithms to generate radar point-scatterer models.” IEEE Transactions on Evolutionary Computation, vol.4, no.2, p.147-163 (July 2000).

              Jensen, Mikkel. “Generating robust and flexible job shop schedules using genetic algorithms.” IEEE Transactions on Evolutionary Computation, vol.7, no.3, p.275-288 (June 2003).

              Kewley, Robert and Mark Embrechts. “Computational military tactical planning system.” IEEE Transactions on Systems, Man and Cybernetics, Part C – Applications and Reviews, vol.32, no.2, p.161-171 (May 2002).

              Kirkpatrick, S., C.D. Gelatt and M.P. Vecchi. “Optimization by simulated annealing.” Science, vol.220, p.671-678 (1983).

              Koza, John, Forest Bennett, David Andre and Martin Keane. Genetic Programming III: Darwinian Invention and Problem Solving. Morgan Kaufmann Publishers, 1999.

              Koza, John, Martin Keane, Matthew Streeter, William Mydlowec, Jessen Yu and Guido Lanza. Genetic Programming IV: Routine Human-Competitive Machine Intelligence. Kluwer Academic Publishers, 2003.

              See also: Koza, John, Martin Keane and Matthew Streeter. “Evolving inventions.” Scientific American, February 2003, p. 52-59.

              Keane, A.J. and S.M. Brown. “The design of a satellite boom with enhanced vibration performance using genetic algorithm techniques.” In Adaptive Computing in Engineering Design and Control ’96 – Proceedings of the Second International Conference, I.C. Parmee (ed), p.107-113. University of Plymouth, 1996.

              See also: Petit, Charles. “Touched by nature: Putting evolution to work on the assembly line.” U.S. News and World Report, vol.125, no.4, p.43-45 (July 27, 1998). Available online at http://www.genetic-programming.com/published/usnwr072798.html.

              Lee, Yonggon and Stanislaw H. Zak. “Designing a genetic neural fuzzy antilock-brake-system controller.” IEEE Transactions on Evolutionary Computation, vol.6, no.2, p.198-211 (April 2002).

              Lemley, Brad. “Machines that think.” Discover, January 2001, p.75-79.

              Mahfoud, Sam and Ganesh Mani. “Financial forecasting using genetic algorithms.” Applied Artificial Intelligence, vol.10, no.6, p.543-565 (1996).

              Mitchell, Melanie. An Introduction to Genetic Algorithms. MIT Press, 1996.

              Naik, Gautam. “Back to Darwin: In sunlight and cells, science seeks answers to high-tech puzzles.” The Wall Street Journal, January 16, 1996, p. A1.

              Obayashi, Shigeru, Daisuke Sasaki, Yukihiro Takeguchi, and Naoki Hirose. “Multiobjective evolutionary computation for supersonic wing-shape optimization.” IEEE Transactions on Evolutionary Computation, vol.4, no.2, p.182-187 (July 2000).

              Petzinger, Thomas. “At Deere they know a mad scientist may be a firm’s biggest asset.” The Wall Street Journal, July 14, 1995, p.B1.

              See also: “Evolving business, with a Santa Fe Institute twist.” SFI Bulletin, Winter 1998. Available online at http://www.santafe.edu/sfi/publications/Bulletins/bulletin-winter98/feature.html.

              Porto, Vincent, David Fogel and Lawrence Fogel. “Alternative neural network training methods.” IEEE Expert, vol.10, no.3, p.16-22 (June 1995).

              Rao, Srikumar. “Evolution at warp speed.” Forbes, vol.161, no.1, p.82-83 (January 12, 1998).

              Rizki, Mateen, Michael Zmuda and Louis Tamburino. “Evolving pattern recognition systems.” IEEE Transactions on Evolutionary Computation, vol.6, no.6, p.594-609 (December 2002).

              Robin, Franck, Andrea Orzati, Esteban Moreno, Otte Homan, and Werner Bachtold. “Simulation and evolutionary optimization of electron-beam lithography with genetic and simplex-downhill algorithms.” IEEE Transactions on Evolutionary Computation, vol.7, no.1, p.69-82 (February 2003).

              Sagan, Carl. Broca’s Brain: Reflections on the Romance of Science. Ballantine, 1979.

              Sambridge, Malcolm and Kerry Gallagher. “Earthquake hypocenter location using genetic algorithms.” Bulletin of the Seismological Society of America, vol.83, no.5, p.1467-1491 (October 1993).

              Sasaki, Daisuke, Masashi Morikawa, Shigeru Obayashi and Kazuhiro Nakahashi. “Aerodynamic shape optimization of supersonic wings by adaptive range multiobjective genetic algorithms.” In Evolutionary Multi-Criterion Optimization: First International Conference, EMO 2001, Zurich, Switzerland, March 2001: Proceedings, K. Deb, L. Theile, C. Coello, D. Corne and E. Zitler (eds). Lecture Notes in Computer Science, vol.1993, p.639-652. Springer-Verlag, 2001.

              Sato, S., K. Otori, A. Takizawa, H. Sakai, Y. Ando and H. Kawamura. “Applying genetic algorithms to the optimum design of a concert hall.” Journal of Sound and Vibration, vol.258, no.3, p. 517-526 (2002).

              Schechter, Bruce. “Putting a Darwinian spin on the diesel engine.” The New York Times, September 19, 2000, p. F3.

              See also: Patch, Kimberly. “Algorithm evolves more efficient engine.” Technology Research News, June/July 2000. Available online at http://www.trnmag.com/Stories/062800/Genetically_Enhanced_Engine_062800.html.

              Srinivas, N. and Kalyanmoy Deb. “Multiobjective optimization using nondominated sorting in genetic algorithms.” Evolutionary Computation, vol.2, no.3, p.221-248 (Fall 1994).

              Soule, Terrence and Amy Ball. “A genetic algorithm with multiple reading frames.” In GECCO-2001: Proceedings of the Genetic and Evolutionary Computation Conference, Lee Spector and Eric Goodman (eds). Morgan Kaufmann, 2001. Available online at http://www.cs.uidaho.edu/~tsoule/research/papers.html.

              Tang, K.S., K.F. Man, S. Kwong and Q. He. “Genetic algorithms and their applications.” IEEE Signal Processing Magazine, vol.13, no.6, p.22-37 (November 1996).

              Weismann, Dirk, Ulrich Hammel, and Thomas Bäck. “Robust design of multilayer optical coatings by means of evolutionary algorithms.” IEEE Transactions on Evolutionary Computation, vol.2, no.4, p.162-167 (November 1998).

              Williams, Edwin, William Crossley and Thomas Lang. “Average and maximum revisit time trade studies for satellite constellations using a multiobjective genetic algorithm.” Journal of the Astronautical Sciences, vol.49, no.3, p.385-400 (July-September 2001).

              See also: “Selecting better orbits for satellite constellations.” Spaceflight Now, 18 October 2001. Available online at http://spaceflightnow.com/news/n0110/18orbits/.

              “Darwinian selection of satellite orbits for military use.” Space.com, 16 October 2001. Available online at http://www.space.com/news/darwin_satellites_011016.html.

              Zitzler, Eckart and Lothar Thiele. “Multiobjective evolutionary algorithms: a comparative case study and the Strength Pareto approach.” IEEE Transactions on Evolutionary Computation, vol.3, no.4, p.257-271 (November 1999).

              Pay special attention to the checkers and the FPGA ones. In the checks one, the researchers only told the computer it’s win rate out of every 5 games. In the FPGA one, the engineers still don’t know how it works, but it still does work.

              These are examples of evolutionary programming without a target. Only that comparison to the environment to determine which ones survive. In the checkers case, more wins is survival… not unlike more kills is survival for a lion.

              If you want to write a program for evolution, why not just use ones intended for the purpose? Why do you feel the need to ignore the large body of programs and literature on the subject and make up your own?

              Here, let me google is for you: https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=genetic%20algorithm%20software

              Here’s the rule of evolution that most of these employ. Random selection, comparison to each other or a fitness goal, removal of non-competitive individuals or promotion of fit individuals.

              What’s so hard about that.

              Look, let me give you an example. Just because programmers can make a genetic algorithm doesn’t mean that evolution is wrong and all the targets are actually designed. Look at the research, in most of those cases, the computer system surprised the heck out of expert engineers. The computer evolved devices and processes that were orders of magnitude better than teams of engineers could come up with.

              Evolution is similar. Change over time. Way more organisms born than could possibly survive. Mutations (and related changes to the genome). Selection. Survival. Rinse and repeat.

              Let me ask you (and I know the answer you will give) how do you explain how the same genes in fish are in humans? How the gill arches in fish and human embryos become shoulders and ears and the larynx? And the thousands of other things that make sense only when you look at them from an evolutionary history of an organism.

            • cryptoguru

              thanks for that … very handy list.

              the problem with all your examples (and I’ve skimmed over many of them, so point out any that don’t fit my generalisation) is that they are OPTIMISATION algorithms. http://en.wikipedia.org/wiki/Genetic_algorithm
              They are evolutionary algorithms, in that the algorithm is called an evolutionary process (in general terms), but none of them model the biological evolution process you are describing happens in the real world, they are not equivalent problems to solve:-

              1) select each entity described by a program
              (i.e. that defines its properties and behaviours)
              2) self-replicate its program to create clones
              3) randomly mutate the clone programs
              4) run programs and apply a selective pressure that kills less fit/performant entities
              5) go to 1

              All the examples you gave mutate parameters within a program, the program itself is not being mutated. You’re therefore not allowing the mutations to actually mutate anything other than the optimisation parameters
              e.g. wing shape, way of walking, material properties etc.

              If real mutations were modelled they would affect the replication functionality and other core behaviours.
              e.g. allow the gears in the clock model to mutate randomly in shape and you’d likely NEVER get a clock. The degrees of freedom of the problem establish whether it is truly random mutation or intelligent mutation, which all the evolutionary models are guilty of. The selection model is also problematic and often either compares to a future target or measures an attribute of the entity, rather than applying a selective pressure in general.
              Forcibly removing “less fit” entities is not equivalent to setting a natural requirement on the survival of the entity and letting it run till it dies.

              Don’t get me wrong, these are all very helpful approaches to problem solving, as I’ve mentioned before … but they DON’T model biological evolution as you or anyone else I’ve heard describes it. If you can describe the process; we should be able to model it and prove it is true.

              I will write a computer model which demonstrates the process that you describe IS evolution … you can then tell me how I’ve got it wrong, as I have told you how these others have got it wrong … unless of course you can point to one algorithm in that list you gave that doesn’t behave as I suggest and I will look at it in more detail.

              NOW we are having a sensible conversation!

            • SmilodonsRetreat

              The problem isn’t the programs… the problem is your understanding of evolution.

              What is evolution, but an optimization alogirthm for a particular environment. Organisms that are more fit FOR THAT ENVIRONMENT preferentially survive and pass on their genes… with mutations.

              1) Organism born
              2) Competes against offspring and other species for survival
              3) If offspring is succesful, then it will reproduce
              4) The genes of that offspring will be passed to it’s offspring
              5) Possibly mutations will happen
              6) repeat.

              That’s exactly what you wrote, except for biology.

              And please don’t patronize me about having a real conversation. I’ve been trying for days to have one. You’re the one who is rejecting evidence.

            • cryptoguru

              Just because optimisation is a subset of some general evolution concept and biological evolution is also a subset of general evolution; it can’t be derived that optimisation is biological evolution, that has not been demonstrated. That is an Association Fallacy, let me use a similar argument as an example of what you’re doing …

              definition: “Transport is a system or means of conveying people or goods from place to place.”
              premise 1) A car is transport
              premise 2) A train is transport
              conclusion) therefore a car is a train.
              I have demonstrated the concept of transport, not that the car is a train.

