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Posted by on Feb 20, 2014 in Biology, Evolution, featured, Genetics, Science | 62 comments

Most Mutations are Harmful

There’s actually two statements that I’d like to deal with here. The first is, of course, that most mutations are harmful. The second is that selection only removes alleles from the gene pool and therefore removes the variation that exists because of mutations.  These two together or either separately is used as an attack on evolution. Both of these charges are wrong and the topics are closely related so here we go.

Mutations, as we all know (and I’ve only met a very few people who don’t think mutations even happen), are changes in the DNA of an organism. It can be something as minor as a single nucleotide in the DNA changing or as major as the loss or gain of an entire chromosome.  The average rate for mutations in humans is something on the order of 175 mutations per diploid genome per generation. This link also tells us that substitution mutations are 4 times as likely to occur as deletions or insertions.

A substitution is when one nucleotide (A,C,G, or T) is replaced by another letter. A deletion removes a nucleotide completely from a gene, while an insertion puts one in. Since most mutations are substitutions, it can easily be shown that the vast majority of mutations do not even change the resulting protein. The reason is shown below.

codon1

This is a codon chart. DNA is transcribed into messenger RNA (mRNA) that can leave the nucleus. A ribosome then translates the mRNA into a protein. THe ribosome reads three nucleotides at a time. This three nucleotide set is called a codon. Each codon has a unique amino acid that matches it. (The process is more complicated than this, but this will get us to where we need to be today.)

There are four nucleotides in RNA (A, C, G, and U). There are three spots in the codon. Some simple math tells us that there are 64 possible combinations of nulceotides.  But there are only 20 amino acids in use in the human body.  There’s also a STOP codon that tells the ribosome to stop adding amino acids. So, we only need 21 spots, but we have 64. The result is that many amino acids have multiple codons that will code for them.

For example, from the chart, we see that leucine (something of an overachiever) has six codons that will work for it: UUA, UUG, UCU, UCA, UCG, and UCC.

Now, that means that the particular codon can be hit with a variety of substitution mutations and it will not change the amino acid that fits in that spot.  No change at all. Think of this like using a thesaurus. To describe Rocket Raccoon one might use the word short, tiny, diminutive, petite, runt, or any of a dozen other words that mean pretty much the same thing.  A writer might choose a particular word for a reason, but any word will describe the height (or lack thereof) of the character.

This gets even more interesting.

1xbb_proteins

 

This is a protein (actually, it’s two proteins). Click to enlarge the picture.  You see that little area of orange and white in the lower center?  That is what is called the ‘active site’. That’s the part of the protein that does all the work. It may store an oxygen molecule, it may change ATP into ADP, it may bind two amino acids together, or any other of a million possible things. But that miniscule area is what is critical to the function of the protein.  I’ll note here that proteins may have more than one function.

But anyway, every part of the protein that is not the active site only has one function. To make the protein fold into that shape. That’s all. A lot of the amino acids come in families with similar chemical or physical properties. Some (three) have a positive charge in a particular spot. Some (two) have a negative charge in that same spot. Some are attracted to water and some are repelled by water. In quite a few cases, it doesn’t matter what amino acid is present… provided that it meets one of those criteria.

For example, arginine, histidine, and lysine all have a positive side chain. If it’s not in the active site, then it may be likely that any of those three will do in that spot. Now, there are ten possible codons that will produce the same result. Any mutation that changes from histidine to arginine won’t change the protein in any appreciable way.

I will say that it is possible for these kinds of mutations to set-up larger changes in the future. These are called potentiating mutations. For example, in Lenski’s work, a certain mutation happened long before the E. coli developed the ability to utilize citrate. If that mutation doesn’t happen first, then the remaining changes still don’t allow citrate forms to evolve.

It gets even easier, because, even if the active site changes, the protein may still work. There can be different versions of a gen called an allele. These alleles may do something similar, but not exactly the same. One allele might give you a widow’s peak, while the other gives you a straight hairline.

There are several with many possible alleles. Due to genetics, you only have two of them (one from mom and one from dad… unless one of them mutated, then you may be unique). The HLA-B gene is also something of an overachiever. There are 3,285 alleles that construct 2,459 unique proteins. All of these proteins re similar enough to do the same thing (help the immune system recognize the difference between your cells and invading cells). You could have dozens of mutations in this gene and the protein would be perfectly fine. It’s very amenable to change… some proteins aren’t so amenable to change.

Don’t get me wrong. It’s entirely possible that a mutation occurs which kills the organism before it’s first cell division. That happens.  Indeed, it probably happens much more frequently than anyone ever realizes (it takes weeks before a human female even knows she’s pregnant).

But mutations aren’t the massively detrimental problem that many people seem to think.

Which brings us to part two of our story. Selection is a removing factor. That’s true.

