• Why Specificity is Not an Argument Against Evolution

    In dealing with creationists, they will often steer the conversation to something like specificity. They will say that no new information can be added without a designer… with the requirement that they get to define information and then they define it in such a way that only a designer can add information.

    One of their constant complaints is that randomness cannot create the specific genes/proteins that do very specific things using very specific interactions with other very specific genes/proteins. The issue is that our bodies require a specific gene to create a specific protein and, if at any point, something changes, then the whole system crashes and the organism probably dies. They say that this deep interaction among very specific systems is evidence of an intelligent designer, since humans are intelligent (generally) and specify very complex things that require very specific systems to run. Go ahead, run 7.5 volts through your USB port instead of the 5 volts required by specification and see what happens.[1]

    But most 8th grade students can explain why this objection makes no sense. There are things things called alleles, variations of a gene that has a slightly different result. The HLA family of genes has thousands of alleles.

    Ah, but the creationists are saying, those are all just minor variations on the same thing.

    Ok, fine. Whatever. But let’s look at this paper. Functional proteins from a random-sequence library[2].

    There are countless variations of amino acid  sequences. There are 20 amino acids used in the human body and there are no limits (of which I am aware) of how large a protein can be. Tintin is the largest known human protein. At over 34,000 amino acids in length, it approaches visibility by a good microscope. Now consider how many variations you could find of any combination of 20 choices (feel free to reuse them) and count every length from 2 to 34,000.  It’s a pretty big number.

    Creationists love to use scary big numbers. That’s their whole shtick in this case. “See, 1 protein out of all those nearly infinite number of combinations.”

    But is that really the case?

    The thing about proteins is that, unlike creationist claims, there are many, many paths to a protein that works.

    In the paper I present, the authors build a random database of 1,000,000,000,000 proteins, each of which is 80 amino acids long. That’s just a fraction of the total number of proteins available in that size range.

    They set an experiment (which, I’m given to understand, is very clever and very accurate), in which they could search this huge field of proteins for one very specific function. Binding to ATP. Now, ATP is the energy source of cells. It’s a nucleoside (adenosine) combined with three phosphate groups (Adenosine TriPhosphate – ATP).

    I need to talk about the experiment and it’s kind of technical. Basically, the authors had these gel beds that had ATP on them. Proteins that could bind to the ATP would attach themselves to the ATP on the beads. Any proteins not attached where rinsed away. Then a wash was done with ATP in the wash. The proteins would preferentially bind to the free ATP, then be carried out in that wash for the next round of selection. Everything in that second wash was amplified using common practice and run through the sequence again.

    Remember that the proteins were totally random. After 8 rounds of the experiment, where they looked for specific activity with ATP and chemically selecting those that bound to ATP[3], they found that 6% of the proteins had that activity.

    We cloned and sequenced 24 individual library members, which showed that the population was now dominated by 4 families of ATP-binding proteins (Fig. 3a). These families show no sequence relationship to each other or to any known biological protein. The members of each family are closely related, indicating that each family is descended from a single ancestral molecule, which was one of the original random sequences.

    First of all, that’s all pretty cool and it shoots the idea of specificity pretty much out of the water. In a random collection of proteins, at least one was capable of reacting with ATP. But it’s not the one used by any known organism.

    This also shows that there are 4 different methods (at least) of accomplishing that goal, reacting with ATP. So another creationist notion is destroyed. There can be changes to proteins and have the remain functional. In fact, there were so many changes that there were four different families of proteins that all did the same thing.

    Here’s where it gets moderately interesting though. The researchers took those proteins and subjected them to mutagenesis. They mutated them, probably by copying them with a low fidelity polymerase. For three more rounds of the experiment. Then six more rounds with out being mutated.

    The amount of ATP binding proteins rose to over 30% of the total. Which neatly destroys one of Casey’s complaints about mutation and selection (#4 on this list) that natural selection struggles to fix traits in a population. In 9 rounds of the experiment, the percentage of ATP binding proteins when from 6% to 34%. Interestingly, all of the individual proteins sampled were from the same family. Showing that particular family had a real advantage in the selection process.

    In conclusion, we suggest that functional proteins are sufficiently common in protein sequence space (roughly 1 in 1011) that they may be discovered by entirely stochastic means, such as presumably operated when proteins were first used by living organisms

    Science is really impressive when you realize that, even obscure papers such as this single-handedly destroy multiple notions and complaints of creationists. It was never the authors purpose to do this. But it shows just how fragile and edifice that the creationists have created. Pick an evolution paper almost at random and it will devastate an argument of the creationists.

    I need to add that I wrote this post specifically (get it?) as a counter to a couple of creationists that are pissing me off with their refusal to learn. However, the paper is really cool in and of itself. One thing that the authors suggest is that this may be a method to find proteins to do something that other researchers need a protein to do.

    Designing a protein from scratch to specifically accomplish a specific reaction is impossible. There is too much going on in proteins. The sequence is not the only factor. There are multiple levels of folding involved and a host of other things that take super-computers to calculate even for one protein.

    Maybe designing proteins from scratch isn’t the best approach. What if, a random search followed by evolution is a viable approach. In probably a couple of weeks, the authors found a highly efficient ATP bonding protein that isn’t already used by an organism (that we’re aware of). This is something that a team of people with supercomputers couldn’t design in a hundred years (probably).

    Evolution beats design.

    P.S. Many thanks to the commentors at Larry Moran’s Sandwalk blog for help with the biochemistry.

    __________________________

    1 In case you’re wondering, yes, that was an attempt to use specify in as many variations and as many times as possible.

    Keefe, A. & Szostak, J. Functional proteins from a random-sequence library. Nature410, 715–718 (2001).

    3 I say chemically selecting those that bound to ATP because the authors did not look at all the molecules and preferentially select those that did what they wanted.

    Category: ChemistryCreationismEvolutionfeaturedScience

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    Article by: Smilodon's Retreat

    • Rob

      I’m currently reading “Arrival of the Fittest” by Andreas Wagner that discusses this research. I get somewhat lost in his writing style (don’t always track so well with his analogies) but I’m trying to grasp the basic ideas.

      • SmilodonsRetreat

        I haven’t read that one yet. Please let me know hos it is.

        I’ll be happy to try and answer anything you’re having trouble with.

    • RexTugwell

      Before I ask the obvious questions, I have to ask what’s on the minds of 8th graders the world over. The above-mentioned experiment corresponds to what cellular processes? Are they known cellular processes in operation today or does this experiment correspond more to the origin of life as the authors suggest?

      Choose one:
      A. Currently known cellular processes
      B. Processes in operation at the origin of life
      C. Both A and B
      D. Neither A nor B
      E. I don’t know
      F. It doesn’t matter because Meyer is a liar
      G. It doesn’t matter because Behe is a poopyhead
      H. Don’t bother me with details

      • SmilodonsRetreat

        None of the above in any way shape or form. But nice red herring.

        • Doc Bill

          The paper read perfectly clear to me. Why does Rex need to be spoon fed?

        • RexTugwell

          Red herring, huh? Since options A – D contain mutually exclusive answers, “None of the above” is an invalid response. That’s why I didn’t include it in the list in the first place. Try again. Is the above a natural process or not? Yes or No?

          • SmilodonsRetreat

            1) The fact that A-D contain mutually exclusive answers does not mean that one of them MUST be correct.

            The question you asked is the wrong question. It’s a leading question that has nothing to do with anything going on in the paper I described.

            Who was the first president of the US.
            A) Blue
            B) Red
            C) Purple
            D) Morris the Cat

            Just because those contain mutually exclusive answers doesn’t mean that one of them must be correct.

            “Is the above a natural process?” Is not one of the questions you originally asked.

            Depends. Part of it was a natural process… unless you can show me exactly where a designer fiddled with the mutations that occurred.

            On the other hand, this paper, as I’ve already told you, has nothing to do with cells, origins of life, or the other things that you mentioned.

            This is exactly like the case where someone (cough) complained on Amazon about no one dealing with the paleontology in Darwin’s Doubt, then when Donald Prothero trashed Meyer’s ideas about paleontology, complained that Prothero didn’t deal with embryology or epigenetics.

            If you want to talk about the work that I presented, then we can do that. But you’re just casting about for anything to get away from the fact that the ID ideas of specificity are basically meaningless.

            • RexTugwell

              I see Meyer’s book still haunts you.

              You’re in no position to be teaching me logic. Looks like a review of Logic 101 is in order. Don’t feel bad though; many new to it have trouble with the logical NOT operator. Your sample test question illustrates your complete lack of understanding of what mutually exclusive actually means. Morris the Cat could be blue and red and purple at the same time. Just give a 5 year old some paint and a cat and it’ll happen. I’ve seen it.