              I agree that your 6 points above are the theory of biological evolution. I’ve never contested that’s what evolutionists claim is going on … I do contest that none of the models you posted represent that specific algorithm and not just some generic evolution concept. I’m asking you to show me one that does. How can this be a viable theory if there isn’t an accurate model of it?

              this is how the models I’ve seen do not represent your definition of biological evolution …
              1) their mutation isn’t universal:
              mutation is restricted to only act on parameters that affect the performance of the model or a specific function. They never mutate the program that defines the entity and its core behaviours, or component parts (e.g. morphology of gears or any other component in the clock model is not mutated)
              2) their selection isn’t usually natural:
              specific traits and performance of certain functions are measured or compared to a goal. Only a select few models create an environment and allow purely death to be the selecting agent.
              3) their mutation isn’t usually random:
              often a selection of options are chosen for the algorithm to “mutate” between. This is not purely random mutation, as those options have been intelligently chosen to result in a functioning entity, so the problem is reduced to searching for a combination of components that optimises the function. (e.g. the clock model has only components that we know make a clock to choose from)

              I’ve been writing mathematical models and computer simulations of real-world problems for years (fluid-mechanics, chaotic-flows/mixing, biological transfer functions, blood flow, biological geometry) … there is no such thing as a perfect model. But there are bad and inapplicable models that make unsubstantiated assumptions that are of no use to the real world. All the evolutionary models I’ve observed break one of the rules above, so can’t be used to demonstrate biological evolution. I keep asking you to show me one that doesn’t break the rules. I’d be happy to investigate.

              The definition that you (and others) propose as evolution is a simple algorithm with hardly any variables … it should be relatively easy to model. And I’ve already started writing one.

              Patronising?? You make me laugh … every post I’ve had from yourself and Bilbo has been patronising and insulting.
              You have avoided definitions and specifics and jumped to “you idiot creationist, you don’t understand biology” … not once were you able to justify HOW I hadn’t understood biology in your opinion. What evidence have I rejected? I’m not rejecting anything … I’m looking at the evidence and saying that it’s not saying what you think it does. That’s what we do in science! I didn’t say “I don’t want to see your evidence” … I’ve simply explained that the interpretation of evidence must satisfy our prior understanding of the laws of nature and science … so your relatively young theory of evolution violates my understanding of the laws of nature, unless you can show me how those laws don’t count anymore I’m not going to accept your interpretation of the evidence. The burden of proof is on you.

              Evidence is not proof … evidence is what we observe … we come to our conclusions from the evidence. We’re both looking at the same evidence.

              This is a very frequent evolutionist mistake, to assume that the evidence is proof … evidence is just some facts that we are interpreting and drawing conclusions from. I disagree with your conclusions on the basis that I don’t see how the evidences you have produced satisfy the definitions you give or fit with pre-existing laws of nature and logic.

            • SmilodonsRetreat

              1) the you need to read those reports. I’m not sure what you are looking at, but for a particular “genome”, then entire thing can be mutated.

              2) In some version. Not all. But then, that’s what evolution is. How is that not “natural”.

              3) That’s totally wrong. Read the papers.

              Again, why are you doing this? It’s been done. You may not like then, but they are the software packages that experts are using.

              ” I disagree with your conclusions on the basis that I don’t see how the evidences you have produced satisfy the definitions you give or fit with pre-existing laws of nature and logic.”

              In general, in these discussions, that’s because you have a misunderstanding of how natural laws actually work.

              For example, your ideas on information are wrong. It’s trivial to add information to the genome. It’s even possible to add meaning (which, despite your claims, are not the same thing).

              If there was a “natural law” that prevented evolution, then we wouldn’t see evolution happening all the time.

              It’s not that our evidence actually goes against natural law. It’s that your understanding of these laws are flawed.

              Nothing I say or do can change your mind because until you start using reality to define your rules, then you will never be able to see the evidence in the same light.

              Again, I think we’re done. There’s no point in continuing as you have refused to accept the evidence that’s been given to you that shows your ideas are mistaken.

            • cryptoguru

              “but for a particular “genome”, then entire thing can be mutated.”
              BEGGING THE QUESTION … demonstrate it by showing me the research that supports this.

              “In some version. Not all. But then, that’s what evolution is. How is that not “natural””
              CIRCULAR ARGUMENT … demonstrate the basic premise

              “That’s totally wrong. Read the papers.”
              MOVING THE GOALPOSTS
              show me where … you’re the expert

              “they are the software packages that experts are using.”
              APPEAL TO AUTHORITY

              “you have a misunderstanding of how natural laws actually work.”
              PROOF BY ASSERTION
              and BEGGING THE QUESTION again … how have I misunderstood natural laws? … you haven’t yet demonstrated your basic premise that functional and structured information can come from random mutation plus natural selection … so you can’t claim I’ve misunderstood laws that are not demonstrated in a model.

              “For example, your ideas on information are wrong. It’s trivial to add information to the genome. It’s even possible to add meaning”
              PROOF BE ASSERTION and
              BEGGING THE QUESTION again … this has not been demonstrated … just stated as fact over and over and over again

              “If there was a “natural law” that prevented evolution, then we wouldn’t see evolution happening all the time.”
              HORRIFIC CIRCULAR REASONING again. You claim to see evolution, I’ve not seen any evidence yet that could only be understood as a direct consequence of the algorithm you stated earlier … or even seen that it’s reasonable to assume that the algorithm could EVER possibly do what you say it does.

              “Nothing I say or do can change your mind because until you start using reality to define your rules, then you will never be able to see the evidence in the same light.”
              PROOF BY ASSERTION
              But you have redefined “reality” to include things that I have not seen demonstrated either as the proven sole causation of an observed effect, or as even a viable mechanism from an algorithmic point of view.

              “Again, I think we’re done. There’s no point in continuing as you have refused to accept the evidence”
              ARGUMENT FROM REPETITION

              I’ve clearly and carefully explained why those models do not model evolution … you have not shown how they have, or shown a model that I have not covered that does.
              You have lost this argument!
              OUT OF TIME

            • SmilodonsRetreat

              Why, in Cthulhu’s name do I have to do this for you?

              1) Avida, the checkers program, the FPGA program I’ve already provided references for. Why didn’t you read them?

              2) You used “natural” not me.

              3) I did show you. Read the papers.

              4) IT’S IN THE FUCKING SOFTWARE.. LOOK AT THEM.

              5) Um, no. You have misunderstandings, these have been pointed out to you many times.

              When you look at this using the actual rules of the universe, then your problems with it all go away.

              Again RTFR (Read the Fucking Research). There are dozens of documented cases of genomes increasing in information content, then using that to generate new genes. This is common knowledge among researchers. Here’s a tiny sample:

              vPonce, R. & Hartl, D. The evolution of the novel Sdic gene cluster in Drosophila melanogaster. Gene 376, (2006).
              Long, M., Betrán, E., Thornton, K. & Wang, W. The origin of new genes: glimpses from the young and old. Nat. Rev. Genet. 4, 865–75 (2003).

              Wu, D.-D. D., Irwin, D. M. & Zhang, Y.-P. P. De novo origin of human protein-coding genes. PLoS Genet. 7, e1002379 (2011).

              Zhao, L., Saelao, P., Jones, C. D. & Begun, D. J. Origin and Spread of de Novo Genes in Drosophila melanogaster Populations. Science (2014). doi:10.1126/science.1248286

              Montague, M. et al. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proceedings of the National Academy of Sciences (2014). doi:10.1073/pnas.1410083111

              Lindblad-Toh, K. et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803–819 (2005).

              Stuart, Y. et al. Rapid evolution of a native species following invasion by a congener. Science 346, 463466 (2014).

              A couple of these (especially the Long paper) are seminal works in the field and are regularly cited in any gene study. It’s actually rather stunning that you aren’t aware of these.

              You have CHOSEN to ignore the evidence provided to you. This has been explained to you many times. It has been explained in my writings many times. It has been explained by experts in the field many, many, many times.

              Just because YOU don’t get it and haven’t read it and don’t understand it is not my problem.

              I know you think you’re on to something. Go ahead and keep believing that. Biologists will just keep on making discoveries without you.

              If you want to continue this, I would start with one simple question that I can explain. Start with the basics.

            • cryptoguru

              every bit of research I’ve looked at so far fails for the reasons I clearly accounted for … you’re now saying the real answers are in other things that I haven’t read. Utterly Fallacious

              THE BURDEN OF PROOF IS ON YOU REMEMBER!!!

              Why should I go digging through a million irrelevant papers that you likely don’t understand anyway to be told each time that disproving 1 in a million doesn’t count, it’s in the others?

              Again you seemed confused by the basic premise of your own dogma.

              given a self-replicating entity
              1) random mutation of the WHOLE program (i.e. including that which defines the properties and functions of the entity must occur … like it does in DNA)
              2) selection must be blind … it can’t measure properties and compare to targets, the environment the entity lives in must impose a universal and simple pressure that results in death. (e.g. entities can’t just be filtered out because they’re blue)

              I’m not asking you for biology papers that presume that evolution works before starting … I’m asking for a mathematical model/computer program that demonstrates your basic premise works.
              HOW HARD IS THAT???
              Show me new functional traits appearing in a program in the way that you described it happens. (it MUST satisfy that it models the mechanism that you insist is happening in Biology)
              ONE PAPER WILL DO

            • SmilodonsRetreat

              here we go again… denial, it’s not just a river in Egypt anymore.

              1) random mutation – is mostly random. Yes, in real organisms, some DATA has a larger chance of being affect by mutation that others.

              I think you have another mistake here though. As you yourself describe, DNA is multi-layered. While it is true that traits can be controlled by one gene, those genes are controlled by other genes and a multitude of factors. In this case, evolutionary algorithms don’t handle this very well.

              I want to ask, do you think that evolutionary algorithms act on programs? If so, that’s another fundamental mistake. The “genome” in an evolutionary algorithm is data… not a program. here’s an analogy since I know you like them so much. The DNA is the data. Chemistry and physics are the program that works on the data and uses the data to generate some structure or process.

              2) Why does selection have to be blind? Selection is non-random (mostly, in the real world).

              You are creating an almost unbelievably simplistic system here. Selection is not only death, though that’s a part of it. It’s also competition, both with others in the species and other species (in the real world). The clock algorithm didn’t have to delete that third clock and I’m willing to bet it would have run just fine. By saying that the third clock isn’t fit enough (and it never will be once another generation passes), it’s out of the breeding pool. In evolutionary terms, it’s effectively dead.

              How many of the papers did you read? Everyone one of them describes what I’m talking about. Look at AVIDA (that includes information increases in the genome).

              It’s trivial to provide this information and I have been providing it all along. That you don’t accept it is not my problem.

              AVIDA shows new functional traits. The classic 2003 paper is here: http://myxo.css.msu.edu/papers/nature2003/Nature03_Complex.pdf

              I don’t know why you haven’t read that already. It’s one of those seminal papers in the field.

              http://www.skepticink.com/smilodonsretreat/2013/08/05/complexity-and-evolution-recent-research/

              There’s three papers. Now, go read them. When you can talk about them without ranting, then we’ll see about continuing.

              I predict that you will say that they do not meet your requirements. I predict that will be because of some minor semantic argument or goal-post shift.

              I’m very, very confident that nothing will ever change your mind? Why, because you said so. Your mind is made up. Still.

            • cryptoguru

              How am I in de Nile … when tis you who refuses to accept those models don’t model evolution .. I’ve shown you clearly how they are NOT modelling biological evolution, I’m not making it up. You can investigate for yourself. You have 3 options

              1) deny that the models are doing what they are doing
              2) pretend that I didn’t understand the mysterious law of evolution … again
              3) agree that I’ve got a point
              (you get full marks for number 3)

              you obviously don’t understand how AVIDA works … it does exactly what I contested ISN’T biological evolution. (unlike you, I will proceed to qualify my statement and explain how you have misunderstood)

              AVIDA has 26 functions that it randomly selects and optimises over to maximise or minimise a function … EXACTLY what I said is NOT biological evolution.

              DNA is not 26 nucleotides long, and each nucleotide is not a function, it is a letter, that creates an expression that is evaluated by the cell, through the complex functional pipeline of transcription and translation (yes that’s even a simplistic explanation). DNA IS THE PROGRAM, the functional attributes of the whole cell are defined in the DNA, the molecular machines in the cell execute them (like a PC operating system) through many complex stages.

              Therefore an accurate model of biological evolution MUST
              1) allow the nucleotides to mutate, not just optimise over entire gene sequences.
              2) select based on the survival of the organism.