But when you have 3,285 alleles to choose from and, on average, new ones are being created every day. If one is detrimental, then it’s gone. But so many more have no effect at all (coding for the exact same amino acid) or an effect which is effectively invisible (coding for the same type of amino acid), that there are way more potential alleles in a population than selection can remove.

In other words, mutation adds more alleles to the population faster than selection can remove them.  This is because many of the changes to the genes are simply too minuscule to have a selection effect.

This paper[1] describes it very well. The authors show that, given certain circumstances, that a population will tend to express multiple phenotypes. This isn’t what Darwin predicted, the old ‘survival of the fittest’, but it is, instead, ‘survival of the good enough’. In the real world, there may be multiple ways to survive.  In a gross sense, think of one species dealing with a competitor by becoming smaller, faster, and hiding more and another species becoming larger, stronger, and tougher. This paper is talking about alleles, not large scale features like that, but it’s an analogy to help you understand what I’m describing.

Both solutions may be equally effective. And some of the population will go one way, some the other way, based on what is already present in their genome from all those mutations that have come before.

I have little hope that this will put to bed these creationist tropes.  But still, it’s fascinating to go beyond high school biology, where you might have two traits, each with two options. In the real world, we have thousands of traits, some with thousands of options and mutations which generate more and more options as time goes on.

__________________________________

[1]  Schaper, S., Louis, A. A. & Rutherford, S. The Arrival of the Frequent: How Bias in Genotype-Phenotype Maps Can Steer Populations to Local Optima. PLoS ONE 9, (2014).

 

  • Void L. Walker

    Great post, informative as always

    • SmilodonsRetreat

      Thanks! I try.

      • Void L. Walker

        It is highly unfortunate that you must explain the simplest of evolutionary concepts to nut jobs, though….you are a very patient person.

        • RexTugwell

          Void, you make me giggle. :-)

          Speaking of nucleotides, amino acids, etc, help out an old nut job, will ya? I’m trying to get Smilodon to tell me if there are bonding affinity differentials among the nucleotides like there are among amino acids*. Maybe you can tell me. I’ve asked him several times but he doesn’t seem to want to respond; probably because he knows the implications of such an answer.

          So obviously you know a lot more about gene expression than I, Void. What’s your professional opinion? Smiley seems to think the differences in amino acid bonding affinities has something to do with the price of tin in Bolivia. Curiously though, he’s also a big RNA World fan. I’m trying to reconcile his advocacy for the Protein First theory with his RNA World pet theory. It looks like a contradiction but maybe I’m missing something.

          Let me help you get started with your answer: [head shaking] “Rex, you just don’t understand evolution…”

          *btw Meyer covers this in SITC. I’m not sure if Smiley’s asking about AA affinities was meant to teach me something new or what.

          • SmilodonsRetreat

            Wow, Rex, now you are just making stuff up. You’ve never asked me about binding affinities with nucleotides. If I had, I would say, “Yes, there are differences”. It’s even trivial to look them up.

            It’s not a problem though. I don’t why you would think it is.

            As usual, you try to attack evolution without any support for your own notions.

            As far as Meyers, SitC, why do you think he knows more about biochemistry than about paleontology. Answer, he doesn’t. His work there is full of quotemines and wrong information too. The documentation of this by actual scientists is quite thorough. But, again, you ignore all evidence to the contrary, because it doesn’t support your notions. Which you cannot support.

            As far as RNA world, tell me the evidence that provides a better explanation. Better yet, tell the evidence that supports a designer.

          • RexTugwell

            Actually my post was meant for Void but since you insist on inserting yourself into the conversation…

            I was just kidding before but maybe you do have short-term memory loss. I asked you about nucleotide affinity differences just a few days ago here and here and a couple of times last year also.

            You’re wrong about nucleotide binding affinities. You’re welcome to show me otherwise.

            As for Meyer, you’ve read neither of his books so you’re in no position to judge his work. You lied about reading SITC when you reviewed it on Amazon and you abandoned Darwin’s Doubt just before getting to the substantive chapters. Declare victory if you want but you let A LOT of people down by not continuing with the “review”.
            So which is it? RNA World or Protein First? You seem to be supporting both. It could be one, it could be the other but it cannot both.

            Where’s Void?

          • Void L. Walker

            Also, as Smilodon pointed out, all you do is attack evolution. You haven’t given any empirically supported data to vindicate your views on ID. No peer reviewed papers, no step-by-step processes that point (undeniably) to an intelligent causation. Your argumentation is akin to attacking the evidence for gravity because you want to prove that, in reality, angels are holding us to the ground.