              I’ll simplify things for you so you can grasp it a bit better. Feel free to draw Venn diagrams if it’ll help.

              1. A
              2. not A
              3. none of the above
              “none of the above” is invalid

              Don’t see it yet? Your own example should have been the following if you were trying to show I was wrong:

              Who was the first president of the US?
              A) George Washington
              B) not George Washington
              C) none of the above

              C is clearly an invalid answer because A and B are mutually exclusive. Substitute any other name and B becomes the right answer. Really, Smiley, I’m surprised at you.

              Since you admit that the paper has nothing to do with cells or origins of life and that even simple proteins are obtained only by the intervention of intelligent agents, the question now becomes: why is this obscure paper even relevant to evolution and how can you say that “evolution beats design” with a straight face?

            • SmilodonsRetreat

              All this time and you still haven’t discussed the meat of the argument. You’re just playing rhetorical games that I’m not interested in.

              Your questions are leading questions that are meaningless.

              Congratulations, you have used logic to show that you have no idea what’s going on. Whenever you want to talk about the science let me know.

              If anything in my blog post or the article was unclear, then feel free to ask about it. It seems obvious that you didn’t understand it. Instead playing your cute little “gotcha” games, I’ll discuss the science, when you’re ready.

            • SmilodonsRetreat

              “Since you admit that the paper has nothing to do with cells or origins of life and that even simple proteins are obtained only by the intervention of intelligent agents, the question now becomes: why is this obscure paper even relevant to evolution and how can you say that “evolution beats design” with a straight face?”

              Because, AS I SAID IN THE POST and in responses to you, NONE of that has anything to do with anything.

              The point is, AS I SAID IN THE POST, that specificity, which is required in Intelligent Design is meaningless. This is because there are multiple way to achieve the same effect… as shown in the paper.

              Therefore any argument about specificity is fatal flawed and can be ignored. This is what the paper shows (among other cool things, such as evolution happens).

              Rex, you (and all creationists I’ve found) have a talent to completely missing the point (see the Prothero comment *cough*). You know that this destroys a fundamental aspect of intelligent design and therefore you are doing everything you can to cause confusion. You can keep whining about it all you want, but this paper (among the dozens of others that I post about) shows that the fundamental tenants of Intelligent Design are simply wrong. The assumptions of Intelligent Design are wrong.

              Until INTELLIGENT DESIGN changes and comes up with some useful way to test itself… which will almost surely require the discovery of a designer… then these are the only tools we have to show that ID is flawed. Sadly, ID changes so much, even in a single conversation about it, that it’s truly meaningless.

              There are no predictions of ID. There are no theories of ID. There are no experiments that support ID. There’s nothing. Except for a bunch of people who desperately want it to be true and will do anything to make it true.

              Again, if you want to talk about this paper, fine. It’s not hard. This paper shows that multiple random proteins can do the same function. And after evolution, can do that function extremely well. This defeats one of the premises of ID that only the proteins that currently exist can do the job. It’s call specificity.

              “Just as the meaning of a sentence depends upon the specific arrangement of the letters in a sentence, so too does the function of a gene sequence depend upon the specific arrangement of the nucleotide bases in a gene. Thus, molecular biologists beginning with Crick equatedinformation not only with complexity but also with �specificity,� where �specificity� or �specified� has meant �necessary to function� (Crick 1958:144, 153; Sarkar, 1996:191).3 Molecular biologists such as Monod and Crick understood biological information–the information stored in DNA and proteins–as something more than mere complexity (or improbability). Their notion of information associated both biochemical contingency and combinatorial complexity with DNA sequences (allowing DNA’s carrying capacity to be calculated), but it also affirmed that sequences of nucleotides and amino acids in functioning macromolecules possessed a high degree of specificity relative to the maintenance of cellular function.”
              FROM http://www.discovery.org/a/2177

              This is now known to be untrue. There is not a high degree (no measurement given), because there are multiple solutions. You may disagree and that’s fine, but before we go any further, we need to establish numerical values for this and explanation of why those values are valid.

              This is another creationist tactic, forced ambiguity. What does “high degree” mean. One? Two? Four out every 8,000,000? Why?

              Until ID does this, then there’s no point in going any further with discussing it. Because it’s just a discussion without any supporting evidence. You say “nuh uh!” and I say “whatever”.

              But that’s totally typical of creationists.

              BTW: Remind me again of why you think Meyer is so great, considering that he lied multiple times in that book, took numerous quotes out of context and ignored (or couldn’t find) research that directly contradicted his claims? Oh yeah, because he says what you want to hear.

            • RexTugwell

              Golly, Smilodon, all I asked was if the process employed in the paper to obtain proteins by the researchers had some real world, cellular counterpart. You answered my question. Thanks.

              As for Meyer: One last time. You may not like my answer but here it is so stop asking and deal with it. Your review left the main arguments of the book largely unanswered. [If you ask me what the main arguments were, then you haven’t read the book. If you misunderstand the main arguments, that’s your problem] You tried to limit your “review” to the introductory and concluding paragraphs. Curious. If it weren’t for my prompting, chapters 11,12 & 13 would never have been attempted and even then you couldn’t finish those! I’m someone who believes that what is not said is as significant as what is said.

            • SmilodonsRetreat

              OK, so you accept that the central tenant of ID is refuted by the paper. You must since you refuse to talk about it.

              As far as Meyer, it really doesn’t matter what his point was, there’s so much wrong information that his book is useless.

              You prompted me to look in certain chapters and time and again I found mistakes, quotemines, and research that refutes Meyer’s claims.

              You’re someone who believes whoever agrees with you and to hell with the evidence.

              I’m glad we cleared all that up. There’s really no place for you here anymore.

            • RexTugwell

              It’s tenet Smiley. Central tenet not tenant! I find it extremely amusing that you and the PhD impersonator sit in judgement of my intelligence.

            • SmilodonsRetreat

              If that’s all you got… my spelling.. well… I guess that answers that.

            • RexTugwell

              No it’s not all I’ve got. Not by a long shot. It’s merely the latest in a cumulative case to show that you’re not the sharpest knife in the drawer and when you and Bag Man Billy call into question the intelligence of ID proponents, it’s really more comical than anything else. Wouldn’t you agree?

            • SmilodonsRetreat

              So far, you have YET, in this discussion to even comment about the research I presented. You have YET to show that ID says something different. You have YET to do anything but cast red-herrings and change the subject to tone-trolling and ‘I don’t care if ID is wrong, because you can’t spell and that means you’re stupid.”

              Whatever.

            • chienblanc4csi

              Alfred Mosher Butts was a bad speller. Don’t know who he was? I didn’t till my board game addict friend reminded me that Butts invented Scrabble.

              Just another red herring for the net.

            • Doc Bill

              Certainly Scrabble is more reasonable than Rexy! Difficult to find a 7-letter word to describe Rexy. IsMoron, that’s a word? I’d need help to play Numbskiull on a triple, although Rexy is definitely a triple numbskull.]

            • RexTugwell

              Smilodon didn’t misspell anything. He used a completely different word showing his unfamiliarity with the term central tenet. Funny how the three of you can’t see the difference. No worries. The entertainment continues as Smiley with his BS in Earth Science has the hubris to criticize other far better educated than himself.

            • SmilodonsRetreat

              You continue to create personal attacks instead of dealing with the science.

              This continues and it’s recorded here permanently.

              Any time you want to talk about the science, we can. It’s obvious that you can’t.

              You have not refuted my claims of the central principle of ID, in spite of my word choice.

              You have not refuted my claims of how this process refutes those claims, in spite of trying to tie the paper to something that it has nothing to do with.

              Honestly, this has been a classic study in the tools of debate by creationists. Thanks for that.

            • RexTugwell

              “You continue to create personal attacks instead of dealing with the science.

              This continues and it’s recorded here permanently.”

              Are you addressing me or the Smilodonian Sage?
              BWAHAHAHAHAHAHAHA!

              I’ll see if I can sum up my objections to your shoehorning this obscure paper into your Darwinian worldview.

            • chienblanc4csi

              Oh, I am humbled indeed to be one of “the three of you” . . . I don’t have a PhD, I am an artist, not a scientist, but interestingly, I am a good speller. In this case, spelling is beside the point, a distraction. Nice try.

            • Doc Bill

              No, Rexy, you are wrong, wrong, wrong! As usual!

              It is tenant, not tenet. It’s a notion that is resident in the Disco Tute, dwells there and lives nowhere else. Pays no rent, I might add.

