Friday, September 20, 2013

Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different Rates

Stephen Meyer is promoting the idea that God made all the various types of animals over a short period of time about 530 million years ago. The molecular data refutes that speculation because it shows that the various phyla share common ancestors and many of those ancestors appear long before the Cambrian Explosion.

This data creates a serious problem for the IDiots so they have to discredit it in order to dismiss it. As we've seen in earlier posts, Meyer argues that the molecular data is wrong because: (a) there are no transitional fossils, and (b) different molecular phylogenies do not agree in all detail [see The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes and Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates]. He has five anti-evolution arguments altogether [Darwin's Doubt: The Genes Tell the Story?]. The third one is that different genes evolve at different rates.

It's been known for decades that different genes evolve at different rates. The earliest comparisons were between the proteins; fibrinogen, globins, and cytochrome c. Those are the examples often shown in textbooks. Cytochrome c is well conserved. Most of the residues don't change very much because mutations would be lethal. The rate of change (evolution) is determined by substitutions that occur at neutral sites.

Globins are not as highly conserved so the sequences change more rapidly. The molecular clock ticks at a faster rate for globins because more neutral substitutions are allowed. Fibrinogens (fibrinopeptides) are not well-conserved. There are very few residues that can't be mutated. Fibrinogens are practically useless for constructing phylogenetic trees [The Modern Molecular Clock].

Some histones (H3 and H4) are highly conserved. Just about every amino acid is in contact with other histones in the nucleosome or with DNA and substitutions are lethal. H3 and H4 genes yield molecular clocks that tick so slowly that the genes can't be used to detect the relationships between animal phyla. Their sequences are almost identical.

The idea that different genes evolve at different rates has been around since 1970 and we have a good explanation. If you want to look at the relationships of the various animal phyla and you want to date their separation then you have to choose genes that evolve at the appropriate rates. Modern studies are not based on single genes: instead, it's common to use dozens or hundreds of concatenated genes in order to filter out stochastic noise and get accurate dates from calibrating the rate of evolution.

But here's how Stephen Meyer explains it ...
Reported Precambrian divergence times would vary even more dramatically were it not that evolutionary biologists and molecular taxonomists ignore certain molecules in their studies to avoid grossly contradictory results. Consider, for example histones—proteins found in all eukaryotes involved in packing DNA into chromosomes. Histones exhibit little variation from one species to the next. They are never used as molecular clocks. Why? Because the sequence differences between histones, assuming a molecular rate comparable to that of other proteins, [my emphasis LAM] would generate a divergence time at significant variance with those in studies of many other proteins. Specifically, the small differences between histones yield an extremely recent divergence, contrary to other studies. Evolutionary biologists typically exclude histones from consideration, because those times do not confirm preconceived ideas about what the Precambrian tree of life should look like.
Meyer wonders how scientists choose the appropriate genes and concludes that they pick the ones that conform to their preconceived notions of what the animal tree ought to look like.
... as one widely used textbook euphemistically puts it, evolutionary biologists must choose "phylogenetically informative" data. By this, they mean sequences that exhibit neither too little nor too much variation—where too much and too little are determined by preconceived consideration of evolutionary plausibility, rather than by reference to independent criteria for determining the accuracy of molecular methods.

The subjective quality of these considerations, where scientists "cherrypick" evidence that conforms to favored notions and discard the rest, casts further doubt on the extent to which molecular comparisons yield any clear historical signal.
This is so wrong. It's evidence that Meyer doesn't understand the science he criticizes but that's not a surprise. He is not an expert in biology or in evolution and we already have plenty of evidence of that.

What IS surprising is that a passage like this demonstrates that the book was not reviewed by anyone who is knowledgeable about the field. Any undergraduate who had completed a course in molecular evolution would easily spot the error. Even Jonathan McLatchie would have caught it!