          • RexTugwell

            There’s a lot of stuff to unpack here so I’ll fisk certain statements from your comments with my own:

            Now, be a good chap and read away

            I read both links. Not impressed. I read Prothero’s review long ago. He’s still miffed from being spanked by Meyer in a debate about evolution. You should see it. Smilodon refuses. Prothero, like Smilodon doesn’t address Meyer’s primary arguments. The quote mine example is a bit of a stretch and shows what happens when we rely on Panda’s Thumb for the truth. Meyer’s full reference to the quote in the endnotes specifically states: “13. Marshall, “Explaining the Cambrian ‘Explosion’ of Animals,” 357, 372. For an authoritative refutation of this version of the artifact hypothesis, see Conway Morris, The Crucible of Creation, 140-44; Conway Morris, “Darwin’s Dilemma: The Realities of the Cambrain ‘Explosion’,” 1069-83.”
            Notice the 357, 372? Nothing nefarious after all. The pages were cited. What’s the problem? Does Conway Morris qualify as authoritative? That’s up to you?

            I’ve read much of his work, and this fact is as plain as day

            Have you read SITC and/or Darwin’s Doubt in their entirety?

          • RexTugwell

            “But void, you merely asserted that Meyer is a quote miner. Where is your evidence?”.
            to which you will blindly assert I am not qualified to even discuss anything at all
            you may call this a goal shift
            But let’s face it, you don’t really care about science Rex
            The one dogmatically defending a position here is you

            You’re putting words in my mouth that I’ve never said.

            Smilodon has already given a better response to you than I could hope to

            Smilodon hasn’t replied at all to my satisfaction.

          • RexTugwell

            my primary area of expertise is Cosmology/Astronomy, and with regard to evolution, Paleontology

            Oh good! So what’s your take on Lawrence Krauss’s bibliography-free book “A Universe From Nothing”? Do you really believe in the creative power of nothing?

            all you do is attack evolution

            I don’t attack evolution. I am a strong believer in evolution. Just look at Lenski’s E. coli or malaria in the first half of the 20th century. What I reject is the inability of unguided RM & NS to produce information-rich organisms.

            I used to be a christian, then an ID advocate

            And what made you go from an ID advocate to full blown atheism. From what you wrote, I’m sensing some personal loss in your life and a lot of anger and pain because of it. Is that true? If it is, I’m truly sorry. I’ll pray for you.

          • Void L. Walker

            Personal loss is hardly involved at all. And you presuppose; I am Agnostic.

          • RexTugwell

            Well I guess the honeymoon is over. No more giggles from the
            Voidmeister. I ask a simple question and I get an 800-word hissy fit
            over 3 comments. Void,you make me giggle. Glad to hear there’s no loss though.

          • Void L. Walker

            Hissy fit? Wow….did you actually construe my comments thus?

          • RexTugwell

            Indeed I did. This will be my last comment tonight. I’ve got a family to be a father to.

          • Void L. Walker

            I see….enjoy that…

          • RexTugwell

            For ease of tracking, I’m just going to put these at the bottom:

            Smilodon:

            Meyers’ books are so filled with incorrect information

            I see you didn’t use the mine quote excuse this time. You’re learning. Now give us a good example of incorrect information e.g. from SITC chapter 11 where he talks about bonding affinity differentials among nucleotides.

            Can you calculate the CSI of a system (your choice)?

            I don’t have to. Dembski has already done that with the bacterial flagellum in No Free Lunch. All you have to offer in desperate reply is T3SS and exaptation. This is from NewScientist: “It has been
            proposed that the flagellum originated from a protein export system. Over time, this system might
            have been adapted
            to attach a bacterium to a surface by extruding an adhesive filament.” I always get a kick out of such “optimistic” language. No, the flagellum is irreducibly complex and until real evidence is given for a stepwise evolution (not wishful thinking), ID is a valid hypothesis.

          • RexTugwell

            Void

            My, thank you for probing my brain when I was a
            believer; how miraculous that you apparently know more about my past christian self than I (speaking as, well, myself) know.

            Sorry but I don’t believe your story that you lost your faith due in large part to SITC. You may deny it but I’m not buyin’ it. If you want to share your journey to agnosticism, be my guest.

            Anyway, you seem to take offense that I questioned your motives for rejecting faith and then you turn around and start
            psychoanalyzing my motives for believing. You sound like Freud. Question: if evolution selected FOR religious belief/thought, isn’t that a good thing? And
            isn’t the contrary (atheism/agnosticism) counter-evolutionary? Do I have that
            right? Evolution selects for religion yet you reject it? I guess I’ll be the one surviving.

          • RexTugwell

            My objections to “fine tuning” ARE scientific.

            They are not for at least two reasons. 1. You imply “God would not have done it this way”. This is a theological statement and not one based on science. 2. Your examples of sloppy design have been shown to be in fact good design e.g. blind spot – not a problem since our binocular vision cancels out the blind spots. As I type this, I can’t see my blind spot. Can you see yours? Junk DNA? Really?