              Nope, you’re wrong.

              Hey, how’s the chemistry studying coming along? Mastered Boyle’s Law yet?

            • Doc Bill

              The irony is that I’ve forgotten more chemistry than you’ll ever know!

              Sucks to be you, Dumbo Rex!

            • RexTugwell

              Oh yeah, how could I forget? You keep telling us “I’m smart” “I’m educated” “I’m rational” “I’m a DOCTOR!” If it helps your low self-esteem then go for it.

            • Doc Bill

              That’s right, Rexy, and if you learn anything, learn that!

              So, this paper is really a great demonstration that randomly generated polypeptides can exhibit some specificity. It’s not a lot different than using ordinary river clay to catalyze certain organic chemistry reactions, then by treating the clay with certain reagents and metals and adjusting the temperature and pressure, even greater catalytic efficiency can be achieved. Similar to the experiment described in this paper, in the old days chemists basically tried random stuff to see what worked: walnut shells, Aunt Sally’s teapot, dog hair and what have you.

              This paper blasts a big old hole in Dembski’s and Marks’ contention that “random search” (whatever they mean by that, and they never define it) of the “fitness landscape” will never result in specificity. It turns out that “random search” is good enough.

            • Tim Tian

              Ay no, rite, speling iz soe relavant at teh ponite at hand rite?

      • Doc Bill

        Rex writes stupidly, as usual, “The above-mentioned experiment corresponds to what episode of Friends?”

        I think it’s the episode where Rachel and Monica get the same hair style and hilarity ensues.

        Rex, poor baby, you suffer greatly by your willful ignorance of chemistry in general and biochemically specifically. I know it’s hard work for your little punkin brain but that’s the nub of your confusion about the world. According to ID the “probability” of a random sequence of amino acids forming a polypeptide with catalytic activity is so small as to be impossible; the Edge of Evolution, according to Behe. Yet, there it is: random sequence, catalytic activity. As for corresponding to a cellular process, Rexy wexy, what is it about ATP binding that you don’t understand? Oh, yeah, now I remember – everything.

        • RexTugwell

          If you’re going to invoke Behe, at least be minimally informed about what he says. It makes you look foolish when you don’t. According to Behe, one binding site is well within the edge of evolution. Sorry to disappoint you. There’s really nothing in this obscure paper that causes problems for ID. Try again.

          • Doc Bill

            Hey, pot – kettle here. What Behe said was that two SIMULTANEOUS mutations leading to a binding site was beyond the edge of evolution. He wrote that two SIMULTANEOUS mutations were required because a single mutation would have no advantage and get “weeded” out by evolution.

            Turns out not to be the case. So sad for Behe – again! Studies have shown that between 2 and 6 sequential mutations can and have led to CC-whatever resistance and that the potentiating mutations are not “weeded out” as Behe falsely claimed.

            In an astounding turn of events, Behe tried to walk back what he had written IN PRINT by still claiming that simultaneous mutations were beyond the edge and that sequential steps were not possible, either, directly in the face of the evidence. Astounding cognitive dissonance! What Behe was saying, essentially, was that since you can’t walk across the Atlantic Ocean there is NO WAY to cross the Atlantic Ocean.

            • SmilodonsRetreat

              This is trivially easy to show as well. In less than 72 hours, four mutation GROUPS increased the efficiency of a ribozyme by 98-fold.

              Behe didn’t know that because that paper was published about 9 months after Edge of Evolution.

              What I have noticed though is that ID proponents consistently make claims that are refuted by future work. Then they ignore that work. Unless of course, they are Meyer, in which case they ignore previously written work that conflicts with their ideas.

            • RexTugwell

              Nope. Try to do a little more speed reading on Behe before you comment further so you don’t continue to make an ass of yourself.

            • RexTugwell

              “CC-whatever”
              Sounds like you’re really up to speed on all of this.

            • Doc Bill

              And you need to jack off some more, dolt. So far you haven’t addressed a single scientific point. I guess it’s because you’re really, really stupid, or really, really ignorant or, OMG, a toxic brew of both.

              Does it hurt to be stupid, Rexy?

              Hey, I’m going down to the Chevy dealership to order my Z06. Should I get yellow or red? I’m thinking red, but you know us intelligent science types, always overthinking things!

            • RexTugwell

              Reminding us how smart you are isn’t enough. Now you’ve got to tell us how well off you are financially being able to buy a Z06. Your self-esteem must really be taking a hit this week. I’m starting to get embarrassed for you.

              As for color, you know which one I think fits you best. However, red may boost your self-esteem a bit. Your call.

              Buying American, huh? Better get the extended warranty.

            • Doc Bill

              Yeah, I went for red. A friend of mine has a yellow one and my next door neighbor had a navy blue one with a vanity plate that read “NAVY.” I guess he was in the Navy but I never asked. He moved, anyway. Also, I chickened out on the Z06 and went for the Stingray. Cheap bastard always wins in the end. Yes, I’m both cheap and a bastard, with no self-esteem.

              You’re right, though, I should’ve gotten yellow with a vanity plate that read “Stain.”

    • I’m a curious layman and prepared to ask, what may appear to be a rather obvious, question. I have no doubt that it is “very clever” but, as you say, “the authors build a random database”, design and “set an experiment” then intervene to execute a number of (no doubt) planned stages and select those that “did what they wanted”…

      If Meyer/creationists are talking about ORIGINS of life, how can the argument be ‘dismissed’ by presenting a paper that, essentially, requires ‘intelligent design’ prior to its commencement and throughout a number of, no doubt, carefully planned interventions?

      I would have thought that a statement like “designing a protein from scratch to specifically accomplish a specific reaction is impossible…etc.”, in the 21st century with all the knowledge, tools – super-computers et al – and techniques available to us, suggests that the underlying biological complexity (that enables such thought, research and discussions) requires much more than this!

      • SmilodonsRetreat

        It’s not really an obvious question, it’s a good one. And there’s two parts.

        The first and easiest to deal with is the idea that because a scientist did something, that means an intelligent agent was involved and this is really support for ID. I’ve heard that argument several times before.

        The response is that experiments are carefully controlled by the experimental designer. They are very carefully designed such that only one variable changes and any changes in the result can only be attributed to that variable. But careful design of the experiment does not mean that the results are carefully designed. In this case, for example, the experiment could have shown that no other proteins out of the millions randomly selected were capable of attaching to ATP. Or it could have shown that most proteins were capable of attaching to ATP.

        There’s a huge difference between a carefully designed experiment and a carefully designed result. ID proponents are talking about the result (humans, complex proteins, etc). Scientists are talking about careful design of the experiment. I’ve used this analogy before. Casino equipment is carefully designed, but that doesn’t mean that casino equipment engineers can predict the results of an specific spin of the roulette wheel.

        The second question is about the proteins themselves. ID proponents argue that specificity is a hallmark of an intelligent designer. That only those proteins that exist can do the job and that a random protein can’t. Many of their works calculate the probability of a specific protein or DNA sequence and then say, see it’s so improbable that it couldn’t have happened without a designer. In fact, Behe used this argument in the Kitzmiller trial.

        The response is two-fold. First, this experiment shows that there isn’t just one protein that can do a particular job. There are many, so every probability calculation is now wrong. Until ID proponents determine ALL the functions of every single POSSIBLE protein, then there is no way to calculate the probability of a random sequence of amino acids being able to do or not do any particular function.

        The second, of course, is that no biologist thinks that these proteins appeared, fully formed. Every protein extant today, every DNA sequence extant today, has a multibillion year history. Even those nearly formed genes came from previously existing genes by various known (and well understood) mechanisms. Which, also neatly destroys another ID principle, that new genes can’t appear. I wrote about one of these recently too. http://www.skepticink.com/smilodonsretreat/2015/02/28/gene-duplication-may-be-the-cause-of-human-brains/

        I hope that helps.

        • Thanks…but!

          I get that the results are not “carefully designed” and that adaptation occurs but, back to origins. What is the source of the information that, after millennia, we are still only scratching the surface of identifying and interpreting? Highly complex life emerging, undirected, from (dead) matter and energy that must have gone through so many failed random attempts but still, eventually, led to US and the vast array of life thriving, surviving and (unless you can suggest otherwise) without evidence of new species emerging from random interactions.

          I understand why the scientific community would have an issue with the concept of Creator and an innate desire to gain understanding from experimentation. For that reason I have a great admiration for those scientists who have a faith and are prepared to approach THE issue with open minds, apply their skill-sets in the face of such consistently ferocious (even coordinated) attacks.