              “Selection is not only death, though that’s a part of it. It’s also competition, both with others in the species and other species”
              WRONG! Selection can only be death, the selective pressure can be anything e.g. weather, food availability, predators etc. But the selective agent is ALWAYS death … THAT IS EVOLUTION 101
              This isn’t American Idol … Organisms don’t get scored according to their performance and voted out and sent home. The evolutionary principle insists that the propagation of an advantage is through the death of the less fit or those who are less able to reproduce. Death removes the weaker versions and leaves the stronger to reproduce and persist the advantages. Therefore death must be the agent of selection and can’t be used intelligently .. e.g. an organism can die when it can’t find food or reproduce or gets eaten … NOT when it’s shorter or slower or more purple than its siblings. I’m not saying that being shorter or slower or purple won’t get you killed, it might. But you have to let death do the killing and not just apply a metric at an atomic level. A good example of this is … getting closer to a target is not a selectable parameter. In biology, the target is usually food/water … it’s not the closest organisms to the food that get to carry on; any organism that doesn’t reach the food will die, irrespective of how close they get.

              In AVIDA the original functions are never evolved and can never change (they can only be sequenced) … this is not like DNA, where anything can change at an atomic level. So although this is dressed up to look like it is modelling evolution … it isn’t at all. It’s now not modelling the proposed evolutionary algorithm. If you DO model the real evolutionary algorithm, it doesn’t work … because you can’t create new functionality from an optimisation algorithm, you can only optimise the combination of existing functions. (you will disagree … but we’ve yet to see this actually happen)

              Let me use a very simplistic version of this approach to explain so you can understand this:

              This is an analogy of how AVIDA works:
              1) I have 4 functions (forward, backward, left, right) that controls a robot, which has legs.
              2) I randomly select 3 functions and try them from a starting position and do that 100 times.
              3) I measure how close the robot gets to a target position on each attempt.
              4) I choose the sequence of functions that gets the robot closest to the target
              5) go back to 2) and repeat until I reach the target

              This should eventually find the quickest route to the target if I have enough tries (100 would probably work) and I keep the number of functions I randomly select low (3 should work with 100 tries). This is NOT evolution. Real evolution would be able to mutate the functions themselves, and wouldn’t be able to measure how close the robot gets to the target.

              A better model for evolution would be
              1) Write a program that automatically builds a robot that has legs and builds a software driver that has an API to send messages to the different servos once it is built.
              2) the program is copied 100 times
              3) each copy is randomly corrupted a small amount by inserting, changing or deleting bytes of code
              4) the robot closest to a target is kept, the rest killed
              5) go back to 2) and repeat until you reach the target

              You getting the picture yet? This will go nowhere, they have no functionality to move, just the ability to send data to the robot’s servos .. it doesn’t have code that sends the data. And the corruption is more likely to stop the program from building the robot than it is to randomly get to writing the correct code to send a walking cycle to the robot.

              This still isn’t a fair model, as really step 4 should be “if a robot doesn’t reach the target it dies”. All robots will die at the first generation … how will they ever get the chance to evolve the ability to get to the food they need?

              (cue the response … “this is not evolution” … “you misunderstand evolution”)

              HOW HAVE I MISUNDERSTOOD IT WITH MY MODEL?

              (DNA is run by the cell like a program, it is randomly mutated at an atomic level anywhere, the organism must develop new functions for survival and reproduction)

            • SmilodonsRetreat

              If you think the selective pressure is always death, then you don’t know anything about evolution.

              Sorry.

              The problem is not with the programs, it is with your misunderstanding of evolution.

              To you, every non-dominant creature dies. You fail to understand things like alpha males, which drive off less successful males. Competition among males (and females) for mating privileges. These things are evolution based processes and do not result in death, just more or less opportunity to mate. This has been explained to you before.

              In AVIDA, which organisms get to reproduce are those which compete most successfully for logic functions in the environment.

              Did you read the paper I linked to? (I have asked this of you several times and not gotten an answer.)

              So, let’s see, some random creationist on the internet says that AVIDA organisms do not evolve. Dr. Lenski (an evolutionary scientist), and two researchers in computer science, say things like

              “The ancestor could replicate but could not perform any logic

              function. However, an organism that evolved one or more of nine

              logic functions would obtain further energy. The benefit increased

              exponentially with the approximate difficulty of each function

              (Table 1). Functions could be performed in any order during an

              individual’s life, but no extra energy was obtained by repeatedly

              performing the same function. No single mutation in the ancestor

              can produce even the simplest of these functions. Instead, several

              mutant instructions must appear in the same lineage, and such that

              they are coordinately executed, to perform even a simple function.

              Nonetheless, this population (and many others) evolved the

              capacity to perform EQU, the most complex of these functions.”

              In other words, the organisms evolved. They increased their information. Using mutations and selection, they gained multiple new functions that did not exist in the ancestors.

              “The presence of deleterious mutations along the line of descent is

              more surprising. Fifteen of the 18 deleterious mutations reduced

              fitness by ,3% relative to the parent, and might have hitchhiked

              with beneficial mutations that arose soon after in the same genetic

              background. However, two mutations reduced fitness by .50%.

              One was a point mutation that disrupted replication efficiency. Its

              harmful effect was eliminated by the next mutation in the line of

              descent, which occurred at a distant site in the genome. The other

              very deleterious step was a point mutation, at depth 110, that

              knocked out NAND, one of the simplest logic functions. Only two

              individuals had this maladapted genotype, yet their descendants

              emerged as eventual winners. In fact, in the very next step, this

              genotype produced the mutation that gave rise to EQU. Was that

              deleterious mutation extremely lucky to hitchhike with such a

              beneficial mutation? Or was the deleterious mutation a prerequisite

              for producing the EQU function within that genome context? To

              distinguish between these hypotheses, we reversed this one-stepprior

              mutation in the genotype that first expressed EQU. This

              reversal eliminated the EQU function. Therefore, a mutation that

              was highly deleterious when it appeared was highly beneficial in

              combination with a subsequent mutation. The evolution of a

              complex feature, such as EQU, is not always an inexorably upward

              climb toward a fitness peak, but instead may involve sideways and

              even backward steps, some of which are important.”

              and

              “The most

              complex function, EQU, evolved only when several simpler functions

              were also useful. Some simpler functions were accessible from

              the ancestor by relatively few mutations, and these served as a

              foundation on which more complex features were built. The

              foundational role of simpler functions in the origin of more

              complex ones was evident in the overlap of the genetic networks

              underlying their expression, and the frequent loss of simpler

              functions as side-effects of mutations yielding more complex

              functions. Our experiments demonstrate the validity of the hypothesis,

              first articulated by Darwin1 and supported today by comparative

              and experimental evidence2–16, that complex features generally

              evolve by modifying existing structures and functions. Some readers

              might suggest that we ‘stacked the deck’ by studying the evolution of

              a complex feature that could be built on simpler functions that were

              also useful. However, that is precisely what evolutionary theory

              requires, and indeed, our experiments showed that the complex

              feature never evolved when simpler functions were not rewarded.

              Our experiments also show that many different genomic solutions

              produce the same complex function. Following any particular path

              is extremely unlikely, but the complex function evolved with a high

              probability, implying a very large number of potential paths32.”

              This is exactly what you say doesn’t happen.

              Tell me, what is your definition of evolution?

            • Doc Bill

              Sorry, but how about you fuck off until you learn some actual science. Why, for example, do you assume there is a “VERY simple and universally repeatable algorithm of evolution” unless you are a manipulative twit erecting a straw man? Which you are. Seriously, just light a candle, pray for forgiveness for all the lying you’ve done recently, drink 10 pints of ESB for old Bilbo and then go away – forever. Thank you.

            • Doc Bill

              Typical useless god bot. Argument from incredulity. Has to paint science as a faith because of a narrow, restricted, dogmatic worldview. Forest full of straw men, drenched in tard and burning with the fire of the willfully ignorant. Sucks to be you, NotGuru. Enjoy howling in the darkness.

            • cryptoguru

              I paint evolution (non-science) as faith … because it is.
              It’s an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who’ve wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

              You still don’t address any of the gaping black holes that I’ve pointed out.

              It doesn’t suck to be me … me is very happy … it sucks to be you when you eventually accept you got it wrong and have a shameful record of all this stuff on-line. Also it must suck to be a meaningless bag of chemicals … I hope you don’t get outraged about morality at all, that would be extremely inconsistent with your view of meaninglessness and relativistic morality and all the other absurdity they teach in your church.

            • SmilodonsRetreat

              There is no EVIDENCE on non-material causation. Provide the evidence. I’ve been asking this for two decades… nothing. Go ahead.

              Big numbers is not evidence. Designed lab experiments is not evidence.

              I’m very sorry that you can’t think anymore. I’m perfectly happy with my knowledge. I’m also perfectly happy knowing that I can change my mind. Unlike you, who is forced to find a way to discredit all the evidence because it conflicts with your worldview.

              I think we’re done.

            • Doc Bill

              Too bad Dawkins didn’t set the target to “Methinks it’s a willfully ignorant religious fanatic,” although that target would work just as well. It’s amazing how creationists simply don’t understand Dawkins’ little demo program.

              Many years ago there was a huge discussion on Uncommon Descent about Weasel and I think even Luskin participated. They were all convinced that the program “latched” the target phrase and even when the code was published and it was obvious there was no latching, and even a video of the program running showed the “correct” letters appearing then changing and rattling around before settling on a solution, they were CONVINCED that somehow the program was latching the target. Finally, it might have been Luskin, proposed that the program “implicitly” latched and that the published code wasn’t the real code even though it ran the same.

              Unbelievable the contortions these people go through to hold on to their beliefs. If only they channeled that energy into something productive.

              Although I don’t recommend going to Gary Gaulin’s thread at AtBC for any length of time, it is amazing that it’s been going on for a couple of years and even though it’s been demonstrated to Gary that he’s simply wrong, it doesn’t matter. He keeps pounding that nail.

            • Doc Bill

              I wish we could create a Bill Maher rule that creationists have to announce themselves on science forums like Hovind did in his thesis: “Hello, my name is Kent Hovind.”

              That would save a lot of time going through my Stages of a Creationist culminating with The Flounce. Alas, it seems that NotGuru has done a double reverse pike position flounce back!

              “Hello, my name is NotGuru and I’m going to make up a bunch of shit that you won’t agree with, then complain that you don’t agree with it, then call you a bunch of evil atheists, give you a sermon about how you can accept Jeebus into your flinty hearts, then go kick a dog or something.”

              That would certainly save a lot of time!

            • Doc Bill

              Well, this is your whole problem, NotGuru, you’re a willfully ignorant closed-minded creationist suffering from a religious delusion and probably sociopathic tendencies. Aside from that I bet I could still beat you in 301 down, not to brag.

              Sorry, we’ve heard the “evolution is faith,” “evolution is religion,” “you worship Darwin” and so forth for decades. Nothing new there. In the United States, at least, this science-is-faith notion has been struck down by the Supreme Court, so it doesn’t wash in public schools.

              Factually you are incorrect. Evolution is an observation, a fact; biology evolves. That has been observed for centuries. What Darwin did was to put the pieces together in a theoretical framework which not only explained the diversity of life as individual variation acted upon by natural selection, but also provided predictive abilities that have been demonstrated to be correct. Faith has nothing to do with it. It’s all observed, measurable, objective science. Faith is how you look at the world, NotGuru. You’ve got it exactly backwards.

              Second, the modern theory of evolution is not an absurd unsupported set of stories. What you just described is your religion. The modern theory of evolution is supported by facts, data, observations, experimental results and verified predictions spanning chemistry, physics, genetics, geology, population studies and all branches of science; all of them.

              Third, science is definitely not based on “no possibility of non-material causation.” You just made that up. What is “non-material causation” anyway? Magic? Science is not based on the proposition of no magic, rather science has no need of that hypothesis. That’s what you religious freaks get wrong every single time. Science isn’t against magic. Magic would be great! I’d love to have a wand and conjure up demons. However, magic has never been demonstrated. Nothing is learned by invoking magic. Magic is not necessary. The origin of species is explained quite nicely without magic. So, simply put, on this proposition of yours, you are wrong. Wrong. You made a false statement.

              Fourth, what is a “god hater?” That’s the most ridiculous phrase ever. Laughable. That’s your paranoia and insecurity, NotGuru, not mine. You’re the one living in fear, not me.