David Klinghoffer might have reviewed the book before publication1 so I'll let him have the last word from: The American Spectator Warmly Welcomes Darwin's Doubt.
You might not like what Stephen Meyer has to say in Darwin's Doubt, but a competent critic knows you need to react to what the author actually argues. By contrast, Meyer's critics have mostly refused to grapple with the main contentions of the book, the categories of evidence it advances. When you call them on this, they refuse to respond. Or in Farrell's case, they reply with name-calling.

Tells you something, doesn't it?


1. A case of the blind leading the blind.

40 comments :

  1. Replies
    1. I will reserve my comments on the molecular clock for an ENV blog post.

      I have been ignoring Billy's repeated claims that I am mistaken about the optimization of the genetic code for minimizing the impact of point mutations. I thought, however, that I should perhaps weigh in and set the record straight. My position on this is in fact quite mainstream. Granted, most biologists would reject my claim that the optimization reflects evidence of design. But my claim that it *does* exhibit this optimization is agreed upon by many. I have a whole electronic folder of scientific papers pertaining to this topic. Here's a couple of quotes:

      From http://mbe.oxfordjournals.org/content/17/4/511.long,

      "The fact that codon reassignment is not always lethal indicates that the amino acid/codon assignments of the canonical code need not be a “frozen accident” of history, but, rather, require explanation. One hypothesis is that the arrangement of amino acid assignments results from natural selection among different codes favoring those that minimize the phenotypic impact of genetic error by maximizing the similarity of amino acids assigned to codons differing by only a single nucleotide."

      From http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468,

      "Even a perfunctory inspection of the standard genetic code table (Fig. 1) shows that the arrangement of amino acid assignments is manifestly nonrandom (4–7). Generally, related codons (i.e., the codons that differ by only one nucleotide) tend to code for either the same or two related amino acids, i.e., amino acids that are physico-chemically similar (although there are no unambiguous criteria to define physicochemical similarity)."

      Jonathan

      Delete
    2. MacLatchie, you refused to acknowledge your serious scientific errors in the previous thread, or apologize for your false accusations about the 4 people you banned, then bad-mouthed when they could not respond.

      Now you change the subject by misrepresenting-- lying about-- your previous bizarre statements about the genetic code. You now attempt to trick us into believing you had said the genetic code was merely optimized. This is a lie.

      In fact, no one would have criticized you had you merely said that the genetic code was optimized. But that's not what you really said, was it Jonathan?

      Copy and paste the words you really wrote over at Facebook that caused this controversy. Copy and paste your actual words. Do not try to rewrite the past. Stop it.

      You cannot neuralyze us. You cannot give us amnesia.

      Copy and paste your actual words.

      Delete
    3. @McLatchie shows Luskinian courage: "I will reserve my comments on the molecular clock for an ENV blog post."

      ENV. Where comments are not permitted. Real courageous.

      Jonathan, I don't dislike you and I already apologized for calling you a bad name.

      But I worry about you. I mean: do you want to turn into Casey Luskin? Really?

      It's not too late for you. You're young. Is Casey Luskin so attractive that you would want to turn into him? Because every day it's like ... science blunder... ban criticism... admit no mistakes... Try to neuralyze witnesses and rewrite history...

      We're used to this from Luskin, no hope for that one. Luskin has no choice, it's in his bones. But somehow I get the feeling you've got a choice.

      You need to be realistic about this ID thing and what it demands. A true IDer can never admit he's wrong, no matter how great the mountain of evidence against him-- because IDers are always insecure, all they have is their authority, and they can't admit mistakes because it would undermine their authority. They're nailed to the cross of "scientists disagree", so they have to pretend they're scientists even if they're not (Luskin, Meyer, Berlinski, Dembski, and Oller all do) and nothing can undermine that, ever.

      Does that sound fun to you? Is it attractive? Doesn't sound fun to me.

      Compare it to our side. We can have fun-- we can be proven wrong, which in real science is a great pleasure. We don't need to guard our authority in a state of perpetual fear. We can admit our mistakes. I can say Dawkins is dumb as a box of rocks and he was dead wrong about that Nilsson and Pelger paper. I can yank Larry's moustache-- he's come this close to banning me twice. I can tell you everything I know about philosophy I learned from Wikipedia, and everything I know about math I learned from Schoolhouse Rock. We don't need authority-- we have evidence. If we don't have evidence, we can say "I don't know"-- and there's a good research project.