          I do appreciate your response but ORIGIN is what perplexes me and am amazed how many are prepared to ‘gloss over’ that/THE question.

          Best

          • SmilodonsRetreat

            Once again, there are several answers that we have to consider and some other things to consider as well. I’ve written about this a lot on this blog, but I will try to summarize.

            1) First, to consider a supernatural creator, one must evidence of some supernatural creator. That is, evidence that could ONLY come from such a supernatural entity. No such evidence exists.
            2) Origins of life is a highly researched area of science. We will never know exactly how life came to be on Earth. But, so far, every molecule needed for life has been shown to be the product of non-living chemical processes. Some of these take place in various environments, including deep space. Some recent research shows that the essential components of DNA can form on comets.
            3) The origin of information is much less complex. First, one must define information. Without a consistent and rigorous definition of information, too many problems can result. For example, most creationists (if not all) conflate information with meaning. For example, speaking to me in Swahili will convey information, but no meaning is transferred.

            Information can easily be produced by non-intelligent means. This is trivial to show. Nuclear fusion in stars results in information that is transmitted through space and tells us about the composition of the star, the mass of the star, the life stage of the star. All by non-intelligent processes.

            There are significant research papers regarding to development of the codon structure, the DNA reading system, and the like. So, these are very interesting questions that are under scientific scrutiny right now. You can read about much of that research on your own.

            I am not prepared to “gloss over” that question. I an answering your questions.

          • Doc Bill

            No scientist I know “glosses” over THE question, it’s just that we have no need of that hypothesis. What is to be gained by declaring that DNA was created by a deity? Nothing. It’s still DNA. Granted, there are otherwise sane people *cough Jim Inhoff cough* who still believe the weather is controlled by their personal god. However, that belief and only that belief does Jim no good at predicting weather patterns.

            So, the scientific community does not, in fact, have an issue with a Creator, it’s just that it’s a superfluous idea that adds nothing to the equation. That said, we all muttered supplications prior to taking that Quantum Mechanics II final exam!

            One final point regarding natural and “artificial” selection. Professional creationist dissemblers, like the Dishonesty Institute, are fond of drawing a big red line between those two processes calling natural selection “Darwinian” and artificial selection “intelligent design.” However, they are being dishonest, although it’s subtle. When the Disco Tute talks about “intelligent design” creationism as applied to life on Earth, they invoke direct, molecular intervention by their Designer (blessed be he). Direct molecular intervention. That means changing or creating genes and/or regulatory processes and so forth with a specific goal in mind.

            But, and this is key, with artificial selection none of that happens. All of the genetic mixing and producing of offspring is done by the organisms themselves, be they dogs, cows, rabbits, pigeons or pumpkins. There is no genetic selection or manipulation or new genes being made or new processes being implemented; the organisms reproduce naturally and without design. The only difference is that instead of the “less fit” or “less desired” being picked off naturally by predators or disease or what have you, the farmer does it. That’s the artificial part. Everything else, and I mean everything, all the chemistry, reproduction, etc is good, old fashioned, bog standard evolution of the Darwinian kind. Sort of ironic, isn’t it?

            • Thanks Doc B but, when I use the term “gloss over” it is, specifically(!) in relation to origin.

              Whether I believe/agree the ID position or not, I respect that creation explains origin for believers: BOOM!

              BANG and, even with all the ‘ingredients’ and environmental conditions coming together, the number of random/undirected mutations required to achieve the sheer complexity of organs let alone the array of fully functional biological systems with reproductive capabilities, also requires a form of faith!

              Thanks, to you both for your thoughts.

            • SmilodonsRetreat

              “BANG and, even with all the ‘ingredients’ and environmental conditions coming together, the number of random/undirected mutations required to achieve the sheer complexity of organs let alone the array of fully functional biological systems with reproductive capabilities, also requires a form of faith!”

              That’s simply not true. There is this thing called evidence.

              So far, in every experiment tested, the precursor molecules of life have been found to be formed by non-life based reactions.

              It has been shown, multiple times, that long chains of RNA and amino acids can form it little more than warm water.

              It has been shown that RNA can catalyze it’s own reactions and that the shortest RNA chain that can catalyze other reactions is a mere 5 nucleotides long (only the middle three of which actually matter, the two on each end can be anything).

              It has been shown that multiple mutations do happen and do improve the efficiency and even change the function of proteins.

              NONE OF IT IS FAITH. It is all based on evidence. I’ve talked about much of that evidence on this very blog. Continually ignoring that evidence is a common problem and it’s frustrating as hell for me.

            • Dr Hal

              You say that “NONE OF IT IS FAITH” but please show us the study that shows that RNA can replicate itself without ribozymes or turn itself into DNA (as in the case of retroviruses) without reverse transcriptase? In your evolutionist view, where did these vital molecules, not to mention the nucleotides needed, come from? The experiments that have “shown” that life could form from inanimate molecules have ALL included conditions that some scientists deem as “this is what the atmosphere on earth must have been like 4 billion years ago”. The truth is that NONE of us were around 4 billion years ago and any estimation that made upon the assumption that things were one way or another requires a great deal of faith, ESPECIALLY if it dates that far back!!! There are soooo many things that science can’t explain so it is a bit naïve of some scientist to take the road of “science knows all, everything outside of science is wrong”. Just my 2 cents!!!

            • Doc Bill

              Ah, the old creationist “show me” gambit. Face it “Dr” Hal, if you’re not smart enough that you have to resort to the “show me ” gambit, you’re not smart enough to understand the answer. Compounding your willful ignorance with the Hambo “were you there” fallacy simply cements your creationist troll credentials. Your two cents are worth precisely 2 -2 cents. Do come back after you’ve learned some science.

            • SmilodonsRetreat

              Please explain in detail why those two things you started with are a requirement. The comparison of what happened 4.5 billion years ago to the organisms (including viruses) today is like asking Henry Ford why the jerk didn’t include anti-lock brakes and sat-nav on a Model T.

              On the other hand, if you actually read my blog, you will find that RNA can replicate itself.

              Lincoln, T., & Joyce, G. (2009). Self-Sustained Replication of an RNA Enzyme Science, 323 (5918), 1229-1232 DOI: 10.1126/science.1167856

              The truth is that no one has shown that any of the molecules needed for life cannot be formed by natural processes. For example
              http://www.skepticink.com/smilodonsretreat/2015/03/19/common-origins-of-rna-protein-and-lipid-precursors/

              I have another 200+ papers on the subject. Interested?

            • RexTugwell

              Dear Dr. Hal aka Smilodon and/or Bag Man Billy,

              If you’re going to try to impersonate a creationist, do try to be a bit more convincing.

            • Dr Hal

              Doc, please reply when you graduate from “super-kindergarten”. Attacking and insulting someone’s intelligence ONLY based on their the fact that they disagree with your point of view is as infantile as one can be.
              Smilelodon, thank you for the legitimate points you make. Nevertheless, my comments were addressing your statement about science not being a matter of faith. You can point at all the studies and the papers you’ve written but it still does not take away from the fact that just as creationist “hide” behind this invisible creator; science, as it pertains to origin AND evolution hides behind time. The truth is that just as creationist require faith to believe something that cannot be proven in a science lab, there is a great deal of faith required to believe beyond a shadow of a doubt what evolutionary scientist say today. Just because there is a POSSIBILITY that given certain conditions, life MAY HAVE begun the way these scientist say if MIGHT HAVE, does NOT mean that this is PROOF that life began that way. Or is that good enough proof to you? If not, then you are on the boat as those you’re criticizing, relying on FAITH (as a result of lack of proof) to justify your believes.

            • SmilodonsRetreat

              Dr. Hal,

              Once again, you misunderstand the entire process and mindset of a scientist. What we have is the best explanation for the information that is known.

              What we do know is that processes that we DO see in the lab are the same processes that we see in the field. We DO know that the same mechanisms are in effect now that were in effect hundreds of years ago (and for physics and chemistry) known to occur exactly the same way billions of years ago.

              Further, unlike creationists, scientists WILL change their minds when presented with new information. For example, if you have information that somehow discredits every single one of the millions of papers published in evolution, population biology, paleontology, biogeography, genetics, molecular biology, etc. Then publish that information and we’ll see what happens.

              BUT, their is no shred of faith involved. There is evidence. We have evidence that biological, chemical, and physical processes happen now in the same way that they happen in the past. We have evidence that organisms evolved. We have evidence that life can come from non-life… even if we haven’t created life in the lab from non-life.

              Creationists would have you believe that until scientists breed bacteria without a flagella in the lab until they get a flagella, then evolution doesn’t work. That’s childish and fundamentally flawed picture of science and the work that scientists do. Further, when applied to their own ideas, their ideas come out looking much, much worse.