              And, finally, the biggest canard of them all and the one that bugs you the most is that I can think for myself, and you can’t. You need threats of eternal damnation to keep your loose morals in check, whereas I have lived an honest, tax paying, productive, fun life all by myself. Really, there are “eternal consequences” for me being married to the same woman for decades, raising healthy children and sending them through college, paying my taxes, giving to charity, establishing a scholarship fund, adopting orphaned pets, volunteering at the local hospital, supporting the arts and watching out for my neighbors? What are those consequences, NotGuru? Only a sociopath like yourself could possibly judge my life as being anything but exemplary. Go ahead, NotGuru, cast the first stone. I double dog dare you.

    • SmilodonsRetreat

      Tell you what, Disqus is becoming full.

      Why don’t you come over to AtBC. Lots of people you can continue to discus with… including me. http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=54b6f45f47f70f97;act=SF;f=14

      • cryptoguru

        sounds fun!

        create a topic called “models of biological evolution?” and I’ll jump in when I get a moment.

        thanks for the interesting debate on here anyway .. I’ve enjoyed it.
        I think Bilbo did too, he was probably just running low on sugar or something, I don’t blame him for his outbursts.

        • SmilodonsRetreat

          We’re both used to people who aren’t getting it. He’s a bit more aggressive than I am. I assume that people want to learn the correct things… I’m usually disappointed though.

          • cryptoguru

            good job you’ve got all the right answers then eh … will make it easy to expose my unscientific rationale … like you so effortlessly did here.

            • SmilodonsRetreat

              I did. The fact that you refused to accept it and continue to have misunderstandings is not my problem.

            • Doc Bill

              Well, that was quick! I guess NotGuru just loves the attention.

            • Doc Bill

              That was sad. NotGuru wanted people to address his “theory” and when they did he went all religious creationist on them. Really sad. He had a real opportunity to engage with the very best.

    • Martin Mayberry

      DNA IS INDEED like computer code! I have my copy of SIGNATURE IN THE CELL and have read it. if DNA is like they claim, it does have code and code is only created by a MIND!! And I also have looked on Wikipedia to get an unbiased opinion and have seen the same thing “signature in the cell” claims! so just tell the truth and shame the devil !

      • SmilodonsRetreat

        The Signature in the Cell was not written by a scientist, contains many mistakes and has been thoroughly refuted by scientists who actually do the work.

        I’ll be happy to teach you real science, but you have to be willing to learn.

        • Martin Mayberry

          I have seen a debate on you tube at Biola University Steven Meyer was on it and they were debating this subject and for every thing the evolutionist were saying that it could not be, Mr. Meyer had an answer for. It was an excellent Debate you can find it on you tube! Evolutionist do NOT want the TRUTH to come out and will refute everything they can about it because it points to an intelligent creator that evolutionist want NO part of. My take is this— flight is a complicated process if it takes a designer to make an airplane, it also takes a designer to make a bird fly! Just because you do not see God with your eyes does NOT mean he did not design the bird to fly! Look at the hollow bones and the working of the lungs of a bird and you see design in it! Intelligent design is real! You can find it in nature! just look at and study the BIRD for an example!

          • SmilodonsRetreat

            Meyer is a liar and the worst researcher ever. I have proven this to be true on this very blog. He has ignored relevant research and lied about what scientists actually said in their research.

            • Martin Mayberry

              Which scientist? The scientist who are anti evolution or pro evolution? Please watch the debate on you tube at Biola university with Steven Meyers and the men who doubt ID is true and you will see the truth! one of the evolutionist even went as far as to say that where the debate was held{ at a Christian university} would have an effect on the out come of the debate ,but Mr. Meyer corrected him on that and said that “where it was held had no impact of the facts presented”. I thought about it a while and said to myself well done Mr Meyer, well done! You really should watch it. It is a hoot!

            • SmilodonsRetreat

              Claiming that scientists are biased is a flawed outlook.

              The scientists who have looked at the evidence and actually work in the field. The scientists who write the papers and don’t lie about what someone else says.

            • Martin Mayberry

              If scientist are not biased why do some say that ID is true and others say ID is false? If I look outside and can tell you I myself see ID in the way a birds wings are Hollow to help them fly and the lungs they have help them fly and that owls see in the dark and I do see ID in the birds and the bees hive is designed if you have ever noticed. I also have read “Darwin’s black box” by Michael Behe and I assume you will try to tell me he is not a scientist either. I’m sure the only people that you will conclude are true scientist are the ones that will agree that evolution is true! and ID is not!! that is BIAS! evolutionist are terrified that the truth will get out and people will get smart to them! Guess what ? We have.

            • SmilodonsRetreat

              No scientist who studies the evidence says that ID is true. There si zero evidence for a designer. You’re welcome to present it, but there isn’t any.

              Michael Behe is a scientist.. sort of. He hasn’t done much science research in the last two decades (two papers I think, but math based and flawed). He also lied to a court of law in the Kitzmiller trial and has had a page put up at his university that says that the rest of the faculty don’t agree with anything he’s said. In fact, Judge Jones specifically said that Behe’s testimony was one reason he ruled that ID is not science. Not that it required a judge to decide that. Scientists have always known it.

              ID has no evidence.
              ID makes no predictions.
              ID does not draw valid conclusions.
              ID does not explain the diversity of life.
              ID does not explain the amazingly poor design of organisms.

              ID is a story that is altered to suit the evidence as it comes in. For decades, the bacterial flagella was a model ID example. But soon researchers discovered that it was just a modified pump. ID people haven’t brought it up in a long time.

              You haven’t asked a question.

            • Martin Mayberry

              Mr Meyer has never recanted his view .I wonder why? I get his face book updates all the time! and he still makes claims as fact.As far as a story altered to fit the facts Evolution is constantly altered to fit the facts. As a matter of fact they claim that is a positive for evolution to be able to change to fit the facts{LOL} But One thing that evolutionist will NOT do is say that I D could be based in truth! and then when a person has an argument that invalidates it the evolutionist say “You just don’t understand how evolution works” I figure it this way, If evolution is not directed by a mind, as they claim, It could NOT be that impossible for any one to grasp it. it would be simple to understand For the very fact that only a mind can do complex things like math and the like. that it takes complex math to understand the universe is proof that a complex mind did it!

            • SmilodonsRetreat

              Let me explain this to you simply. Behe gets a stipend from the Discovery institute for his “work” with them. He’s a tenured professor who teaches one or two classes a semester. He doesn’t have to produce papers. Heck, he hasn’t even written a book in quite a while.

              He’s got it made because of people like you, who want to believe and will do anything to avoid having to deal with reality.

              Lots of people grasp evolution. You have said many many things, but your statements about the actual science tell me that you really don’t understand it. I’ve offered, let me know when you are ready.

              Finally, look at what you haven’t done. Offered a single bit of evidence that ID is real. Is testable. Is falsifiable. We’re all waiting.

            • Martin Mayberry

              I know if a bird wings are hollow and you asked an airplane maker if from flight sense it would make more sense for a birds wing to be hollow or solid in order to fly had he told you hollow that is proof of intelligent design,yes it is! How would a bird know if they needed or had hollow wings in order to fly! and a birds lungs are designed for flight too! that is intelligent design!

            • SmilodonsRetreat

              Sigh… and that was all present BEFORE birds existed.

              You have another misconception about evolution (again, you need to learn and if you read my blog, you will). Organisms do not plan for the future. Evolution does not plan for the future.

              That is wrong.

            • Martin Mayberry

              that is my evidence and it is true evidence accept it or not!

            • SmilodonsRetreat

              It’s not evidence. No matter what you keep saying.

            • Martin Mayberry

              ID does Make valid conclusions and that is a creator made the Universe and I agree to that!

            • SmilodonsRetreat

              Name the creator and the evidence for it.

            • Martin Mayberry

              the “I Am” the God of Abraham . My evidence for it ::: He works in love John 3;16 and things are way to complex to be undirected! The birds wing and lungs for flight! and the Human mind and body! and that evolution is based on it’s ability to constantly change and some consider that a strength I consider it a flaw for the simple reason you never really know if you are at the absolute TRUTH or not, because it can change on a whim!

            • SmilodonsRetreat

              Perfect, thanks. you have just invalidated ID from ever being taught in schools.

              Well done.

              I don’t really want to get into a Bible discussion, but there are so many mistakes and contradictions in that there is no point in considering it a reliable history. If you consider it correct, then you must think that the movie Titanic was a documentary because the Titanic was a real ship.

            • Martin Mayberry

              You are incorrect again says Mr. Spock to captain Kirk. It makes No difference to me if ID is taught in schools or not. The matter that I am mostly concerned with is that I myself Know the Truth. I am 51 years old {way past school age} and love to hone my debating skills. The students in the schools will have to make a choice. will they just accept what they are told by the liars of evolution or will they think for themselves and discover the Truth that I have .that evolution is only believed by the fools and the Ignorant that have splinters in the windmills of their mind. thanks for the GREAT debate! it was fun!

            • SmilodonsRetreat

              Here’s the thing. I’ve asked you several questions and you have not answered them (“birds, because I say so” isn’t an answer). You have not talked about the science at all.

              You keep talking about how much you know the science, but you don’t want to talk about it. I can’t help you. You believe whatever you like. Science will go on without you.

              Let me ask one final question. When the doctor prescribes antibiotics, you do take all of them correct?

            • Martin Mayberry

              I really do love science. I do indeed believe in science and use it everyday! just boiling water can be described in science terms.I do not believe however that science has to begin with evolution. If evolution disappeared tomorrow, science would go on and still be science. Most early scientist were creationist. Science can begin from a creationist view point. Science has just been hijacked by evolutionist and made the courts believe that evolution pseudo-science is real simply because the judges believe the falsity of “separation of church and state” the way it has been interpreted by the courts. However it does not invalidate creation or ID.as Truth!. Science is a TOOL we use to understand the world that God has created., To me that’s all it is and the definition of science. Birds because I say so is not what I said, you can find out for yourself that birds have hollow wings and bones to make them weigh less. Look on Wikipedia for yourself. maybe Hollow wings to make the bird less heavy does not smack if intelligence to you, But if you ask an airplane maker about it they would agree that the less weight the better for flight! and Hollow wings would make birds less heavy. would it not? and the less weight is more logical,don’t you think? and yes if I get sick I do take antibiotics but a Christian who is a scientist could have figured that out too.It does not need to be an evolutionist! or an Anti-Christian!

            • SmilodonsRetreat

              Let me tell you a little bit about evolution. Without evolution, we would not understand antibiotic resistance, herbicide resistance, and insecticide resistance. Which means our crops would be running at about 30% what they are now. We would not understand genetics, breeding, or any of the other systems that feed us. We would have chickens that lay an egg a week instead of one a day. We would have cattle that produced a gallon of milk per week instead of three gallons a day. We would have no corn, no wheat, no brussels sprouts, broccoli, squash, mustard, papaya, or any number of crops and food animals that we have now.

              Without evolution, we would not have evolutionary algorithms, which have created amazing things, transformed factory scheduling, the stock market, weather prediction, industrial design, optics, electronics and dozens of other industries.

              Without evolution, our understanding of medicine would be barely a third of what we have now. We would not be able to deal with any form of resistant bacteria or viral infections. We would not understand and be able to deal with many autism disorders, heart disease, and cancers.

              We would not have the variety of dogs, cats, chickens, rabbits, cows, goats, horses, and other important animals.

              If evolution went away as a science, or stopped working, we would be well and truly fucked.

              There is no way that intelligent design can produce the things that evolution can. I can list dozens of papers and projects where evolution has outperformed teams of expert human engineers. One that I’m aware of, human engineers still don’t understand how the evolved system works, but it does.

              So you keep believing that evolution doesn’t work. Meanwhile, all the food you eat, the medicines you take, the factories that build your shit, and the banks that handle your money will continue to use these processes that you say don’t work.

            • Martin Mayberry

              To put all of that for evolution to have produced it is a big pill to swallow How in the world did the people ever exist before Darwin? I do think we would understand how reproduction of animals worked if we did not have evolution, that you give all of that improvement to evolution is quite amazing indeed, and that all of it happened and we still do not understand how evolution the “evolved system” works proves to me anyway that it took a mind to create everything the way it is. If No mind at all created it then it would only be logical that man with an highly intelligent mind would surely be able to out think it rather quickly and easily figure it out. don’t you think? You are making evolution way, way too smart. Just think if it can keep us guessing this long and we still can’t figure it out .that does indeed make it {evolution} more intelligent than man! and to prove to me that something with no mind or thinking or planning ability can out think man is illogical says Mr Spock to captain Kirk. My analysis is God with a mind must have done it He would be able to out think man, indeed! Think about it for a while and you too should agree that evolution that has NO intelligence should NOT be able to out think man who is intelligent.