      Doesn't that sound like more fun? Really, why anyone would trade real science for something like ID, with the dishonesty it demands of its acolytes, its diminishing returns and ingratitude-- I can't fathom it. You're young and it's not too late for you, but please be conscious if how ID sucks its adherents dry. Just look at Luskin. That's you in 10 years.

      Delete
    4. This will be my last comment in this thread. I did not make "serious scientific errors" in the previous thread.

      It's isn't me changing the subject. It's Billy who wanted to raise the issue of genetic code optimization (see his hyperlink).

      As for what I said regarding the genetic code, I said precisely what it says in the two quotations I cited (anyone can verify this by reading my original article, here: (http://www.evolutionnews.org/2011/11/the_finely_tuned_genetic_code052611.html). I could cite many other papers on this topic as well.

      Billy took exception to the specific example I offered. I wrote "For example, the amino acid leucine is specified by six codons. One of them is CUU. Substitution mutations in the 3' position which change a U to a C, A or G result in the alteration of the codons to ones which also specify leucine: CUC, CUA and CUG respectively. On the other hand, if the C in the 5' position is substituted for a U, the codon UUU results. This codon specifies phenylalanine, an amino acid which exhibits similar physical and chemical properties to leucine."

      I stand by what I said. Phenylalanine, like leucine, is both hydrophobic and non-polar, which means that it can often substitute for leucine without affecting protein structure and function. You can also change the C in the 5' position to an A or a G, which alters the codon to specify isoleucine and valine respectively, which also have physical and chemical properties similar to leucine.

      But I don't wish to engage further in this forum, unless you are prepared to start speaking to me respectfully and cease making baseless allegations. I have some comments to make regarding molecular clock studies, but I will reserve those for a blog post.

      Delete
    5. Mclatchie, how about some honesty
      You write I have been ignoring Billy's repeated claims that I am mistaken about the optimization of the genetic code for minimizing the impact of point mutations.. However, let me remind you or your claim

      "Indeed, the genetic code found in nature is exquisitely tuned to protect the cell from the detrimental effects of substitution mutations. The system is so brilliantly set up that codons differing by only a single base either specify the same amino acid, or an amino acid that is a member of a related chemical group."

      My response

      "Let’s now really demolish your claim with some facts. Here are some examples, there are many more. Let’s play how many you can find.

      Valine (polar uncharged) to Phenylalanine (hydrophobic) substitute GUU or GUC to uUU or uUC
      Valine (polar uncharged) to Glutamic acid (anionic) GUA or GUC to GaC or GaA

      Isoleucine (hydrophobic side chain) to Threonine (polar uncharged and now a possible phosphor acceptor site) AUU or AUA or AUC to AcU or AcA or AcC.

      Theonine (polar uncharged, loss of possible phosphoregulatory site) to Lysine (cationic, potential, methylation, acetylation, ubiquitylation, sumolyation, ISGylation, NEDDylation site ) ACA or ACG to AaA or AaG.

      What’s that, I hear you say? Yes, it does facilitate the co-evolution of new pathways and crosstalk."

      So, you did not make an honest claim about what was exactly refuted, and your incompetence is clear for all to see.

      Delete
    6. Jonathan McLatchie is also continuing to claim that the ENSEMBL database reports that the GULO psuedogene is transcribed. After one keeps repeating the same error after it has been pointed out to youmany times, it starts to look less like an error and more like incompetence, if not outright dishonesty.

      Oh, and this is your "last" comment yet again, Jonathan? Let's see how long that holds this time.

      Delete
    7. mclatchie said:

      "This will be my last comment in this thread."

      And:

      "But I don't wish to engage further in this forum, unless you are prepared to start speaking to me respectfully and cease making baseless allegations."