              Let me say this plainly and if you actually ask biologists they will entirely agree with what I’m about to say. We will NEVER know exactly how life formed on this planet. However, there are two facts that we do know. 1) Life exists here now. 2) Life did not exist on the planet at some point many billions of years ago.

              Therefore life arose on this planet. Now, the massive amount of studies done on the subject all point to the idea that there is no reason that the pieces of life, from base carbon all the way up to self-replicating RNAs cannot come from known chemical reactions under plausible conditions prior to life on the planet. Indeed, for the majority of precursor molecules, there are multiple pathways to get from base stocks that are easily found in nature to those precursor compounds (including sugars, amino acids, nucleic acids, lipids, and chains of all of the above).

              So, it’s not about faith. It’s about evidence.

              Faith is believing something without evidence (indeed, in spite of evidence)… like creationists.

              Science is using evidence to find likely solutions and then changing those solutions when knew evidence is found.

              Please understand, this is a hugely common complaint that I hear from religious and creationists all the time. I first heard it over 30 years ago. It’s not new. It’s not correct. And, except for a few creationists who have no idea what’s going on in the real world, it’s not used anymore.

              I hope that helps.

            • RexTugwell

              My prediction: “Dr. Hal” will be rendered speechless after that thrashing.

            • Doc Bill

              Come on, Rex, the little God-squader needs help. Show him how it’s done!

            • RexTugwell

              “Dr. Hal” doesn’t need my help. You’re channeling him just fine.

            • Dr Hal

              Smilodon,
              Again, thanks for taking the time for the detail explanations. I understand science and trust me, I understand scientists. However, you seem to misunderstand my point which is simply that “the best explanation for the information that is known” does NOT equate evidence let alone proof when it comes to, once again, the subject of ORIGIN. I do not argue against the science, only against some of the conclusions that some scientist reach.
              You seem to have been around long enough to be arguing this for 30 years so you should know that one of the tenets of scientific research is that “correlation does NOT equal causation”. Just because the Biological, Chemical, and Physical process that happen now also happened long ago, enabling us to make correlations, does not mean that unequivocally life sprung up spontaneously. To reach that conclusion there is a lot of assumptions that need to be made and although those assumptions might be based on “evidence”, as you stated the evidence will NEVER reveal how life formed on this planet. Thus if you believe in something that the evidence does not show…well you answered what that means.
              Now I don’t know what “creationist” argue for or against as you seem to be keeping track of arguments you have heard over your lifespan. However, I do believe in a creator and I do believe in science and I don’t see that science disproves religion or religion disproves science. You say that all the studies conducted on this subject point to the “IDEA” that life happened spontaneously but non of the results that I’m aware of show “evidence” that there is NOT a creator. Like almost everything else in life there are multiple sides to a story. You have obviously chosen to listen only to one side. However, if a creator created life to be the way it is, would our experimental results today not be the same as they are? As a scientist you can believe that all life came from one single organism and all our differences are due environmental adaptation and mutations over billions of years (tenet of the theory of evolution) or you can believe that ALL life was created to be different but with similarities, just like the many principles in Biology, Chemistry, and Physics are different but have also share similarities. I subscribe to the latter set of believe because to me our differences greatly outnumber our similarities. Oh and then there is the fact that asides from a few fossils I have not seen any “transitional” species lately (i.e. a monkey in the process of becoming a Neanderthal). Oh wait, but why can’t we test THAT in a lab, ohhh that’s right, it takes millions of years so, darn it, you will never be able to see it. Sounds familiar?
              This is getting kind of long but I’ll make one last additional point, you can’t make generalized statements such as “scientists WILL change their mind if presented with evidence”. The truth is that this is a matter of individual choice. Just because someone is a creationist doesn’t mean they will not listen to reason and just because someone is a scientist doesn’t mean that they WILL listen to reason or vise versa. See your assumption would lead one to believe that NO scientist is a creationist and NO creationist is a scientist which is a very narrow point of view. If you’ve looked at ANY court case you should know this, almost all “evidence” can be debated as individuals WILL inherently see the same set of information differently based on a plethora of biological, psychological, and sociological factors.

            • SmilodonsRetreat

              If you require “proof”, then you don’t understand science.

              “although those assumptions might be based on “evidence”, as you stated the evidence will NEVER reveal how life formed on this planet. Thus if you believe in something that the evidence does not show…well you answered what that means.”

              You say two things here wrongly. First, if it is based on evidence, then it is based on evidence. Whether that evidence comes from a modern biochem lab or 4 billion years in the past is inconsequential. It is still, as you rightly agree, evidence.

              Then you go on to say that that evidence will NEVER reveal how life formed on the planet.

              That is both correct and wrong. It is correct in that we cannot know how it happened. However it is wrong in that we cannot know how it happened.

              The evidence DOES show that life can arise from non-life. Do we know exactly HOW? No. Is it possible? Yes.

              Now, if you want to argue the particulars of a RNA first model or a metabolism first model, then we’ll have something interesting to talk about. But, you cannot pick and choose which sciences you like and which you do not.

              You seem to have a very different definition of creationists. It is used on this blog solely as one who believes that life and possibly the universe was specially created by a deity. Very, very few scientists are creationists in that regard. Even the majority of religious scientists are not creationists in that regard.

              Yes, evidence can be debated. But you seem to not be interested in doing so. Again, I can provide you with hundreds of papers showing the steps of abiogenesis. It’s pretty easy to find them on google scholar should you choose to look for them. But you aren’t doing that, you are rejecting the practice of science instead. Not that scientists don’t look at evidence, but that they believe things without evidence. I can’t speak for anyone but myself, but having talking to a number of researchers doing abiogenesis research, none of them take anything on faith (as I previously defined it) and all look ONLY at the evidence that they generate and generated by others, which is subsequently confirmed.

              You are mistaken.

            • Doc Bill

              I often use a traveling analogy. I’m in Austin and I tell you that I came from Houston. Does it matter to know every inch of the way or just plausible pathways? You might determine I came by car and even discover how much gas I used. That might enable you to narrow down the route. It’s probably irrelevant whether I came up highway 99 or 36 as they are about equivalent in time and distance. No faith involved, no proof required.

              Alas, talking to a brick wall it is.

            • Dr Hal

              Wow!!! Some how I am not too surprised that we disagree even on what science is ABOUT. I’m not a blogger, I’ve never done this before but I felt compelled to intervene here in large part because Smilodon seems to use some logic in arguing his point so I thought we could converse on the basis of logic as it applies to science, which is a very logical field. I did NOT expect you Smiley to hide behind that coward excuse used by some evolutionist that “science is not about proof”.

              You throw around the word “evidence” in the name of science but say that science is NOT about proof. So lets break things down to a basic level since the occasion seems to dictate that. What is the definition of this word “proof”? Lets ask our friend dictionary.com

              “noun

              1. evidence sufficient to establish a thing as true, or to produce belief in its truth.”

              So then, what do this word “evidence” mean? Since it seems to appear so often in our arguments and all. What say you dictionary.com?