            • SmilodonsRetreat

              Can you explain to me what every line on the circuit board of your laptop does? No? OMG…. computers can’t ever work.

              That sounds stupid, but that is exactly the argument you are making.

              And no, I’m not making evolution sound smart. Evolution is NOT a person with a brain. It’s a process. It’s a process that inevitably leads to complex systems that are highly adapted to their environments.

              To make any claims about god doing it, then you have to provide evidence that god exists. You don’t have any. There isn’t any and there never has been. Better minds than both of us have spent their lives looking for evidence of god and couldn’t find anything.

              You have your beliefs, that’s fine. But don’t pretend you understand evolution.

            • Martin Mayberry

              a mind made a computer board, it did not accidently happen.that prooves my point to me!

            • SmilodonsRetreat

              Computer boards don’t self reproduce. They are not subject to mutation, selection, and any other biological processes.

              It doesn’t “prove” anything, except that you will believe whatever supports your belief.

            • Martin Mayberry

              he brought up the computer issue not me, but the computer was made by a mind anything complicated is. and that is the same thing God does, is make complicated things like the universe and flowers and trees and birds and bees. and God has given man the same ability and with it we makes cars and rocket ships and computers and air planes and ice cream and wonderful things to make our life special isn’t that cool? that knowledge is so awesome!

            • SmilodonsRetreat

              Then you have to have evidence that a god exists. You don’t.

              Proven fact, biological things change. Populations of organisms change over time. This is non-controversial. If you deny it, then you may as well go away, because you are totally ignoring reality.

            • Tim Tian

              Just by the way, Evolution has had billions of years to our hundred thousands.

            • Martin Mayberry

              It does not matter how long it has had with out a mind directing it ,it could accomplish Nothing! a mind makes all the difference,you do understand that concept ? right?

            • SmilodonsRetreat

              Yes, I understand that the ability think makes someone think that that trait is necessary. I even know the psychology behind it.

              It’s still wrong and you still have no evidence for any designer.

              Why are we repeating this again and again. I will change my mind, but only with evidence that you don’t have. I have all the evidence to support my theories, but you won’t accept any of it.

              What is your purpose here?

            • Tim Tian

              If you flip a coin a million times, it will most likely have a run of heads at least 500 long. Did a mind make the coin flip heads 500 times in a row? No. Probability did. I’m lighting a Bunsen burner right now. Does a mind tell methane to react with oxygen to make carbon dioxide? You should be very much aware of the fact that things happen with or without a mind, especially since you do seem to be, in fact, accomplishing something.

            • Martin Mayberry

              Birds are an example of intelligent design! that is my example! that is true!

            • SmilodonsRetreat

              You can say it all you want. It’s not true.

              Birds came from dinosaurs… in fact, they are dinosaurs, by definition. Dromeosaurs in fact. You might be interested to know about some recent research on feathers. http://www.skepticink.com/smilodonsretreat/2014/12/04/historyoffeathers/

            • Martin Mayberry

              I read an article that said they plastered the wings on it after the find but it di not originally have feathers when they found it. they put chicken wings down in order to place the wings outline on it! and birds look nothing like dinosaurs LOL so that I do not accept! wing and fethers and scales are two different things wings are made of feathers and are soft scales are not!

            • SmilodonsRetreat

              Congrats. You read an article. Was it peer-reviewed? or just someone on a creationist site making stuff up?

              DID YOU READ MY ARTICLE?

              Of course you didn’t. Can’t let any actual knowledge interfere with your beliefs.

              There are dozens of known dinosaurs with feathers. There were dinosaurs with hollow bones before that. Do you want the references?

            • cryptoguru

              Hi Kevin (me again), let me take a poke at your dino->bird evolution claim.

              how do you explain modern birds found in dinosaur rock layers? (Cretaceous)

              Monony*us and Hpeoni

              This text was recognized by the built-in Ocrad engine. A better transcription may be attained by right clicking on the selection and changing the OCR engine to “Tesseract” (under the “Language” menu). This message can be removed in the future by unchecking “OCR Disclaimer” (under the Options menu). More info: http://projectnaptha.com/ocrad
              https://www.youtube.com/watch?v=C5eTNoTHewY

              http://www.berkeley.edu/news/berkeleyan/1998/1118/fossil.html

              Quoting the article in case you don’t want to read it:-
              “Until now the only modern bird fossils uncovered from the Cretaceous have been water birds: loons, duck-like waterfowl, shorebirds and tube-nosed seabirds like the albatross. The oldest of these dates from about 80 million years ago”

              Archaeopteryx was a bird and appears in Jurassic sediment, before (according to evolutionists) the Cretaceous Theropods, which birds are claimed to have evolved from. Birds in modern form (including parrots) are observed in the same layer as the dinosaurs they were meant to have evolved from. Then we have even more evidence … Protoavis, a bird found in Triassic layers … and bird footprints (Melchor et al (2002)) in Triassic layers, again before birds were meant to have evolved.

              Hardly a watertight theory eh!

              “No scientist who studies the evidence says that ID is true”
              Even you must see what a ridiculous statement that is?? No?

              You should change that to …
              “No scientist who studies the evidence, under the assumption that there is no designer, could say that ID is true”

              We are all biased, Kev. However, your world-view only permits slow and gradual unguided natural processes to explain origins … my world-view allows natural processes too, but also includes that a supernatural (outside of the natural world) designer both can and did intervene at points in history, so things don’t have to happen slowly or automatically. So which one of us has the closed mind? (My world-view allows a set of possibilities that is a superset of yours.)
              My science allows me to look at the world and determine which things could have been originated under natural principles and which things were supernaturally initiated by the creator. Your science can only look at the natural principles, which are deficient when it comes to origins.

              So I’m assuming that you think that most of the greatest scientists of all time who believed in a creator weren’t real scientists?
              (Einstein, Compton, Pascal, Haekel, Schrodinger, Bacon, Collins, Galileo, Leibniz, Mendel, Marconi, Newton, Maxwell, Kepler, Eccles, Pasteur, Planck, Faraday, Copernicus, Descartes, Boyle, Millikan, Heisenberg, Harvey, Kelvin)
              Atheism has been acceptable especially in educated circles since the 18th Century, so they all had the choice to reject a creator if they felt that was intellectually superior.

            • cryptoguru

              Apologies … ignore the bit that says

              “Monony*us and Hpeoni

              This text was recognized by the built-in Ocrad engine. A better transcription may be attained by right clicking on the selection and changing the OCR engine to “Tesseract” (under the “Language” menu). This message can be removed in the future by unchecking “OCR Disclaimer” (under the Options menu). More info:http://projectnaptha.com/ocrad

              that was my browser automatically pasting weird stuff invisibly into the text editor.

            • SmilodonsRetreat

              While your worldview my allow for supernatural explanations, there’s still no EVIDENCE for said supernatural explanations.

              I love the bird thing. Somehow you think that if birds and dinosaurs lived together, then one couldn’t come from the other?

              Let me quote from that same article
              “A separate line of evidence — molecular studies of modern birds and the rate at which their DNA has changed with time — also has placed the origin of modern birds, including parrots, in the Cretaceous. The new find confirms this hypothesis from molecular divergence data.”

              Archeoptryx was barely a bird, I personally disagree with the authors. I written about this before. Going from memory, out of 21 characters, Archeoptryx had 17 that were strictly dinosaur and only 4 that were strictly bird.

              It was TRANSITIONAL between birds and dinosaurs.

              I totally disagree with your claim that I think those you list weren’t scientists. Their BELIEFS did not influence the science that they did. Sometimes they were right and sometimes they were wrong. But they did proper science. If ID wants to ever do proper science, then those people would be good choices.

              Sorry, but thanks for playing. AtBC is waiting for you.

            • cryptoguru

              there’s plenty of evidence that slow and gradual natural processes could not produce the diversity we see and definitely can’t explain the origin of life itself.

              – ORFan genes (DNA)
              – lack of transitionary forms (Geology)
              – lack of provable evolutionary mechanisms (Biology & Informatics)
              – Lack of observable evolution in experiments (beyond basic regulatory mutations)
              – inability to recreate or even define realistic pre-biotic conditions
              – the hiding of fossils from the public that “confuse” (disagree with) evolutionary pathways or timescales
              – dating methods are inaccurate and provably flawed, yet still used to justify dating rocks
              – geologic processes for sedimentation are assumed to be slow and gradual, when observable science has seen layered sedimentary rock laid down in hours in catastrophic conditions

              I could go on like this for hours. The proof for supernatural causation is that we don’t have the time or the processes for life, biology, geology, cosmology to happen by accident. And no natural process can explain the origin of the laws of nature, logic, morality and human consciousness. Now don’t get all excited and start jumping all over those things I’ve said … let’s stay on topic.

              The arguments you are giving are just stories … they aren’t backed by evidence.

              When did you think birds evolved then? And from what?

              If T-Rex existed at the same time as birds he couldn’t be an ancestor of birds. So which dino became birds? I thought they drew feathers on T-Rex and on others because they assumed they turned into birds?
              So Velociraptor (late Cretaceous dino) never became a bird either … like Jurassic Park said it did? *sad face*

              So you’re basically trying to claim that even though evolutionary scientists claim that Archeoptryx was a bird, you think it was a transitional form and therefore ancestor of birds. Where’s the bit inbetween??? Or the bit before where it came from something else in the fossil record? What about the Triassic birds?

              It seems to me like you’ve got one fossil that some say is a bird, but you don’t want it to be a bird because it could be used to link dinos to birds … yet there were still LOADS of dinos for millions of years afterwards all in the same form they all appeared originally in the fossil record.
              I find it flabbergasting that you think this is a logical or even remotely scientific line of reasoning.

              (and no I don’t want to go to a fundamentalist blog where I have to argue with 30 people who are just like you and change the subject with every vigorous post … I’d prefer to argue with the person who is making the extraordinary claims … I may go back again there again sometime when I have the time)

            • SmilodonsRetreat

              Sadly, the things you mentioned are not correct. I’ve shown so on this very blog. The stuff on that list has been debunked for decades in some cases.

              You need to learn about the things that you are arguing against. Sorry, but you are wrong.

              You are also offering a false dichotomy. If not evolution, then supernatural, is a logical fallacy.

              So, let me see if I understand this. If I don’t answer your questions about birds to your satisfaction, then you are justified in believing the supernatural. No thanks. I can look up the actual papers and read them (and I have previously written about some of them) AND YOU CAN TOO. But you won’t because it will show that you are wrong.

              Evolutionary scientists may say that Archeoptyrx was a bird. They would be wrong. It’s a dinosaur with bird features. I’d like some quotes and links to those quotes… I don’t trust creationists with quotes from anyone. You may not be a liar, but if you promote the quotes from someone else without confirming them… it’s not good.

              I’m flabbergasted that you’re still here. I don’t understand. You have no evidence to support your ideas. You don’t understand evolution. You don’t know that the things you are saying are wrong. And you can’t be bothered to learn about them because it would interfere with your beliefs.

              I don’t care. Believe what you like, but don’t pretend that you know anything about the actual science. Because it’s obvious you don’t.

            • cryptoguru

              YOUR RESPONSES ARE SO VAPID AND LACKING IN ANY ACTUAL INTELLIGENCE IT ALMOST MAKES ME DOUBT INTELLIGENT DESIGN. HERE IS HOW ARBITRARY YOUR LAST POST IS (READ CAREFULLY)

              Sadly the rebuttals you’ve given against the things we’ve mentioned are not correct. I’ve shown so on this very blog. The rebuttals to the stuff on that list have been debunked for decades in some cases.

              You need to learn about the things that you are arguing against. Sorry, but you are wrong

              You are also wrong about my offering a false dichotomy. Supernatural vs Natural causation is not a false dichotomy.

              So, let me see if I understand this. If I don’t answer your questions about all of science to your satisfaction, then you are justified in believing in evolution. No thanks. I can look up the actual papers and read them (and I have previously written about some of them) AND YOU CAN TOO. But you won’t because it will show that you are wrong.