      I'm sure that this will shock you jonathan but you are not entitled to respect that you haven't earned and don't deserve. Like other IDiot-creationists you obviously believe that you are a big shot (not just "competent") scientist who should get special treatment, just because you say so, from people who actually ARE competent and accomplished scientists.

      And, like most or all IDiot-creationists, you hide or run away when anyone criticizes you, even when the criticism is constructive, and it is all essentially constructive. You get, for free, the benefit of criticism from people who are very knowledgeable yet you ignore, distort, and run away from what they tell you.

      When it comes right down to it, you're an ungrateful cry baby with the typical creationist inflated ego and sense of entitlement. You're also dishonest, which is typical too. If you don't change your ways in a BIG way you'll never be anything more than a lame mouthpiece for ridiculous, religious fairy tales and the dominionist ID agenda. Wake up, before you waste your life pushing crap. Wouldn't you like to be free of the ball and chain of your religious brainwashing?

      Delete
    8. Well, it's hardly surprising, But Mclatchie's at it again. I have been blocked again, as has Fiona. His thread of shame count rises.
      Expect a dire article on operons to appear in ENV soon. Vincent Mulholland has already destroyed it, but will that stop him?

      Delete
    9. I got blocked by him for daring to tag Vince Mulholland. Vince spent 20-odd years working on bacterial flagellar genes. Prior to becoming a molecular biologist I was a microbiologist. It seems that Jonathan just doesn't want comments from anyone who may bring down his house of cards. Expect Vince to be blocked pretty soon.

      Delete
    10. Oh and just to add, the subject in question was the organisation of bacterial flagellar genes and operons.

      Delete
  2. Does the molecular data show this and that.?? Creationists ask for the evidence!
    What is the scientific evidence that molecular data of today ACCURATELY extrapolates backwards to conclusions about origins of life forms.
    Is this extrapolation based on scientific methodology on molecular processes OR is it based on a mere presumption that its reasonable to extrapolate backwards from the present and a sincere but false, science wise, error is being made about the scientific evidence behind the extrapolation.
    To persuade creationists one must first demonstrate the scientific methodology is the foundation for the molecular data claims about origins.
    What is and is it science about this subject.

    ReplyDelete
    Replies
    1. Is this extrapolation based on scientific methodology on molecular processes OR is it based on a mere presumption that its reasonable to extrapolate backwards from the present and a sincere but false, science wise, error is being made about the scientific evidence behind the extrapolation.

      There are thousands of scientists who devote their life's work to understanding molecular evolution and population genetics.

      Do you honestly believe that it's possible they have overlooked a "sincere but false, science wise, error" that invalidates their work?

      You really don't understand how science works. Any scientist who discovered such an "error" would become instantly famous. I would love to be that scientists but it ain't gonna happen because there is no such error.

      To persuade creationists one must first demonstrate the scientific methodology is the foundation for the molecular data claims about origins.

      I wish that were possible. Unfortunately, many creationists will never be swayed by evidence. That's why we also need to keep reminding them that their imaginary designer does not exist.

      Delete
    2. Hey robert, do you have any scientific, biological evidence to show that the biblical characters satan, yhwh, jesus, angels, demons, noah, adam, eve, moses, the three wise men, jonah and the fish, jesus's disciples, the talking snake, the talking donkey, fire breathing dragons, the tree of good and evil, and the holy ghost ever existed? Just wondering.

      Delete
    3. Well, robert? Let's see the scientific, biological evidence! You do have and can show the evidence, right? I'd hate to think that you believe in all of that fairy tale stuff on a "hunch".

      Delete
  3. Mr Moran.
    Thank you for answering as I studied to put the right words to what I'm trying to say.

    Your main reply is thousands of scientists couldn't of missed a error in the whole matter.
    Actually any population could especially in science. its defined by new concepts by new people. Darwin was replacing , I think thousands, of scientis on the subject of biological origins. not just correcting religious thinkers. Thats why he's famous.