              “noun

              1. that which tends to prove or disprove something; ground for belief; proof.”
              W-H-A-T???!!!!!!! You mean that evidence is something tend to prove or disprove and proof is the evidence used to establish something as TRUE!!!! If science at it’s core is not about TRUTH, then WHAT IS IT ABOUT??!!! ALL scientific EVIDENCE is collected through experimentation to ultimately PROVE a point. I and ALL scientist are well aware that some things CANNOT be proven and the best that we can do through experimentation is reach approximations based on probability of randomness. However, if something CAN be proven by science beyond doubt, science seeks to and ultimately PROVES it.
              I find it comical that on one of Doc’s many replies he actually used something that science has PROVEN (AgNO3 (aq) + NaCl (aq) —> AgCl (s) + NaNO3 (aq)), and followed that up by saying that science is “not about proof”. Everything that has been possible for science to prove thus far science has proven. Even though NO ONE has physically seen an electron science has PROVEN how an electron WILL behave in a given scenario, and to use Doc’s own words this works “every single time” which means it’s PROVEN beyond doubt!!! Staying in the topic of Chemistry since Doc brought it up, intermolecular forces between atoms (proven), behaviors of say…carboxylic groups in acidic, basic, or neutral environments (proven), behavior of molecules at equilibrium and when that equilibrium is thrown off (prove), and list goes on and on and on in Chemistry as it does in Biology as it does in Physics. Principles in all three of these sciences have been PROVEN to be TRUE, which again is what my version of science seeks.
              If you do not seek to prove something to be true through science then, if I may, what exactly have you been doing with your life for the past 30 years? (I am assuming that you’ve been in the “science” field since you started arguing origin with creationists Smilodon). Does your version of science only seek to reach approximations, estimations, and probabilities to present those as “evidence” for….well, I guess I don’t know what you would present it as evidence for if you are NOT trying to PROVE anything. The sciences that thrive on approximations, estimations, and probabilities are called Behavioral, Social, and Political Sciences so perhaps that is what you’ve been practicing and referring to all along. Yet even “scientists” in these sciences seek to show that their theories and proposals are true.
              Let’s bring this back full circle, to the point of this entire argument, ORIGIN. Since our friend Doc used an analogy in another one of his many replies, let me use an analogy to summarize my point in this WHOLE conversation. Lets go with the law analogy since, for centuries now, it has been the best forum of settling disputes as fairly as possible. In a court of law each of the two opposing sides presents their case and shows their evidence which is meant to PROVE their case (the ultimate goal). In the event that the evidence presented by both sides to a fair judge or jury does NOT PROVE one side over the other, then a verdict CANNOT be given. That is all I am saying here folks, you CANNOT say that scientific evidence shows that creationist are wrong and therefore no deity exists, science does NOT show that. The jury is still out on this topic of ORIGIN and evolutionists can argue their side, creationist can argue their side, yet neither PROVES anything. To say that science has settled this debate in favor of the evolutionist is blatant lie. If a creationist argues that the sky is blue because God created it that way and an evolutionist counter-argues explaining in detail the science of how electromagnetic energy derived from the sun interacts with the atmosphere and ultimately ends up being processed by our occipital cortex. Does the science here demonstrate that God didn’t create the blue sky? Are the scientific processes (Physics, Chemistry, and Bio) involved in the explanation proven and correct? YES, they are true and correct!! However, correct as they may be, they don’t settle the argument in court because used as evidence for either side (creationist can very well use science to argue their points), science does not prove that one side is true and/or the other is not true.
              Keep the faith fellas!

            • Doc Bill

              It’s difficult to believe that Hal could be any more ignorant, but there’s PROOF.

              Good night Hal.. Enjoy your little make believe world.

            • Doc Bill

              Biggest load of apologetic bullshit I’ve read in years! No, sir, you don’t know jack shit about science. You’re a poser, or in my rough tongue a bullshitter.

              Do run along, now, you’re quite tiresome.

              Where, oh, where is my Rexy!

            • RexTugwell

              Oh I’m right here, Bag Man. Speaking of bullshitters, your career as a biochemist is coming up on its two week “anniversary”. Congratulations! Have you decided on your next career move?

              Now I know why Smiley keeps you around. Compared to you, he looks like a genius.

            • SmilodonsRetreat

              Do you have any point of discussion other than to provide more evidence that creationists are jerks?

            • Doc Bill

              Hey, “Dr.,” you can blow it out your vacuole!

              No, faith-head, science is not based on faith. It’s called science. You should read about it. Fascinating subject. Hey, “Dr.,” did you know that silver nitrate added to sodium chloride in aqueous solution produces silver chloride precipitate every single time? I know, amazing, huh! Even if I stand in a pentagram and summon the Dark Lord it still happens.

              Your arrogant ignorance about how science works is profoundly insulting to me. Rule Number 1: Science doesn’t do proofs.

              Number 2: Science isn’t a point of view.

              So, run along and light some candles or something.

            • Doc Bill

              Nice one, Rex! Imma gonna steal it!

            • Doc Bill

              Well, no, David, nobody proposes BANG or BOOM. Chemistry happens. Fatty acids or phospholipids, for example, can be formed in steps catalyzed by clays and minerals, and they form membranes spontaneously, orienting their hydrophilic and hydrophobic ends.

              You have to put things in perspective and in the proper context, David. Life percolated in the oceans for over 2 BILLION years (approximately) before multicellular organisms took hold on the sea floor. And even those appear to have been accretions or extensions or aggregations of simpler but similar or identical organisms. A volvox is a good example of such a colony.

              It appears that gene regulatory networks played a significant role in what is now studied as evolutionary developmental biology or evo-devo for short, enabling cells to differentiate.

              It’s not difficult to see, even today, the development of more complicated organisms. You can start with protozooans and study their organelles which perform similar functions as organs in multicellular creatures: energy production, waste management, movement and sensory ability. And you can then study more and more complex organisms to understand, for example, how a neural bundle transforms into a brain, and a straight in-line gut becomes a folded intestine.

              It does not require faith at all. It requires study. It’s all there for you to understand. Nothing is hidden. There are no miracles.

              One final comment. “Random/undirected mutations” is creationist jibber jabber and it’s wrong, not true and you should be ashamed for repeating such nonsense. Natural selection is anything but undirected. Natural selection IS the “intelligent designer” or as Dawkins put it, the blind watchmaker. Simply put, life is an equilibrium maintained by natural selection. It is not undirected nor does it have a purpose, other than to maintain the equilibrium. That you are here is because you are a lucky ducky and you should thank your stars for that, and all of the billions of creatures who survived in your past so you could be here.

            • RexTugwell

              You’ve got it backwards, Bill. Forgive me for quoting Behe again but the guy does make sense.

              In Darwinian thinking, the only way a plant or animal becomes fitter than its relatives is by sustaining a serendipitous mutation. If the mutation makes the organism stronger, faster, or in some way hardier, then natural selection can take over from there and help make sure its offspring grow numerous. Yet until the random mutation appears, natural selection can only twiddle its thumbs.

              The Edge of Evolution: The Search for the Limits of Darwinism

            • Doc Bill

              First of all, Behe is a creationist and a liar. That doesn’t make his argument false but I would never take what Behe says or writes at face value. The key to Behe’s dishonesty is right there in the front: “In Darwinian thinking, the only way…” That’s hundred year old thinking and creationists are very, very fond of calling things “Darwinian” because most lay-people don’t know otherwise. I don’t think Behe is stupid, illiterate or ignorant, but his use of “Darwinian” as the only mechanism is false. Evolution is much more complicated than Behe lets on and I’m sure he knows that by the way he is so very careful not to discuss anything that jiggles his house of cards.

              Random mutation occurs in EVERY single offspring. You, dear old Rexy, have about 100 random mutations in your DNA, so even nodding to Behe using his own words, natural selection doesn’t have to twiddle its thumbs for very long.

              Genetic drift which is the change in gene frequency within a population is also a huge factor. I don’t think Behe talks about genetic drift at all, and it’s a complicated subject and it kicks the legs out from under his argument.

            • SmilodonsRetreat

              This, like most things creationists say, is not 100% true. You have been told this multiple times with documentation. You continuing to promote this misunderstanding can only be construed as a deliberate lie.

    • RexTugwell

      It’s said that the coldest place in this universe, spanning tens of billions of light years, is right here on earth in labs like those at MIT and elsewhere. Conditions made possible by the design of intelligent agents, temperatures only billionths of a degree above absolute zero can be reached. Even in the deepest space, temps can’t get that cold. We’d have to wait for the universe to be approaching heat death for it to reach very close to absolute zero; many billions of years from now.

      So it is with proteins. I did start off by asking you, Smiley, if there was any known parallel cellular processes that could accomplish the task that the researchers had in the above experiment. You emphatically answered no. I thought that was a significant admission. Don’t you? Basically, it can’t be done in nature but intelligent agents could get the job done in the lab. I agree.

      This paper is Intelligent Design from beginning to end. Why evolution even enters into the discussion is beyond me. First, Behe admits to 2 protein binding sites as the edge of evolution. He’s even got a chapter in his book entitled, “The Two-Binding-Sites Rule” Go figure. And 20^80 is well below Dembski’s UPB so this paper doesn’t come close to single-handedly threatening ID.

      Natural processes and surely, cellular processes don’t have the capacity of searching through libraries of fixed-length, random-sequence polymers. And they certainly don’t have the luxury of gel-filtration and amplification. And why 80 AA length polymers and not the average protein length of 300? Because of the likelihood of instability of the protein folds with the longer lengths.

      You made the ridiculous assertion that “Evolution beats design.” Unfortunately, your denial notwithstanding, the paper by Keefe and Szostak was about the origins of life or at least life when it first arose.

      In conclusion, we suggest that functional proteins are sufficiently common in protein sequence space (roughly 1 in 1011) that they may be discovered by entirely stochastic means, such as presumably operated when proteins were first used by living organisms[Emphasis mine]

      I love that level of confidence – “such as presumably operated”

      I just don’t have that kind of faith, Smiley.