              Evolutionary scientists may say that Archeoptyrx was a bird. They would be correct. It’s not just a dinosaur with bird features. I’d like some quotes and links to those quotes that show it’s a dinosaur … I don’t trust evolutionists with quotes from anyone. You may not be a liar, but if you promote the quotes from someone else without confirming them… it’s not good.

              I’m flabbergasted that you’re still here. I don’t understand. You have no evidence to support your ideas. You don’t understand science. You don’t know that the things you are saying are wrong. And you can’t be bothered to learn about them because it would interfere with your beliefs.

              I don’t care. Believe what you like, but don’t pretend that you know anything about the actual science. Because it’s obvious you don’t.

            • SmilodonsRetreat

              Let me explain.

              Do you honestly think that you are the first person to come up with these “arguments” against evolution?

              Man, you aren’t even the hundredth.Your issue have been dealt with, thousands of times over. You choose not to accept them, that’s your problem.

              Here; http://www.skepticink.com/smilodonsretreat/2013/04/05/assumptions-of-radioactive-dating/

              http://www.skepticink.com/smilodonsretreat/2013/04/07/radiometric-dating-part-ii-isochrons/

              http://www.skepticink.com/smilodonsretreat/2013/02/22/weaknesses-of-evolution-part-7-transitional-fossils/

              http://www.skepticink.com/smilodonsretreat/2013/03/02/intelligent-design-gets-peer-review-sort-of/

              It gets very tiring to write the same thing over and over again to someone who refuses to make any effort to learn. But, you’re not here to do that are you?

            • cryptoguru

              do you really think you’re the first person to claim that you have rational responses to these arguments?

              On all your blogs you do exactly the same thing. You don’t address the science, you just make a list of assertions … then you get all emotional that anyone should ever question you.
              THAT’S NOT SCIENCE!!!
              Real scientists make a case and then open it up to query. You are not open to query, you just make dogmatic statements that everything you believe is backed up by science without explaining the scientific reasons for your assertion.

              Tell you what though … I may jump on some of those blogs and raise issues with what you claim. Let’s see how that goes (tries to muster energy)

              You will undoubtedly simply claim that I am “wrong” in every case without giving any rational reason why. And appeal to fallacies such as “thousands of people know this” and “all good scientists agree” to make your case. Let’s see shall we.

              Remember Kev, I expect some actual science here, not just rampant emotionalism … that’s the hallmark of a religious nutter and not an objective truth-seeker.

            • SmilodonsRetreat

              Then you haven’t read my blogs.

              I would love to talk about actual science, but you aren’t. Just the same old creationist nonsense.

              I’m honestly tired of dealing with it.

            • cryptoguru

              hehe … you are very funny.

              I’ve posted on your dating blog (which is choc full of unsupported statements)

              http://www.skepticink.com/smilodonsretreat/2013/04/05/assumptions-of-radioactive-dating/

              please explain how any of my statements are scientifically invalid … by that, I mean explain HOW, don’t just say they’re invalid like you just did above.
              Oh, I should probably go back and say something about Isochron dating before you claim that solves everything.

            • SmilodonsRetreat

              You mean, I should rewrite what I’ve already done in order to debunk your unsubstantiated claims?

              I’ll get right on that.

              If you wanted to learn, then there’s plenty you could do for that. You can see for yourself. But you won’t. That is obvious.

            • cryptoguru

              NO KEVIN!! You are the one making unsubstantiated claims … I’m challenging them, you are unable to counteract my arguments.

              So what you’re really saying is … “I don’t know how to answer your challenge, I will just pretend you’re a stupid creationist, claim you’re unscientific, and tell you to get lost”

              If you can’t handle questions, don’t make bold statements!

            • SmilodonsRetreat

              Claims made without evidence can be dismissed without evidence.

            • cryptoguru

              Sandwiches made without chicken can be eaten without chocolate.

              I have no idea what you’re talking about … you talked about birds coming from dinos … I gave you some pretty clear evidence that calls your claim into serious question.
              You had no rebuttal, you now say I have no evidence.

              What about the parrot Kevin, the parrot??? Surely the parrot counts for something?

              Nice chatting again … feel free to answer my Carbon14 post, I’m sure you have a fantastic rebuttal for that one too.

            • cryptoguru

              ooh my bad, you did respond to C14 … I wasn’t watching … NOW we’re talking … a proper discussion.

            • SmilodonsRetreat

              This is in no way a proper discussion. If you think that it is… well… that explains a lot.

            • SmilodonsRetreat

              I know you have no idea what I’m on about. I’ve tried to help you, but you don’t listen.

              I read the article, there is still plenty of evidence that birds came from dinosaurs. The quote I listed refutes your claim.

              That’s called quotemining. When you take a quote out of context in order to present someone as holding an idea that they don’t actually hold.

              Anyway, there’s plenty of literature on the origin of birds (no, they aren’t from T-rex and velociraptors… and velociraptors are not as big as in the movies either).

              The article you mentioned pushes the date back to WHERE IT AGREES WITH MOLECULAR EVIDENCE… In other words, now two pieces of evidence support the evolutionary model. Thanks.

            • cryptoguru

              BTW: what about the birdies?
              You’ve gone awfully quiet about that one.

              Can you not say anything about Velociraptor? Or T-rex? I thought they evolved into birds? But it seems birds predated even them … at the very least they co-existed with birds that are in their current form.

              You evolutionists keep saying “JUST SHOW ONE FOSSIL THAT’S OUT OF PLACE AND WE’LL BELIEVE YOU HAVE A CASE”
              There’s a LOT there … hundreds of modern-form birds in dinosaur rock layers. And still no transitions! Proof enough? Nah I didn’t think so.

              What’s today’s rescuing device Kevin?

            • SmilodonsRetreat

              “Can you not say anything about Velociraptor? Or T-rex? I thought they evolved into birds?”

              You are wrong.

              Archeoptyrx is a transitional fossil. It has features of a dinosaur AND of a bird.

              Please look up the definition of “Transitional fossil”. You will find that there is no requirement to be exactly in between specific time frames or specific organisms. In other words, an organism can be transitional between two groups that have already diverged… as long as it has some characters of both groups.

              What’s today’s rescuing device? The truth. I don’t need rescuing from you. What you say is mostly wrong and it doesn’t matter what I say, you won’t listen anyway.

            • Martin Mayberry

              evolution is just a religion and it is not true!

            • SmilodonsRetreat

              Saying things over and over doesn’t make them true.

              EVIDENCE. Science has it, religion doesn’t.

            • hyperzombie

              Saying things over and over doesn’t make them true.

              True, unless you chant it while wearing ruby red magic slippers while clicking them together, then you only have to say it 3 times. This has been proven by science, and the great powerful OZ.

      • Doc Bill

        Hi Martin!

        I am a Doctor of Chemistry!

        I am much more educated than you and much smarter than you!

        You, Martin, are a fucking idiot!

        First, please park the exclamation mark. Nobody is impressed by that.

        Second, spend some time learning chemistry before you spout off your ignorant bilge.

        Third, we, the rational and educated people on the planet, have heard your ignorant spouting for decades and are not impressed. Instead of learning something perhaps you could simply crawl beneath the rock whence you came.

        Love and kisses,
        A real scientist.

        • Martin Mayberry

          chemistry does not need a doctor because it does NOT GET SICK ,maybe you are the idiot for thinking chemistry gets sick! what kind of crappolla are they teaching you now days! LOL and further more I would not go to any doctor who cussed like a sailor!LOL

        • Martin Mayberry

          and usually when evolutionist can’t win they call names, and that weakens their position! LOL

        • Martin Mayberry

          I frankly don’t give a hoot if you are Dr Frankenstein, to convince me you are correct you have not done!

          • SmilodonsRetreat

            I have already asked you this. What evidence will convince you? You have not answered it.

            I suspect it’s because you know that I will say that your required evidence is not possible and you know that I will demand that you provide equivalent evidence for your own notions, which you cannot do.

            • Martin Mayberry

              What evidence would convince you that God did create the world other than looking up in the sky an seeing God looking at you? How ever much evidence it would take for you to be convinced God did it, it would take exactly the same evidence from the evolution perspective to get me to believe that evolution did it! If you don’t believe a bunch of preachers that say it was created by God, I’m not going to believe a bunch of scientist claiming evolution happened just because they claim it did just by accident with No mind at all to direct it!

            • SmilodonsRetreat

              God is like Bigfoot. Nothing less than a body will do. Fortunately, we have bodies… and DNA… and observational investigations and lab experiments and biogeography and known factors that alter DNA and regulatory sequences and known factors that form the molecules of life from non-living materials (heck, high school students can do this) and literally millions of individual research papers that all lead to one inescapable conclusion. All life on this planet is related and evolution works.

              You have a book that describes talking snakes, an impossible flood, miracles that suddenly ceased to happen once the book was finished… oh and you have no idea who wrote most of that book or when.

              I don’t believe what anyone SAYS. I look at the evidence. Something you, apparently, won’t do. I’ve done some of those experiments. I’ve seen it happen with my own eyes. We can trace fossils back through time and see the changes in organisms.

              The world is so much more amazing than you’ll let it be.

              BTW: evolution does not equal accident. You can stop lying about that now.

            • Martin Mayberry

              so a bird is related to a worm and ends up eating it and a worm is some how related to an elk. you said all living things were all related. now talk about believing in Santa clause or fairies LOL how do you connect these living things from the very beginning of time?

            • SmilodonsRetreat

              Yep. I thought you said that you studied this stuff. This is High School level material here. http://mbe.oxfordjournals.org/content/15/11/1481.full.pdf+html

              This is one gene, a gene that exists in every species that has mitochondria (i.e. almost every living thing on the entire planet). The difference in the gene between all bird species is much less than 20%. Between all mammals, a few are as different as 25%. And the same for all amphibians and reptiles. Fishes are a tiny bit more variable, with one group going slightly beyond 35%, but the rest are all 25% or less.

              But what’s really interesting is that when you analyze the cytochrome c genes for animals… the more closely related the animals, the more similar the cytochrome c is. What we would expect to find if evolution were true.

              To give you another example, humans cannot manufacture Vitamin C, we have to eat it to get it. The same is true of gorillas, chimpanzees, gibbons and tarsiers. But what is really interesting is that all of these species have THE EXACT SAME MUTATION IN EXACTLY THE SAME PLACE that breaks the vitamin C production gene. Some other mammal species, that are not a small group of primate, also have a broken vitamin C gene, but it’s a different mutation. But again, closely related species have the same break.

              It’s basic genetics.

            • Martin Mayberry

              Ok sounds cool!

            • Martin Mayberry

              here is a tid bit of science knowledge from the web site called “genetics home reference” Mitochondrial DNA contains 37 genes, all of which are essential for normal mitochondrial to function! that is NOT me that is your science telling you that! You do understand what that means do you not? irreducible complexity is also true, if that is true. so now we have irreducible complexity screaming creation is true also! Plus the lungs and hollow wings of birds to help them fly!WoW

            • SmilodonsRetreat

              You assume that such systems appeared fully formed. You assume that NO changes to those systems can happen without the entire system breaking down.

              Both of those things are not true. Therefore, your conclusion is invalid.

            • Martin Mayberry

              If it needs all its genes to function properly maybe you can tell me which came first and why it says all the genes are essential for proper function? if you read the web page all any lack of genes are abnormal and a break down of the normal. you claim a creationist believe in Santa, evolutionist are so hard headed they will tell you that real science not even made up by creationist is a falsehood and lie. Now you have given me real reason to doubt you!LOL

            • Doc Bill

              Martin, I admire the fact that English is a second language for you and, in general, you communicate well; all things considered. Certainly, your attempt at writing English is far better than my French.

              However, your level of education coupled with your religious handicap prevent you from understanding anything above science as taught in the 3rd grade (9-10 year old), or scientific knowledge beyond the medieval period in history.

              At this point you are simply a troll and, frankly, a boring, inept troll. We’ve certainly seen better trolls around here, right Creepto and Rexy? But, on the bright side, with a little work, improving your English composition and possibly developing a unique persona, you could elevate yourself to a really nasty pest and ultimately get your very own Orkin designation.

              All the best.