            Besides your area of expertise is comsology/astonomy. No? You’re telling me the values of the forces in nature and the 20 or so universal constants are not finely tuned? Why don’t you tweak the nuclear weak force and see what happens.

          • Void L. Walker

            Wrong, so much wrong….it hurts. My arguments are not theological at all (yours are, even though you mask them with I.D). My point remains: it is one thing to posit intelligence for the construction of the universe, another ENTIRELY to assume that said intelligence is a loving, caring entity. since you are arguing from the LATTER point, my arguments are valid. And you have yet to address them. It’s funny that you still haven’t conceded to the inherently theistic nature of the intelligent design movement; why are you dodging the issue here?

            The human blind spot could easily be corrected (and yes, you CAN see it; I suggest looking up a visual test that clearly indicates it’s presence) if the “designer” had of made a few tweaks. The presence of said blind spot is hardly indicative of a supreme intelligence at work. You accept descent with modification, acknowledging that evolution is fact, yet have difficulty with the contentions I’ve raised?

            “Junk” DNA….Yeah: http://www.huffingtonpost.com/3013/05/13/hunk-dna-health-organism-gene-study_n_3265375.html. This study was done on a plant, but the implications are quite clear. Do a little actual research, Rex. It never hurt anyone. Your designer made plants too!

            As for the human blind spot and the nature of the eye being purported as any evidence for design: idiotechnica.com/blog/2015/Debunking-Creationism_-part-2%3A-The-human-eye-is-to.html. And please, read; do not brush this off merely because the websites main goal is debunking such a comfortable little notion as yours.

            I’m apparently the only one responding to questions consistently.. I’ll ask you to admit to me that your variant of ID is decidedly theistic, as well as the entirety of the ID movement. To deny this is so absurd that the very thought of you doing so makes my head ache.

            So, because the universe allows for the emergence of life, you’re making the giant leap that A: it was designed to permit it (ignoring multiverse theory, among other things), and B: the designer in question was your God (as stated prior, not one of the thousands of other gods that countless others believe in) You call this scientific? What the fuck are you smoking? You have already reached your conclusion, and are working OUTWARD from it to find support for it. This is not scientific, and if you cannot see that then there truly is no hope for you, Rex.

            So now you’re accusing me of lying about how I lost my faith? Jesus you’re a deluded one. I was completely honest about how i lost it, if that offends you then tough shit. Do not accuse me of something you have ZERO evidence for.

            One last time….admit to me (thou shalt not lie ring any bells?) that Yahweh is the designer you believe in. Stop skirting the issue and positing aliens or some other unknown intelligence. You know, as well as I, that at bottom you are a Creationist. If you continue to refuse acknowledging this, you are wasting my time.

            Also, if you’re going to make such bold claims regarding the nature of the universe and life’s origin, then how about forwarding some actual empirical evidence to support your claims? I’m waiting.

          • RexTugwell

            Void, I do believe you’re coming unhinged. You’ve gone from giggles to profanity.

            My point remains: it is one thing to posit intelligence for the construction of the universe, another ENTIRELY to assume that said intelligence is a loving, caring entity.

            So you don’t have a problem with intelligent design per se. You just have a hang-up about Christianity. That’s quite an admission. Thanks.

            I have a friend who is an engineer. In his field, you DO NOT “compensate” when designing something; you optimize said design from the
            outset!

            Now ask your friend to explain to you the concept of constrained optimization. Oh, I suppose the designer could have given Richard Dawkins the eyes of a giant squid (his favorite example of “perfect design”) but he’d look pretty silly, no?

            One last time….admit to me [LOL!]… that Yahweh is the designer you believe in.

            I’ll admit nothing; you’ll have to make an inference to the best explanation. I will say, however, that with regard to your evolutionary theory on religion, I am remaining true to my naturally selected heritage.

          • SmilodonsRetreat

            “I am remaining true to naturally selected heritage”

            This is EXACTLY the case. If you were born in Iran, you would be Muslim. If you were born in India, you would be Hindu (or possibly Muslim). If you were born in Mexico, you would be Catholic. If you were born in the US, you would be Catholic or Protestant.

            Your religion (and the biases that come with it) are reflected, not by any thinking about it on your part, but by your heritage.

          • RexTugwell

            Don’t read too much into my “heritage”. It was a tongue-in-cheek reference to Void’s Darwinian explanation of religion as a result of evolutionary fitness. Relax.

            As I’m writing this, a thought just occurred to me. Atheists (Dawkins come immediately to mind) always pride themselves on being more intelligent and more enlightened than their religious friends. However, according to your argument (we are who we are based on where we’re born), you’d be a Muslim or Hindu or Catholic or Protestant depending upon where you’d be born. So intelligence has nothing to do with whether someone’s a theist or atheist. Hmmm…thanks for that.