      • SmilodonsRetreat

        You just don’t get it do you. Apparently, according to you, because playing cards are intelligently designed, the results of every dealt hand can be predicted by engineers. Since every roulette wheel is designed, then the results of every spin are 100% predictable… except that reality is different than what you think.

        I’ve written about this MULTIPLE times. Just because an experiment is intelligently designed, it doesn’t mean that the RESULTS are intelligently designed.

        For the third or fourth time now, this experiment shows that the specificity required by ID proponents to exist in natural systems… doesn’t exist.

        There’s no reason why our ATP proteins have to be the ones we have. It could have been any number of ATP proteins… as shown from the RANDOM collection of proteins.

        Why don’t we try this experiment with another million or so random proteins and then another million or so random proteins. I bet that we will find another 4-5 proteins with high ATP affinities in each batch of a million. For ID to be correct, this MUST be wrong.

        I find it interesting that you say that exactly what happened IN THIS VERY PAPER… doesn’t actually happen.

        You said
        “Natural processes and surely, cellular processes don’t have the capacity of searching through libraries of fixed-length, random-sequence
        polymers.”

        And yet, that’s exactly what happened. Those proteins, from a random collection of proteins, that had an affinity for ATP were SELECTED and, just like in the Darwinian Evolution on a Chip experiment, the selection process removes those proteins that do not match the “environment”, in this case, an affinity for ATP.

        The “natural environment” doesn’t say, “Hey, I need a protein with an affinity for ATP”. It’s just, if there is a protein that works, it is used. It’s called chemistry. You should investigate this.

        You also said
        “And they certainly don’t have the luxury of gel-filtration
        and amplification.”

        So, please, describe for us exactly how those two processes were used in this experiment. I bet you can’t. Cite the page numbers.

        “And why 80 AA length polymers and not the average
        protein length of 300? Because of the likelihood of instability of the
        protein folds with the longer lengths.”

        I don’t know, why not ask the authors?

        Average protein length is another red-herring and has nothing to do with this discussion. Why not use the smallest proteins? Or the largest? Or the median? Or the mean? Or any other arbitrary length? It’s a meaningless question. I’ll be happy to do the work that you could do, but won’t. I’ll ask the authors for you, if you like.

        Once again, Rex doesn’t say anything that discredits the paper or the results or the conclusions drawn from the paper. Just desperately tried to confuse, misdirect, and befuddle.

        • Doc Bill

          Behe writes that the collection of mutations required to confer maximum resistance to chloroquine is a mark of complexity in a protein. Behe invented a term for it, calling it a “chloroquine complexity cluster,” or CCC. (I call it a “BCF” or Behe Cluster Fuck, but that’s old yellow stain in action.) Behe suggests that the odds of any protein developing a SIMILAR complex feature, such as a binding site for another protein, would be on the order of 10^-20, based on a rough estimate presented in a footnote of a 2004 paper by Nicholas White suggesting the odds of resistance occurring in a single parasite would be this magnitude. Note that Behe takes this resistance estimate and applies it to a binding site.

          On what basis? None. But, let’s move on.

          Since this probability has been suggested as achievable by evolution, Behe has to convert this number into an argument against evolution and he does this by squaring it. Behe proposes that if the odds of evolution producing one binding site is 10^-20, then the odds of evolution producing TWO binding sites, as would be needed for a signaling pathway, for example, would be the product of 10^-20 x 10^-20 or 10^-40. Given Behe’s estimate that fewer than 10^40 cells have existed during the entire history of life, that means that the evolution of even a moderately complex system of interacting proteins is far beyond the “edge” of what evolution can accomplish. Behe calls this the “two binding sites rule.” Whenever we see two binding sites in a protein, we see the hand of design.

          If you thought Behe was being dishonest above, we’re just getting started! When calculating probabilities you can only multiply individual odds of two events if they are completely independent, like simultaneously flipping two coins. By squaring 10^-20 Behe assumes that both binding sites must appear at the same time in a single individual cell by pure, random chance and, furthermore, the appearance of one or the other binding site by itself is useless and will be weeded out by natural selection. Behe ignores standing research that demonstrates that CCC can be achieved by stepwise mutations, some involving SIX or more mutation steps occurring in sequence, not simultaneously. Intermediate stages are not weeded out as each stage can confer SOME advantage, if not maximum advantage produced by the final stage. Behe’s ignorant book audience doesn’t know any better, of course, which is why he gets away with this subterfuge, and also why Behe is ignored in scientific circles.

          Behe’s two binding site rule makes two critical assumptions: that all of the features of each binding site must appear simultaneously, against great odds; and that each binding site is absolutely useless until the second appears. In fact, both of these assumptions are wrong.

          Behe’s “argument” is total fiction. He pulls a probability number out of a footnote, uses it in an analogy to a different process, invents a world in which that process has to be produced in such a way as to make it impossible, and declares Design! The intellectual dishonesty not only of the gross and incorrect use of simple probabilities, coupled with deliberately ignoring known research that makes his argument moot, and presenting this mess as serious, scientific work is simply staggering.

          (thanks to Ken Miller and Nick Matzke for the meat of this deconstruction)

          • RexTugwell

            Hey Bag Man Billy, brave soul that you are by getting your info on Behe from secondary sources, you get just about everything you’ve written about Behe in this thread wrong. I’m preparing my response but in the meantime, would you be so kind as to explain your allergy to simultaneous mutations? Thaaaaaaaaaanks

            • Doc Bill

              Hey, Rexy, feel free to point out my errors. I’m always looking to improve. Meanwhile, no allergy to simultaneous mutations. It’s Behe who says they’re impossible, not me. None whatsoever. Behe claims they are REQUIRED. He’s simply wrong; they’re not. Stepwise evolution 1, Behe 0.

              This is Behe’s one trick pony, the same pony he used to push the “irreducibly complex” scam. Turns out that every single system he proposed as being impossible to evolve has been demonstrated to be possible to achieve by stepwise pathways. The ruse only still works on the feeble minded and deluded, apparently.

            • SmilodonsRetreat

              Actually, I think that Behe retracted his own ideas along these lines in the Kitzmiller trial. I don’t have time to reread the testimony now, but I seem to recall him saying that the mutations don’t have to be simultaneous.

            • RexTugwell

              Just like you seem to recall Behe not teaching any courses at Lehigh. Tell us, Smilodon, what stated ideas was he retracting if Kitzmiller was two years before The Edge was published?

            • SmilodonsRetreat

              I’m sorry Rex, I thought we were talking about his actual paper… not his book. You have read the paper right?

              Here’s what he says in the Kitzmiller trial

              “Q. Could you read into the record the text to the end of the paragraph beginning with, we strongly emphasize?

              A. We strongly emphasize that results bearing on the efficiency of this one pathway as a conduit for Darwinian evolution say little or nothing about the efficiency of other possible pathways. Thus, for example, the present study that examines the evolution of MR protein features by point mutation in duplicate genes does not indicate whether evolution of such features by other processes, such as recombination or insertion/deletion mutations, would be more or less efficient.

              Q. So it doesn’t include recombination, it doesn’t include insertion/deletion of the mutations?

              A. That’s correct.

              Q. And those are understood as pathways for Darwinian evolution?

              A. They are potential pathways, yes.

              Q. This study didn’t involve transposition?

              A. No, this focuses on a single gene.

              Q. And transpositions are, they are a kind of mutation, is that right?

              A. Yes. They can be, yes.

              Q. And so that means, this simulation didn’t examine a number of the mechanisms by which evolution actually operates?

              A. That is correct, yes.”

              Q is Rothschild (I believe) and A is Behe.

              So Behe admits that he didn’t simulate anything but a point mutation. He specifically mentions that he ignores most of the mechanisms of evolution to focus on one. You, and other ID proponents, seem to have taken that to mean NO form of evolution can work.

              Let’s continue shall we.

              “Q. And one last other question on your paper. You concluded, it would take a population size of 10 to the 9th, I think we said that was a billion, 10 to the 8th generations to evolve this new disulfide bond, that was your conclusion?

              A. That was the calculation based on the assumptions in the paper, yes.

              MR. ROTHSCHILD: May I approach the witness, Your Honor?

              THE COURT: You may.

              BY MR. ROTHSCHILD:

              Q. What I’ve marked as Exhibit P-756 is an article in the journal Science called Exploring Micro–

              A. Microbial.

              Q. Thank you — Diversity, A Vast Below by T.P. Curtis and W.T. Sloan?

              A. Yes, that seems to be it.

              Q. In that first paragraph, he says, There are more than 10 to the 16 prokaryotes in a ton of soil. Is that correct, in that first paragraph?