            • Martin Mayberry

              Oh tell me please please could I ever be as good of troll as You? usually when a person puts another person’s writing down. I think you are spiffy! I think it is wonderful that I show up on these evolution web sites. some one has to put the liars and the stupid people who just want to push evolution garbage in their place, I consider that my job I will never think evolution is correct, It is brain washing at best ,it is NOT true science, it is an evil bias that turns men into mindless evolution Zombies that claim it is true, even when science can be proven to be against them! they close their minds and ears and scream NO NOT true. I do not hate you,and I hope you don’t hate me. I simply wonder why you are so hard headed? And I wonder one more thing since you are so hard headed, do you make it a practice to go to JC Penny’s and argue with the mannequin’s in the store? that just seems like that’s about as hardheaded as you may be to do just that!

            • Doc Bill

              Brain washing is brainwashing and Zombies is zombies. Please take a course in English composition. You are embarrassing to read.

              No, I don’t shop at JCP because JCP is too low-end. Only stupid trolls like you shop at JCP.

              Meanwhile, you only wrote to support my thesis that you are an idiotic , foolish troll.

            • Martin Mayberry

              I did not say you shopped there, you just go in to argue with the mannequin’s, see you can’t read that’s your problem it is not my spelling LOL!!

            • SmilodonsRetreat

              Again, you assume that everything in the mitochondria DNA is exactly that same as it has been forever.

              You assume that NO changes can be made to the genes without the system failing.

              Even if you talk about cars and computers this is completely untrue. It’s even more untrue for organisms.

              Therefore, your conclusion is incorrect.

            • Martin Mayberry

              again you assume that it has changed can you tell me which part could possibly change in order for it to continue to work and still be considered working as normal? just because you say it has changed does not meant that it has changed if you can not prove that it has changed, that is like me saying that “God exist and I have no proof of it” as you so often say! to keep changing the evidence around to fit your conclusions is like a shell game.when something don’t fit, just say it did not happen that way.

            • SmilodonsRetreat

              Gen duplication. Look it up.

              So, what you seem to be saying is that, if I can’t explain every detail of the entire history of a single molecule over the last 3.5 billion years, then you are justified in your belief in a supernatural creator?

              So hypocritical. You demand of me what you can’t begin to provide of your beliefs.

            • Martin Mayberry

              No all I want to know is do you believe that Mitochondrial gene contains 37 genes all which are essential for normal mitochondrial to function?yes or no.

            • SmilodonsRetreat

              No,. I don’t believe it. I’ll have to look it up.

              It’s not that I don’t trust you… but I don’t.

              Let me check.

              Nope, I don’t agree with you.

              The C. elegans mitochondrial DNA is typical of animal mitochondrial genomes in its size and gene content. It is 13,794 nucleotides in length and encodes 36 genes

              Mitochondrial gene content is highly variable across extant eukaryotes. The number of mitochondrial protein genes varies from 3
              to 67, while tRNA gene content varies from 0 to 27

              http://sites.bio.indiana.edu/~palmerlab/Journals/197.pdf

              So, no, you are wrong. While you are correct for humans, you are incorrect for other species. But what’s really important is that this destroys your entire idea. The mitochondria genome is highly variable (as shown in that research paper), therefore your idea that there is only one possible genome and it must be that way to function is wrong.

              I would suggest you stop reading creationist garbage.

              BTW: I found all that in less than 5 minutes on google scholar. Again, YOU CAN do this. i would encourage you to.

    • yor mom

      It’s obvious from reading this that the author has very little knowledge about computer science and so makes some pretty ridiculous assertions in order to categorize biology into a distinctly different field from information technology in order to shake the uncomfortable notion that any of it may have had an underlying intelligently guided design.
      I don’t particularly care, but I think it’s silly to put blinders on for the benefit of any pre-conceived conclusion so without further ado, here’s some of the bullshittery in this article;

      1.) He says that since DNA can contain both instructions and data it is not “like a computer”. Excuse me? We use the Von Neumann architecture in our computers today which is built off of the fundamental idea that the same devices that store data also contain the instruction set. This is part of the reason why we have so much difficulty keeping our computers secure from unwanted tampering. The Harvard architecture was a competing idea that lost out, which is the type of architecture the author thinks that computers actually use; They don’t.

      2.) He says that DNA doesn’t work in discreet steps. Neither do computers. Apparently the author was unaware of the technology we had since 1996; Multicore processors. Computers often do many things simultaneously. That doesn’t make them any less computery.

      3.) He also says that computers will crash if you change some code. No they don’t. It’s perfectly possible to run bad code and even to change it during run time. It’s good programming practice to make the computer crash when the code is doing something it shouldn’t, but it’s not necessary. PHP for example won’t cause your computer or program to crash under most circumstances where it should. Here’s a real world method in java;

      public void tryMakeCrash(){
      try{
      #Write any compilable code you like under here, the program won’t crash.
      #If you want to get anal about “compilable”, you can do the same thing with reflection.

      }Catch(exception e){}
      }

      4.) You need lots more bits than 4 to store the data. So? I’m perplexed as to why this was even brought up. Just because there’s alot of data in the system, and even multiple types of storage devices doesn’t make a thing less of a computer.

      The demarcation point between Computer Science and Biology is getting increasingly hazy as we learn more about both.

      I dislike this idiotic fascination some people have with out-of-hand rejection of any discussion about intelligent design. We take for granted that we live in an intelligible universe and at the same time reject any notion of intelligent guiding force. That isn’t to say I’m convinced by the idea, but that it’s also not some outrageous barbaric notion.

      • SmilodonsRetreat

        1) not DEVICE, but INFORMATION. The exact same code that represents the data is also the same code that is the processing system. Computers use completely separate code blocks for data and for processing, not the least of which are the CPU instruction set.

        2) Show me a computer without a clock. That’s how we measure computer steps… in number of steps per second. Multicore has nothing to do with it. A thousand core Beowulf still does one operation per clock cycle.

        3) OK, I’ll give you this one… to a point. Now, change the code in the CPU instruction set and see what happens.

        4) Because most ID proponents seem to think that DNA contains only four bits per nucleotide.

        I dislike people who think that because they work with intelligently designed, complex systems that ALL complex systems MUST be intelligently designed. This is trivially not true.

        I do not dimiss ID out of hand. I dismiss ID because there is no evidence to support it. There are alternative methods with are much more effective than those proposed by ID. There is no evidence of the “I” in ID. There are no predictions made by ID (well, at least ones that have turned out to be true). There are no research plans to support ID.

        Do I need to go on?

        • yor mom

          You’re not really saying anything intelligible when you’re saying “The exact same code that represents the data is also the same code that is the processing system.” Is the “code” data or is the “code” a processing system? “Code” is typically a digital instruction set. Information on a computer can be either “data” or “code” and can reside in the same physical spaces. This is where the Von Neumon architecture comes into play. So if I look at RAM in a computer and ask, “Does this thing store data, or does it carry instructions on how to manipulate the data?” the answer is that it does both at the same time. When the CPU pulls this information from RAM it is likewise storing and manipulating data simultaneously.
          The fact that we keep particular instruction sets separate in the CPU is a convention that gears the computation toward our particular use cases, but that’s not a rule that governs the field of Computer Science. If you really wanted to create a computer that keeps its instruction set in the same areas as it’s data, you can do that. Though inadvisable it would still be a computer.
          Now, the buck has to stop somewhere. You have to have some kind of metadata that informs the system how to take inputs and produce specific outputs. 0’s and 1’s by themselves can’t produce an opera. Some kind of assumptions need to exist in order to translate information into some desired output. Biological systems also carry these assumptions. Instructions for nano machines that split DNA exist, as well micro machines that “know” how to replicate dna both backwards and forwards. Countless different machines exist that don’t carry data themselves, they perform one specific function on a strip of DNA, or whatever else, that ultimately translates data into biological products.

          As to “discreet operations”, I can see that you were referring to time now, but again this is just convention. We don’t need clocks on computers. In fact here’s someone that’s trying to do computers without them, calling it an “asynchronous system”;
          http://www.cs.virginia.edu/~robins/Computing_Without_Clocks.pdf

          I wouldn’t argue that cells are computers. They’re obviously different in their history, materials, and products, but they do computation, and the fields of microbiology and computer science are not cleanly divided.

          • SmilodonsRetreat

            Sigh… that’s exactly what I’m trying to say. You have said yourself that there is “data code” and there is “processing code”. In DNA, those two pieces of code can be the same piece of code.

            There isn’t memory in DNA. There isn’t a CPU in DNA. There isn’t data code in DNA. There isn’t processing code in DNA. There isn’t CPU instruction sets in DNA. There is just DNA and it does all of those things. That’s why it’s different than a computer.

            And the instructions for those “nano-machines” (which everyone else calls enzymes) is in the DNA.

            Here’s the problem. Computers require a designer. DNA does not. Claiming that DNA is a computer is used to claim that DNA requires a designer. It does not.

            Now, we can argue all day long about the specific instances of things that may or may not apply to computers and DNA. But DNA as a computer remains, at best, an analogy. And it’s a false analogy. Because you can’t talk about all the things in a computer that you can with DNA.

            As I’ve said dozens of times now, why not just talk about DNA? Why do we have to bring in a false analogy? The answer is because it supports the idea of DNA having a designer. Which is simply not true.

            There are tons of papers that talk about how DNA works. It would be better to talk about that, than try to fit DNA into a poor analogy to talk about it.

            • cryptoguru

              Kevin, you really are confusing yourself (and probably others) with this dodgy reasoning.

              (I couldn’t help but chip in here after such a well-made argument from Yor Mom)

              Let’s try and mop up your fallaciousness a bit here.

              If I claimed that cells have transport systems (which they do) but you said they don’t because they don’t have wheels with rubber tyres or remote-controlled central locking mechanisms or seat belts, then your argument is fallacious equivocation and the fallacy of a Complex Question (Tying). You would be saying that because the transport system in question doesn’t have the same attributes as another well-known transport system, then the subject cannot be considered transport.

              A “computer” is a generic term for a device that performs computation and can be defined as that which fulfils the requirements of a Turing machine. A personal desktop computer is an instance of this, as is the biological cell. However a Desktop machine is not the same as a biological cell, they are similar in many ways, but not the same. Yet, the cell is still a computer.

              To hammer it home:-

              1) is THIS a computer? http://www.extremetech.com/extreme/152074-stanford-creates-biological-transistors-the-final-step-towards-computers-inside-living-cells

              YES

              2) is it the same as this (http://www.apple.com/uk/macbook/?cid=wwa-uk-kwg-mac-com) in all its features?

              NO!

              … they both are computers, they’re different kinds of computer.

              So what’s the difference between the biological computer in 1) and a naturally functioning cell? Have we artificially made it from a cell into a computer? Nope! It was a computer before too (according to Turing completeness), it’s just that we don’t know how to write our own code that runs in natural cells, we can only currently hack them.

              Biological computers are a hardware hack that allows us to do things that we understand (from electronic computers) with biological computer hardware that works in ways we currently only partially understand. So we’re adopting unfamiliar computer hardware, and adapting it to work in ways that we are used to. (but we can still tell it’s a computer … just the same way we could tell an alien spaceship is a form of transport even if we didn’t know how to build or use it)

              Many scientists believe that one day we will understand enough about the way DNA natively executes to be able to write code that runs in the cell, without having to hack the way it works.

              In case you didn’t know this already … the biological cell has vastly superior processing, language, runtime translation, storage, error correction, energy efficiency, durability, flexibility, functional complexity over anything we have designed or thought up. We’re starting to copy some of these ideas to use in our own computers, because they’re better.

              I think what you’re struggling with is the fact that the chemistry is just the medium of representation of this system, it’s not the actual system. The system is abstract in the sense that it comprises language and algorithms … DNA is a physical (chemical) representation of the information, or code (which is abstract). Desktop computers use electricity to represent information and to process it, the electricity isn’t the computer; it’s just a medium. The biological cell is much less limited than our electronic computers, in fact it is able to build and install an operating system on an electronic computer (the human brain), so it is both able to compute abstract non-material processes (such as differential RNA processing on the micro scale and programmed behaviours in organisms on the macro scale) and also produce physical output (e.g. proteins and protein assembly). So the biological cell is a much more flexible and complex computer than any we’ve built.

              The reason you seem unable to accept these obvious and undistputable truths seems to come down to the fact that you don’t like where the reasoning might lead … and that a creationist may use it to argue a case that random mutation couldn’t ever cause improvement.

              Shame on you!

              Accept the facts! Argue your case for evolution on the basis of truth, not lies … or is that too difficult?