          • SmilodonsRetreat

            You are actually correct. Atheism comes from the ability to think rationally about all religions and the intellectual courage to stand up in the face of overwhelming majority and say “The emperor has no clothes”.

            I don’t know why that’s a point. You may be a very intelligent person, but you absolutely refuse to subject your religion (including belief in intelligent design) to the same level of scrutiny that you subject science to. If you did, you would see that ID STILL has no evidence to support it.

            You still have yet to point me to a page in Meyer’s book where there is evidence to support intelligent design.

          • RexTugwell

            That’s funny because IDists view you in the exact same way. “The emperor has no clothes”. Whether it’s the origin of the universe or macro evolution or climate change, there is no evidence.

            You still have yet to correct your math and explain protein genesis. How does life create novel proteins without information input? Frankly, I don’t think you have a clue.

            This is getting boring.

          • SmilodonsRetreat

            Yet it is getting boring. You refuse to read the evidence I’ve presented (which is dozens of peer-reviewed papers). Even when you do read them, you refuse to accept them as evidence. Which is hillarious since ID doesn’t have any evidence at all.

            You seem to be under the mistaken assumption that if you somehow prove evolution is wrong, then ID is right. That’s such a simplistic view of the world that it’s hardly worth bothering with. Really, that’s 5 year-old logic.

            Only positive supporting evidence can show that your notions are correct. There isn’t any. Even if there was positive supporting evidence, ID doesn’t do anything. It doesn’t make predictions (hint: Junk DNA isn’t junk, isn’t a prediction, especially since it came AFTER scientists said it). ID doesn’t provide any new processes or systems to learn or use. It just sits there, hoping that everyone will ignore the theological implications. What if the designer was Odin? What would you say then?

            How does life create proteins? For the third time: DNA is transcribed into messenger RNA which exits the cell and is translated by ribosomes using transfer RNA to attach appropriate amino acids in a chain that we call a protein.

            How does life create novel proteins? Mutation. Duh.

            Someone doesn’t have a clue, but it’s not me.

          • Void L. Walker

            Coming unhinged? More like bored and interested in making an old fart such as you open his eyes. This is, of course, wholly unreasonable of me….and if you don’t like “swearing” (what is this, leave it to beaver?) then my apologies. (sigh) What a profound waste of my time.

          • Void L. Walker

            I never went Freud on you; I never even mentioned you directly (but rather faith in general). I spoke of most religionists that I know and have conversed with. But clearly you are not exempt from this. You’re in denial of the reasons for subscribing to ID, and cannot even admit this to me.

          • SmilodonsRetreat

            But you aren’t learning. There is nothing Meyer’s books that are correct. That has been established time and again and you still use him as a reference.

            Link to Dembski’s work or it didn’t happen. In fact, I find it very curious that you would say this since Dembski has specifically declined to make said calculation numerous times.

            Even he did do the calculation (which he hasn’t), he has not explained why a specific value indicates design and why another value indicates not-design. He HAS said that a value is used to determine the difference between design and random. Of course, we all know that evolution isn’t random, so Dembski can’t tell if something is designed or evolved.

            So, to you, evidence linking something as it was and as it now isn’t as good as “something, somewhen, did something, somehow”.

            Got it thanks.

          • RexTugwell

            You keep saying there’s nothing correct in Meyer’s books with no specifics. Try again.

            No Free Lunch, Chap 5, section 5.10 Doing the Calculation, location 4322, Kindle Edition.

            Since it’s a book, I can’t provide a link. And don’t tell me that since it’s not in a peer-reviewed paper, it doesn’t count. You don’t get to weasel out of it that easily.

            Protein formation is random unless you can explain otherwise. Maybe you can write an article on it and educate us cause all I’m seeing is the same statement that “proteins don’t form that way” without much to back that up.

          • SmilodonsRetreat

            Really? Because the 30,000 words I’ve written explaining, in detail, why Meyer is wrong isn’t enough. Prothero’s response to Meyer’s mistakes isn’t enough? Nick Matzke’s detailed responses to Meyer’s mistakes aren’t enough? Larry Moran’s detailed explanations of Meyer’s mistakes aren’t enough?

            I guess no matter what is done, you’ll never be satisfied. As long as one statement in the book is true, then the entire book must be absolute truth. Must be how creationists read the Bible too. Egypt exists, therefore the Biblical stories of the plagues and exodus must be true.

            Protein formation is not random. They are formed by protein coding DNA that is transcribed into messenger RNA that ribosomes read an translate into proteins. There hasn’t been a randomly assembled protein in the last 3.5 billion years or so. And there’s no guarantee that proteins came first. This isn’t a super secret Biology paper that’s being hidden. This is fundamental basics of biology. This is 5th grade stuff.