    Yet I'm not saying thousands of scientists made an error in their work!
    I'm saying there is a error in methodology conception here. As opposed to any one scientist's personal work in molecular theory.
    Is there a careless acceptance or presumption that there is ONLY one option for conclusions about molecular past history? That is simple extrapolation from today equals results about some life form in the past?!
    I think there is this error of thinking.

    Its a error of methodology and not the intimate subject itself!
    In short its not been scientifically demonstrated that modern molecular processes demand extrapolation to the past accurately portrays molecular evolution and so biological conclusions.

    Its just a grand presumption extrapolation is the only option or even a option.
    Where is the scientific molecular evidence for past origins besides mere extrapolation from the present??
    I think there is a grand flaw that really is a famous flaw thats been going on about claims of scientific methodology for conclusions in things like this.
    I think creationism has a good point here.!

    ReplyDelete
  4. Re: McLatchie's genetic code optimization argument.

    Colin Miller had posted the following response from Claudia Schaffner on facebook:

    "Every "tuning" argument is just an appeal to incredulity surrounded by ever fancier wrapping. His genetic code argument is problematic on several statistic levels besides, but I can't comment on it without being a member of Glasgow skeptics.
    If you want my opinion you can paste this. Even without having the time for the statistical analysis of this statement, it is easy to see it is untrue. All codons are triplets. It is true that if you substitute the third nucleotide in the triplet you will often get the same amino acid, but this redundancy is far from complete and also hardly shows a clear bias towards subsitutions of "related" groups. So for instance Histidine (positive charge, code CAU or CAC)) will change to Glutamine (polar uncharged, code CAA or CAG) with the subsitution of just the third letter. However this concentration on the third letter ignores the fact that mutations are just as likely on the first and second letter of the triplet, and there is very little redundancy there. Change the first or second letter of a triplet and you will likely get a change in aminoacid, with no bias towards similar amino acid "types". Given that mutations in any of the three nucleotides in a codon are equally likely, you get that even when the third nucleotide is totally redundant (which, again, is not the case for all amino acids) there is still a good chance of a single nucleotide subsitution causing an amino acid subsitution, or even a catastrophic STOP codon (UAA, UAG and UGA) that ends the protein at that mutation altogether.
    In short, even with a certain level of redundancy, any claim that the genetic code is "exquisitely tuned" to protect from detrimental effects does not stand up to an even casual analysis of the facts."


    McLatchie further claims:

    "I stand by what I said. Phenylalanine, like leucine, is both hydrophobic and non-polar, which means that it can often substitute for leucine without affecting protein structure and function."


    But Billy had pointed out that the following paper shows how a leucine to phenylalanine substitution in E. coli cysteine tRNA synthetase reduces catalytic activity by a 1000 fold:

    http://www.ncbi.nlm.nih.gov/pubmed/8916927

    ReplyDelete
    Replies
    1. Folk may be interested in this. McLatchie is now going about saying I didn't know how to use the database. This guy is far along the path to the darkside

      Delete
    2. Folk may also be interested in knowing that he is repeating his claim that it's all the fault of the Ensembl database for being inaccurate/misleading in saying that GULOP has a transcript. This was thoroughly hashed out in a previous blog's comments section and it beggars belief that he is STILL making this claim.

      Delete
    3. >>>"In short, even with a certain level of redundancy, any claim that the genetic code is "exquisitely tuned" to protect from detrimental effects does not stand up to an even casual analysis of the facts."<<<

      Is that why a paper just came out attempting to explain this feature of the genetic code? http://rsif.royalsocietypublishing.org/content/10/88/20130614

      From the paper,

      "The genetic code, the mapping of nucleic acid codons to amino acids via a set of tRNA and aminoacylation machinery, is near-universal and near-immutable. In addition, the code is also near-optimal in terms of error minimization, i.e. tRNAs recognizing similar codons may be mistaken for each other during translation, yet these mistakes often have no negative impact on translation because similar codons map to identical amino acids or ones with similar physiochemical properties."