              A. Yes, that’s right.

              Q. In one ton of soil?

              A. That’s correct.

              Q. And we have a lot more than one ton of soil on Earth, correct?

              A. Yes, we do.

              Q. And have for some time, correct?

              A. That’s correct, yes.

              Q. And, in fact, he gives us a good way of comparing it. It says, as compared to a mere 10 to the 11th stars in our galaxy?

              A. Yes, that’s what he writes, uh-huh.

              Q. And 10 to the 16th prokaryotes is 7 orders of magnitude higher than the population you included in your calculations, correct?

              A. No. We considered a wide range of populations, and we considered a wide range of number of substitutions that would be — or point mutations that would be necessary. You’re focusing on two, but perhaps I can direct your attention again to that figure from the paper — excuse me. Let me find it.

              The best place I think to look is figure 6, which is on page 10 of the document. Up in the upper right-hand corner, that figure there.

              Q. Sure.

              A. If you look on the bottom, the x axis there, the bottom of the figure that’s labeled lambda, it has the numbers 2, 4, 6, 8, 10, and so on, those are the number of point mutations that we consider perhaps some multi-residue feature might entail. As we said in the paper, forming a new disulfide bond might require as few as two point mutations.

              But forming other multi-residue features such as protein, protein binding sites might require more. And so the number on the X axis lambda 2, 4, 6, 8, those are the number of point mutations that we entertained or we calculated numbers for to see how long such things would be expected to take under our model.

              And if you look up at the top axis, the top x axis labeled N, at the top of the figure. N stands for population size. Okay. So if you look at the figures there on the left, it’s slanted, and it’s not enlarged yet, so it’s hard to see. It says, 10 to the 6th. That’s a million. And then skip a line. These are in every 10 to the 3rd increments of population size. That would be 10 to the 9th.

              The next label is 10 to the 12th, which is a trillion. The next label is 10 to the 18th, which is much more. The next label is 10 to the 24th, which is much, much, much more. The next label, 10 to the 30th, which, again, is very much more.

              So, in fact, we considered population sizes from 1000 all the way up to 10 to the 30th, and multi-residue features from 2, which might involve disulfide bonds, up to many more, which might be involved in protein, protein binding sites.

              Q. 10 to the 30th, that is quite a lot, right?

              A. Yes. That’s roughly what is calculated to be the bacterial population of the Earth in any one year. And so over the course of the billion year, 4 billion year history of the Earth, there would probably be a total of roughly 10 to the 40th.

              Q. And so in the case of prokaryotes, which you said was a good example of what you were studying, 10 to the 16th in one ton of soil?

              A. Yes.

              Q. So a few tons of soil, and we’ve gone past that 10 to the 30th?

              A. Well, no. In the 10 to the 14th tons of soil. 10 to the 30th is the number that’s in the entire world, according to the best estimates, including the ocean as well as soil. So — but I agree with your point, that there’s a lot of bacteria around and certainly more than 10 to the 9th.

              Q. So just with the prokaryotes, 10 to the 16th, 7 orders of magnitude higher than what you were calculating here?

              A. That’s certainly true, but in our paper, we had our eye not only on prokaryotes, but also on eukaryotes as well, which, if you leave out recombination, one can — they certainly undergo point mutations. They certainly have genes and so on. So much of this is also applicable to eukaryotes.

              And the populations of eukaryotes and certainly larger plants and animals are much, much smaller than populations of bacteria. So we view our results not just as supplying that, but to giving us some feel for what can happen in more complex organisms as well.

              Q. Well, you’re not talking about more complex organisms here, are you?

              A. I think we do. I think at the end, if I’m not mistaken, if I remember correctly — okay, yes. On page 11, the second full paragraph, on page 11. It begins on the right-hand column, the second full paragraph. It says, The lack of recombination in our model means it is most directly applicable to haploid, asexual organisms. Nonetheless, the results also impinge on the evolution of diploid sexual organisms.

              The fact that very large population sizes, 10 to 9th or greater, are required to build even a minimal MR feature requiring two nucleotide alterations within 10 to the 8th generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.

              Thus, mechanisms in addition to gene duplication and point mutation may be necessary to explain the development of MR features in multicellular organisms.

              So here we were trying to point out that, because of the results of the calculation, it seems that, when we’re trying to explain MR features in multicelled organisms, then we’re going to have to look to other processes for that.

              Q. Okay. So if we exclude some of the processes by which we understand evolution to occur, it’s hard to get there for multicellular organisms?

              A. I’m sorry.

              Q. If we exclude some of the mechanisms by which we understand evolution to occur, like recombination, it’s hard to get there?

              A. Yes.

              Q. And bringing it back to the prokaryotes. We’re in agreement here, the number of prokaryotes in 1 ton of soil are 7 orders of magnitude higher than the population, you said it would take 10 to the 8th generations to produce the disulfide bond?

              A. Yeah, certainly. Yeah, the bacteria are — can grow to very large population sizes.

              Q. So the time would be?

              A. Much shorter.

              Q. Much shorter?

              A. Absolutely.”

              Wow, straight from the horses mouth. Here’s the paper, which was written slightly before the book, “Simulating Evolution by Gene Duplication of Protein Feature that Requires Multiple Amino Acid Residues”

            • RexTugwell

              You mean Behe’s peer-reviewed paper which concludes:

              The fact that very large population sizes–10^9 or greater–are required to build even a minimal [multi-residue] feature requiring two nucleotide alterations within 10^8 generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.

              Makes sense to me. Didn’t you say you never hear creationists talking about population? But there it is, “straight from the horses [sic] mouth.”

              A thousand pardons, Smiley. According to Bag Man Billy, I’m a fucking moron so why don’t you spell it out for me. I’m just not seeing the point you’re trying to make. And what does this have to do with Behe’s claims in his book? Thaaaaaaaanks

            • SmilodonsRetreat

              You are so caught up in trying to figure out the angle for everything you do, you assume that everyone has an angle too.

              You said something: Behe’s book was written AFTER the Kitzmiller trial. I replied saying that the paper that appears to be directly relevant to this conversation was written prior to Kitzmiller.

              During that trial, it was shown that the paper does not do what you ID proponents wish that it did. Behe only considered point mutations. He did not consider large populations. As Doc Bill pointed out, he also requires simultaneous mutations.

              All of these are significant flaws to his paper… which does NOT say anything about ID (as Behe stated in the Kitzmiller trial).

              Now, maybe I’m referring to a different paper, but it seems to be the same one and you didn’t correct me (as I know you love to do so much), so we’ll assume that it’s the same paper.

              So, let’s see… we have 3 significant flaws, any one of which means that the simulation does not accurately model reality. So what’s the point of the paper?

              To befuddle people like you who want to believe. That’s all it does.

              Here’s a response to Behe’s paper: http://www.genetics.org/content/180/3/1501.full

              And another one:
              http://onlinelibrary.wiley.com/doi/10.1110/ps.041171805/full

              And another one:
              http://www.sciencemag.org/content/312/5770/61.full

              Don’t take our word for it, look at what the scientists say about Behe’s work.

            • Doc Bill

              For the record, YOU’RE the first person on this thread to invoke the Behe when you correctly, and I agree with you most wholeheartedly on this, wrote:

              “G. It doesn’t matter because Behe is a poopyhead.”

              Spot. On. Well done, Rexy, you’re evolving into less of a worthless fart and more human every day.

            • RexTugwell

              Thanks for the non-answer. I’ll be in touch.

            • Doc Bill

              No, you won’t be “in touch” because you are ignorant, illiterate and stupid. Need I go on? You mount a defense of Behe is laughable. Bwahahahhaha! You’re a much better wanker, Rexy, than a thinker. I guess everybody has a gift so good on you.

            • RexTugwell

              Does this mean my evolution into a human has already halted? That was fast.

            • Doc Bill

              A severe case of inbred punctuated equilibrium.

    • Arturo

      If I may interrupt the back and forth with creationists and point out a spelling error 🙂
      The protein mentioned in your post is called “TITIN”, not Tintin (which is a great comic book).
      Titin is an incredibly interesting protein that functions as a spring in muscles. As you point out it is a very large protein. So large that it takes a cell about 4-5 hours to synthesize it!
      Thank you for an interesting post.

      • Doc Bill

        A grad school friend of mine studied titin working on a PhD in physical biochemistry and mostly I remember him tossing freshly dispatched zebra fish into a blender. He had never seen the SNL Bass-o-Matic sketch and my description of it to him was lost in the telling, but it was decades before the Internet and YouTube. Recently I sent him a link and it brought back great memories.