            Interestingly, Demsbki agrees with what I’ve told you

            Wein therefore does not dispute my calculation of appearance by random combination, but the relevance of that calculation to systems like the flagellum.

            This is from (http://www.designinference.com/documents/05.02.resp_to_wein.htm) in which Demsbki is attempting to refute one of the many responses to said “calculation”.

            Again, evolution is not random. Mutations are random, but evolution also deals with selection, which is not random. Unlike what you and Dembski wish were the case.

            If we expected that every protein in our body was assembled from a soup of amino acids by random chance, then and only then would Demsbki have a legitimate case.

            Again, there hasn’t been a randomly assembled protein (if ever) since the first RNA was used as a template. I can provide you with several references on the development of the RNA-> protein codon system and how it was likely to have developed.

            Of course, we both know that will not satisfy you, since it is only “likely” and “we weren’t there”… which argument is truly abysmal and applies to what your notions are as well as notions that have evidential support, like evolution.

            Here are some responses to Dembski
            http://www.talkorigins.org/design/faqs/nfl/

            http://schneider.ncifcrf.gov/papers/ev/dembski/

            http://infidels.org/library/modern/science/creationism/dembski.html

            Indeed, the original authors of the no free lunch theorem say that Dembski is wrong: http://www.talkreason.org/articles/jello.cfm

            Enjoy

          • Void L. Walker

            Nothing can satisfy him. The thing that pains me the most is his refusal to acknowledge the reason for his contentions. I’d rather he just admit to us that he’s a Bible-thumping creationist than skirt the issue at every point. Oh….sorry Rex, forgot you were here.

          • Doc Bill

            Naw, widdle Wexy is more of an intellectual wannabe poseur. Seriously doesn’t have the brainpower of a cabbage. Alas, poor Rexy-wexy also fails to appreciate the High Entertainment Value he has for us. Oh, my, he’s better than JoJo the Dog Faced Boy and at a fraction of the price.

          • Void L. Walker

            Wexy lol :-p Yeah, failing to answer half of my questions and never admitting the true nature of ID is enough for me to throw in the towel. I made an attempt at least.

          • RexTugwell

            Smiley, it could be 3,000,000 words. It doesn’t matter. (wow those words sound familiar) You wrote 0 (zero) words on Part 2 of the book. You made an “executive decision” to skip over chapters 2 through 16; even after I explicitly requested that you tackle chapter 13.

            As for protein formation: I don’t know if you’re purposely being obtuse but recounting the process of gene expression is not what I’m looking for. I think you know that. Maybe I should have said “protein genesis”. You keep saying “that’s not how proteins form”. Fine. How do we get from a warm little pond to hemoglobin.

            Wein therefore does not dispute my calculation of appearance by random
            combination, but the relevance of that calculation to systems like the flagellum.

            That makes 3 of us in agreement. The point of contention is in the relevancy of the calculation.

          • SmilodonsRetreat

            ANd no one, not even Demsbki has ever shown that any calculation of the kind is relevant.

            After I specifically asked for a page number or section, you specifically replied chapters 3-21.

            Does Meyer perform these calculations in Darwin’s Doubt?

          • Doc Bill

            But Rexy, baby, Dembski doesn’t do the calculation in chapter 5. He estimates an “upper bound” by assuming the old flagellum came together by random banging around, Brownian motion, which is absurd. Even so, he doesn’t calculate a value for CSI.

            In fact, nobody has calculated a value for CSI or FCSI ever! Not Meyer, not Dembski, not Behe – nobody. EVER!

            Furthermore, there isn’t even a definition that enables such a calculation to be done. Sure, Meyer writes stuff like “when we see structures that contain high amounts of CSI” or FSCI, doesn’t matter which you pick but never defines either what “high” means, or “low,” nor does he provide any instance of a value.

            What Dembski actually wrote is that the calculation of SCI has “yet to be done” although he claimed to have “done” it back in 1998. Of course, Dembski and Meyer are both transparent liars and only a fool would believe a word they say.

            So, Rexy baby, show me the number. The value of SCI for the flagellum is …

            Waiting. Waiting. Crickets. Yo, Rex, you there?

          • RexTugwell

            So, Rexy baby, show me the number. The value of SCI for the flagellum is …

            777 bits.

            Smilodon should be able to help you with the math.

          • SmilodonsRetreat

            WHICH flagellum? You do know that there are dozens of unique ones right? What species and how was this calculated?

            777 bits? So what? I can easily generate a random number that’s 777 bits. I can also create an intelligently written phrase that stores at 777 bits… is that with compression or not?

            Is that proteins? or DNA? You do know that those two would have different values right? I have actually shown mathematically that it’s possible for a protein to be considered intelligently designed by Demsbki’s “math”, but the DNA that generated the protein would NOT be considered intelligently designed. Isn’t that interesting.