            • SmilodonsRetreat

              It’s funny that you don’t understand anything that I’ve written or that others have written here.

              A computer is anything that computes. That is, takes an input, does something, and forms an output. I am a computer. You are a computer. DNA is a computer. Air is a computer. The solar system is a computer. By that very basic definition, everything is a computer.

              But THEN we move to the “computers are designed, therefore DNA is also designed” argument, which is where the problem lies. We cannot code the DNA into computable bits (at this point), because the whole is not easily represented by the parts. You may be correct and that we will figure this out (probably using actual computing devices that we have built). But it will not be the simplistic version offered by creationists.

              I would suggest that you reread the post, since it was talking about very specific instances. You are, here, talking about generalities, most of which I do not disagree with.

            • cryptoguru

              it’s not that I don’t understand … I don’t agree; that’s VERY different.
              You seem to have this problem accepting that people can disagree with your conclusions. Which FACTS are there that we’re in disagreement over that aren’t subject to interpretation, that could only be explained by me not understanding what you wrote? Or is it just that you made a bunch of baseless assertions.

              In your original article you actually show your incompetence by consistently setting up sequences of weird straw-man arguments
              EXAMPLE:
              “So, if you see someone using this argument and describing DNA using 4 bits, then you are free to call them out on having zero knowledge of DNA or biochemistry. Here’s why. …”
              Err … the symbol set is base-4, but the cell processes codons, which are 3 symbols long (i.e. base-64). None of these refers to 4 bits.
              So in binary (base-2) a nucleotide would be represented 2 bits.
              11, 01, 00, 10
              And a codon would be represented by 6 binary bits. Where did you get 4 bits of anything from?
              Hilariously you refer to “knowledge of DNA or biochemistry”, coding has nothing to do with either of those fields … a code is a mathematical construct. What you said there is as stupid as saying
              “So, if you see someone using this argument and describing a car as having 8 wheels, then you are free to call them out on having zero knowledge of quantum mechanics or material science”.
              In that respect yes I don’t understand anything you’re saying … because it makes no sense at all. But I do understand the thrust of your message
              “creationists are wrong, because they’re wrong … if a creationist tells you that a cell is like a computer then tell them that they are wrong, because who knows what unfavourable conclusions could be drawn from that concession”
              You have yet to demonstrate how a cell is not like a Turing machine (computer).

              “A computer is anything that computes.”
              That’s another straw man! I did not say that’s the definition of a computer, I said that the Turing machine serves as a definition of a computer. “anything that computes” is a vague and wishy-washy term that you can make to mean anything you like (which you did)

              What you are saying is utterly absurd … you are declassifying a clear definition of something because you’ve generalised it and therefore are saying that it’s not specific. YOU applied the definition as a generalisation, not ME. I don’t accept your generalisation of the definition of a computer. I’ll stick with the Turing machine if that’s OK.

              So how is Air, the solar system or you like a Turing machine?
              Again … how is the living cell NOT like a Turing machine?

              I suggest you re-read MY post, it is only YOU who is referring to generalities, which neither of us agree with.

              (BIG FAT STRAW MAN)

            • SmilodonsRetreat

              Again, I responded to a very specific claim in my post. You are arguing against claims that no one has made.

              Again, I disgaree with much of what you say.

              I will say that it is the Intelligent Design proponents that talk about encoding DNA with bits per nucleotide… and I did make a mistake. That should be 2-bits per nucleotide. I explained, in detail, why this is false and cannot be complete.

              Here’s the problem, even if we assume that the DNA is a tape, I still don’t think that it meets the definition of a Turing machine. This is because the information in the tape is not affected by the physical tape (using tape as any generic storage device). This is not the case for DNA, where changes to the physical structure of the storage system can change how the data is interpreted.

              While you are arguing about Turing machines, which again, I could disagree with. That’s not anyone else’s point. YOU brought in Turing machines. Feel free to visit any ID websites, you won’t see a discussion of Turing machine. You will see the discussion I outlined in my OP. It is you that are bringing extraneous material to the discussion.

            • cryptoguru

              I am using Turing machines as a cast-iron definition that you can’t wriggle out of or change. It is a clear explanation of what a computer is … and the biological cell fulfils its requirements.

              You really are clutching at straws now.

              My argument is against your post, which is arguing that DNA is not like a computer (which is a straw man anyway .. creationists are saying that the CELL is a computer, DNA is the storage mechanism for a program). Either way you are claiming that the cell being like a computer is a bad analogy … presumably because understanding the cell works as a computer exposes the stupidity of the evolutionary assumption that random damage to a computer hard drive can write better code.

              I have demonstrated how the cell satisfies the requirements of a Turing machine. You are trying to dismiss it as irrelevant … IT IS NOT!

              If the cell is a Turing machine, then your entire post is wrong and the cell is a type of computer, and DNA stores the program run by the computer. (the stored-program is abstract in the same way as Von Neumann defined in his architecture)

              “This is because the information in the tape is not affected by the physical tape (using tape as any generic storage device). This is not the case for DNA, where changes to the physical structure of the storage system can change how the data is interpreted.”

              completely wrong!! Here try this … open your computer hard-drive (assuming it’s a disk-drive), take the disk platters out carefully … now chop them up with a pair of scissors and splice them back together into a different arrangement (like old-style film editing). Now run your computer, is the data interpreted differently on your machine when you try and run the OS?
              Tell you what, do that to DNA too, take a genome and cut the chromosomes up into random segments, join them together again and try and run the DNA in the cell it was intended for.
              If you’ve cut it up to a small enough resolution (i.e. through code that executes) I can guarantee that something won’t work properly, if anything.

              They are exactly the same concepts realised on different media. A stored non-linear program that is run through a translator and produces measurable output.

              I’m not to be held responsible for ID websites who don’t mention the Turing machine. It’s possibly because they expect everyone to understand the cell works like a computer, and they don’t feel the need to have to go to the levels of pedantry I’m having to in order to get you to concede the absolutely child-level obvious fact.

              So as long as you can keep evolution as this mystical unknowable force that can’t be compared to any other known physical system, because it’s just so magical … maybe people will simply accept what you say about evolution creating everything. But as soon as we start to nail down what evolution is meant to be and try to understand its mechanisms, you get very twitchy and want to change the subject, and want to claim that I don’t understand anything about evolution etc.

              I put it to you that you know nothing about evolution … that it in fact is not real and therefore the reason why you don’t like trying to understand evolution (real science) is because it doesn’t exist as the mechanism you think it is.

    • Steephen Hatfield

      People who believe in ID are proof it never happened.

    • J.S. Shepard

      Since current binary computer code is no more than an analogy to DNA, according to the evidence in this article, could a new computer code be generated to replicate how DNA works? Would it be a computer/machine that is able to learn and get better?

      • SmilodonsRetreat

        Yes. There’s an entire branch of computer science called “evolutionary algorithms” or “genetic algorithms”. Basically, you code the subject matter into a string of data, then allow evolution to modify that string and evaluate the resulting strings in some way (usually mathematically) looking for the optimum conditions.

        I’ve got some older articles, but I haven’t really been keeping up in the field.

        A quick google search resulted in this book http://mf.erciyes.edu.tr/dosyalar/dokumanlar/Intelligent%20Optimisation%20Techniques%20D.KARABO%C4%9EA.pdf
        (large pdf)

        • J.S. Shepard

          Thank you!

    • Sarah Fix

      I still think it’s a pretty good analogy from my understanding of CS and genetics. Granted I only have an undergraduate understanding of both, and I’ve only taken python with experience in HTML, CSS, and maybe some javascript. But adding to code doesn’t necessarily eff everything up. You can add code to areas that the program won’t run or read until something odd and unusual happens. Arguably you could compare this to alleles interacting with each other and to methylation and to diseases that show up only under stress and immunocompromised systems. CS has certainly become pretty complicated in the short time that’s been around. By the time we have artificial intelligence, no one person is going to be able to understand all of the inputs that went in to creating it, just as at this point in time it’s impossible for everyone to understand all of the components of the human body. We have a lot of people that are experts in one tiny area, on one molecule or allele or piece of machinery (DNA polymerase, etc.) or segment of DNA (TATA box, etc.).

      No, I don’t think it’s as simple as DNA being a four bit system. That is oversimplified. But I’m pretty sure that comparing DNA to coding is not very inaccurate.

      • SmilodonsRetreat

        The problem is that is an analogy and not the thing. Making arguments about DNA by referring to computer code is a mistake.

        For teaching purposes, it’s a perfectly good analogy.

        • Sarah Fix

          I understand. Thanks for clarifying.

      • Doc Bill

        I like to use the analogy of a book of recipes in a large kitchen with lots of chefs. Everything is happening at once. Seasoning can change the recipe dramatically. Take fried strips of meat, add garlic and cumin and you have Mexican. Add cinnamon and you have Turkish. Add coriander and bay and you have Indian. Same basic ingredients.

        The computer runs on a clock. Everything is synchronized. Tick tock, shift a register, tick tock, add a bit, tick tock, latch a buffer to memory. Not so biology. It’s all chemistry that just happens.

        Craig Venter took the DNA out of one organism, put it into another organism and it ran just fine. Org B started replicating Org A. It would be like taking my kitchen and replacing all the Italian recipes with German turning the restaurant from Giovani’s to Gunter’s.

        Creationists love to use the computer analogy because it sounds sciency and schmart, and fits with the “intelligent design” creationism meme of “machines in the cell” and all that stuff. I suspect creationists are lousy cooks, too.

    • Dana Smith

      I’m a trained biologist and also a fluent programmer and coder, and I agree in some ways with Smilodon and disagree in others (and don’t worry, I’m not an advocate of Intelligent Design). It seems almost like Smilodon is trying to discredit the notion that the genetic code is similar to computer code in order to discredit IDers, but I think he is throwing the baby out with the bathwater.

      I would absolutely say that the Genetic Code operates like computer code in that programming languages and the “language” of DNA both involve complex procedural algorithms and operators working within the parameters of a given system. In the case of computers, that system is your operating system and hardware, where as in biology its the parameters of physics and chemistry.

      The major difference between computer code and the genetic code is that, well, the language of DNA is totally wacky, weird, and cobbled together as though it were… you know… done without any foresight, just as you would expect with evolution. This fact, I think, is actually evidence that there WASN’T any intelligent design, as you end up with things like repeating microsatellites. One of the reasons that genetics is a science and not just a casual observation is that the architecture of the genetic code is not at all elegant.

      Interesting tidbit, by the way. While I code, I’ve found that some of the bugs I’ve introduced to my code can actually produce unexpectedly favorable results in a similar way that a mutation would.

    • Ray Riemersma

      While comparing genetics to computer science may be a bit off, there are analogies that can be made, for purposes of understanding. Example: Puberty is the point in genetic code formation where the code finishes compiling, or matures and becomes hard wired for the remainder of life (excluding environmental factors such as radiation and chemical poisoning, cancers, etc.). Much in the way a completed, debugged computer program is packaged and runs after it is compiled. The difference is that with genetic code, there are too many variables in the programming to comprehend or predict any changes in interactions with them, that while we may be able one day to selectively “alter” some lines of genetic code, we will not be able to do so to produce any particular goal or intended advantage, but rather only succeed in destroying original information. The odds of succeeding in such an attempt would be equivalent to predicting the winning numbers to dozens of separate lotto drawings…in a row, and getting them all correct.

      • SmilodonsRetreat

        Nope.

        “Example: Puberty is the point in genetic code formation where the code finishes compiling, or matures and becomes hard wired for the remainder of life.”

        Unlike computer programs, living things exist and function perfectly well before puberty (compiling).

        “The difference is that with genetic code, there are too many variables in the programming to comprehend and predict any changed interactions,”

        You’re not keeping up in biology. This is a common refrain from engineers and computer science people. There are multiple research programs that are developing predictive measures of the results of DNA changes.

        “The result of which would be equivalent to predicting the winning numbers to dozens of separate lotto drawings…in a row.”

        But genetics is NOT RANDOM, while lotteries are random. There’s a fundamental difference between a deterministic system and a random system. This is another very common place that these kinds of analogies fail… comparing two things that are not the same.

        While mutation is random and crossing over is as well… the resulting molecules are determined by basic genetics. You will not have a case where TAT doesn’t code for Tyrosine.