            It’s almost like ID itself, what you get is determined by who you are talking to and not any objective data.

          • RexTugwell

            WHICH flagellum? You do know that there are dozens of unique ones right? What species and how was this calculated?

            Do I hear a goalpost shift?

            I can quote you guys all day long.

          • SmilodonsRetreat

            You are completely delusional.

            You said that the value of SCI for the bacteril flagellum is 777 bits. So, which flagellum is this for? There are dozens.

            That’s like saying the fuel economy of cars is 13 miles per gallon. Which cars? Is that an average?

            But please, keep exposing to the world the total inability of ID to do anything.

          • Doc Bill

            Ah, yes, once again a soiled diaper. Fell into that trap didn’t you little Rexy! If a PhD mathematician like Dembski can’t calculate a value what chance has innumerate, illiterate, undereducated Rexy, hmmmmm? Snowball’s chance. Proving once again that ID is just a bunch of hot air expended by windbags like Rexy boy. Pathetic.

          • RexTugwell

            A universe from nothing or an all-powerful, intelligent being. Which one better explains the fine-tuning of the universe and its constants? To ask the question is to answer it.

          • Void L. Walker

            Fine tuning, huh? Look at our own planet. Life has spent billions of years just adapting to it. I hardly call that (and the presence of cancer, terminal illness, germs) “finely tuned” by an intelligent agent. Unless the agent you speak of is a 4th grader with a C average. You’re positing a God of the Gaps. You have zero evidence that “in the Beginning” Yahweh created anything.

            See, the big problem here is one you still haven’t answered. Why did Yahweh create the universe when He did? Why did he create such suffering and pain along with it? How could He have existed if nothing did, and how could He create something from nothing?

          • RexTugwell

            It’s ironic how the only one bringing up the subject of God is you. Listen carefully: ID only states that some features of nature are best explained by an intelligence. THAT’S IT!! Let it sink in!

            From that point, everyone is welcome to venture out of science and into metaphysics to infer what that intelligence might be. Could be God. Could be aliens. Could be super intellects from another universe. Take our pick. You’re the one continually making theological statements, not I. Your objections to fine-tuning are theological NOT scientific.

            As for your loss of faith, if you lost your faith from reading Meyer’s book, you had little or no faith to begin with. I’m starting to think that this whole quote mining crusade is just a ruse to avoid having to talk about the science. Quote mine, quote mine, quote mine but never any specific objections to the science of the books.

          • SmilodonsRetreat

            http://www.skepticink.com/smilodonsretreat/2012/10/06/why-intelligent-design-must-be-religious/

            The leaders of the movement all agree that ID is religious.

            If you disagree with this, then I would encourage you to talk to OTHER ID PROPONENTS and GET A CONSENSUS on what ID is.

            The FACT that ID proponents change their message depending on the audience ought to tell you that ID is a purely made up system to promote a specific worldview.

            If it is not, if ID is indeed science… then no one should have any problem discussing the specifics of ID. Which is something I’ve been asking for nearly a decade. Yet, so far, no one has done so. Meyers’ books are so filled with incorrect information that they are not worth considering. The fact that you can’t see this is your problem, not a problem for science or any science supporter.

            What about it Rex? Can you calculate the CSI of a system (your choice)? What values of CSI indicate design? Why? What values indicate evolution? Why?

          • Void L. Walker

            Rex, I actually pity you at this point. You cannot even see what you’re doing.

            My objections to “fine tuning” ARE scientific. You cannot ignore how sloppily designed (atavisms, vestiges, junk DNA, human blind spot, etc) much of life is, the fact that such maladies and diseases exist, and that our planet has CHALLENGED life to evolve for billions of years; then jump and say that everything is fine tuned. Apparently by a meager intelligents (sic). If none of this were true, and life were far more abundant (even in our own solar system) then I would say you have a point. But not the case.

            STOP denying what the ID movement is. Look up the Wedge Document. For fucks sake Rex. The movement (as well as you) is a religious one. How can you be so ignorant, is it deliberate?

          • Void L. Walker

            Also, I directly mentioned God because you mask the issue using ID.Your entire view presupposes a God, and the only reason you hold to it IS God. You even mentioned in a previous comment that you would “pray” for me. Pray to what? An alien? The church of E.T? I’ve let it “sink in”, only to further my realization that your vehement defense of ID hinges upon a belief in Yahweh.

          • Void L. Walker

            One further point that I meant to address earlier (but due to time constraints was unable to): “if you lost your faith from reading Meyer’s book, you had little or no faith to begin with”. My, thank you for probing my brain when I was a believer; how miraculous that you apparently know more about my past christian self than I (speaking as, well, myself) know.

            Chief among the reasons that I lost my faith is that individuals who espouse any religious view care primarily for upholding it, often in the face of overwhelming evidence to the contrary of their assertions. I.E, your brain on happiness is naturally more adept and efficient than when not; the antitheses of comfort and happiness can often lead to suicide, so it makes perfect sense that evolution would favor cognitive biases.

            To deny the happiness that faith brings is…well, who the hell denies it? I saw Meyer struggling to defend arguments that upheld his particular brand of faith, generally by injecting God into an otherwise natural equation (something I have seen dozens of times before, notably with a certain C.S Lewis; his method of ‘attack’ was a less naturalistic one, but still).

            The demarcation between Lewis and Meyer is thin at best; both individuals use different forms of argumentation, but both desire the same end: vindicating a highly comfortable, cathartic view. You, my good sir, are also guilty of this act. You see the potential for wholly natural evolution to deflate and crush your cherished view, and so promptly rush to defend it. And now, good sir, my rant has concluded. Awaiting your response(s).

          • Void L. Walker

            As for Krauss, I have yet to read that particular work. But here’s a good couple questions. How could Yahweh create something from nothing? Why did he decide to create the cosmos as it is, and when he decided to do it? Did He exist along with nothingness before bringing about the universe? If so, how could there have truly been nothing?

          • Void L. Walker

            Of course it isn’t to your satisfaction, Rex. You (unlike Smilodon) have a God-centric view that must be upheld. As stated prior, we do not have anything even remotely similar to that. Good lord, you are a walking cognitive bias.

          • Void L. Walker

            I’ve read both SITC and Darwin’s Doubt. Ironically, reading SITC was chief among the reasons that I lost my faith. Meyer wants to pretend that he is an authority on the matters discussed, I’ve given you links that expose his quote mining and general lack of knowledge in said fields, and here you are (just as I predicted) maintaining your archaic view unflinchingly. Sometimes I wonder why I even bother to open peoples minds.

          • Doc Bill

            Prothero didn’t get spanked, except in your fetid imagination, Rexy. Meyer and Sternberg conspired to change the topic of the debate the morning of, but Shermer and Prothero still went along with it. Then Sternberg jumped the shark, rather the whale, and went on a tangent about whale evolution and just like his buddy-boy pal Meyer conveniently omitted all the relevant research.

            Anybody who actually knows some science saw Shermer and Prothero laughing hysterically at a couple of fumbling, bumbling creationists. What’s astounding is that Meyer is the Alpha Apex of creationism and his whiney defense is an insipid “is to!” argument that even Pee Wee Herman would be too embarrassed to utter.

          • RexTugwell

            We must be talking about two different debates because that’s not the one I saw.

          • SmilodonsRetreat

            of course not, because your ability to think critically is compromised.

          • Doc Bill

            Oh, yeah, right. Of course. Uh-huh. In your dreams, Rexy.

          • Doc Bill

            Bad choice of Conway-Morris. In fact, in Crucible he supports the hypothesis that the Cambrian Explosion represented a true radiation, but no more extraordinary than other radiations since that time but he also notes that “a substantial proportion of the metazoan genome was probably available well before the Cambrian Explosion.” That destroys Meyer’s thesis right there. Nice job, Rexy, shooting yourself in the foot.

          • RexTugwell

            Look at the reference again. Meyer is referring specifically about the artifact hypothesis. Opinions on Cambrian radiation is irrelevant.

          • Doc Bill

            Are you really that dense, Rexy? Do you even know what the artifact hypothesis is? Apparently not. Conway-Morris 1; Meyer 0.

          • Void L. Walker

            (head shaking) Rex, you really don’t understand evolution. For what it’s worth, Smilodon has already given a better response to you than I could hope to; my primary area of expertise is Cosmology/Astronomy. I do know from much experience that Meyer is a quote mining bigot, though; I’ve read much of his work, and this fact is as plain as day. Perhaps quoting his sources isn’t the most cogent approach?

          • Void L. Walker

            “But void, you merely asserted that Meyer is a quote miner. Where is your evidence?”. Hmm: Pandasthumb.org/archives/2013/08/stephen-meyer-w.html That is but one example. And please, actually read it? I visit your little Evolution news and views den, so the least you could do is flatter me.

  • Ratabago

    Nice article. Thanks for the GENETICS article. I’ve only read the abstract so far, but it looks like fun.

    One nit picking pedant point though, it should be “175 mutations per diploid genome per generation”. I think if the “per diploid genome” is not stated explicitly that eventually, whether by random flailing around, or deliberate design, some one will produce the argument that evolution can’t happen because science proves there’s not enough mutation to support it. Only about 175 per generation, so nearly no one will get one. I wish I could say this is just a dumb joke (which it is, partly). But I can really see it happening.

    • SmilodonsRetreat

      Will do.

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