      I also cited two papers above that make the very same point. How about another one? http://genome.cshlp.org/content/17/4/401.full

      "Other striking properties of the code that seem far from random were revealed. Woese observed that similar codons are assigned to amino acids with similar chemical properties, most notably, similar polar requirement (Woese 1965b; Woese et al. 1966a). He proposed that the code is optimized for minimizing the impact of mistranslation errors. These errors occur when a codon is translated via a tRNA with a near cognate anticodon. The finding that the genetic code is optimized with respect to minimizing the impact of translational misread errors was statistically quantified by Haig and Hurst (1991) and further strengthened by taking into account biased mistranslation and mutation (Freeland and Hurst 1998)."

      Delete
    4. >>>"Folk may also be interested in knowing that he is repeating his claim that it's all the fault of the Ensembl database for being inaccurate/misleading in saying that GULOP has a transcript. This was thoroughly hashed out in a previous blog's comments section and it beggars belief that he is STILL making this claim."<<<

      I lost interest in this discussion long ago. It has no relevance to any argument I currently defend.

      Ensembl states clearly with respect to GULOP in humans, "This gene has 1 transcript (splice variant)." This, however, is not confirmed. At best, it is rather misleading.

      I'm not really interested in having this discussion anymore frankly. It's such a trivial matter with no relevance to any of the questions I'm interested in.

      Delete
    5. NO McLatchie, NO. That is not what you wrote. Not ONE of the papers you cited in any way demonstrates the idiotic point you made!

      I asked you to copy and paste your actual words here, and defend them-- or take them back. You wouldn't-- you pussied out. You won't even copy your own words!

      So I have to.

      McLatchie wrote: ""Indeed, the genetic code found in nature is exquisitely tuned to protect the cell from the detrimental effects of substitution mutations. The system is so brilliantly set up that codons differing by only a single base either specify the same amino acid, or an amino acid that is a member of a related chemical group."

      That sir, is a stupid thing to say.

      You have attempted to neuralyze us, Casey Luskin-style, and make us believe you said something else altogether-- that the genetic code was optimized.

      If you had said the genetic code was optimized, there would have been no controversy. But

      NO. That is not what you wrote. Do not try to trick us into re-writing our memories-- it's insulting to our intelligence.

      Delete
    6. McLatchie: "I lost interest in this discussion long ago. It has no relevance to any argument I currently defend."

      We don't care what YOU are interested in!

      You banned four people from your website, and insulted them and personally attacked them! You don't care about that-- so what? Why should we care about what you care about?

      The ENSEMBL database entry said "Transcript not found" and you blamed it for your error.

      Everybody makes mistakes, but if you try to shift the responsibility off on others, and then ban and insult and personally attack and misrepresent the people who taught you how to read the database, it's not the error that bugs us. It's the dishonesty.

      Delete
    7. So you're back, McLatchie, to make more comments after what you yet again promised would be your "last comment." Is it possible for you to even open your mouth without a stream of lies spewing out? Not to say we don't like having you around, of course.

      Let me attempt to explain this to you in a childishly simple manner, so maybe you have at least a chance of understanding. I assume you know what "books" are, correct? And that some of these bigger books, generally long ones with big complicated words, have what are called "indexes." You are familiar with that as well, right?

      Well, now, let suppose you read the "index" of one of these "books" and find an entry that reads:

      Loch Ness Monster, 123

      Now, suppose there is someone who understands how the "index" of a "book" is supposed to be used. She goes to p.123 and finds the following passage: "There is no evidence that the Loch Ness Monster exists."

      However, let's imagine another person who does not know how "books" and "indexes" are supposed to be used, because he is an ignorant, incompetent, idiot. He just sees the entry listing "Loch Ness Monster" then goes on the internet to say that the Loch Ness Monster exists, because this book says it does.

      Now, is this person's claim correct? Does the book say that? And suppose other people on the internet then pointed out his error and, rather than acknowledging his error, he deleted their comments and went on to say the book was to blame for his error because it was "misleading." Would he be speaking truthfully? Would be be correct? Or would he just be further confirming that he is either ignorant, incompetent or a liar, if not some combination of all three?

      Now, if you do not understand how this applies to your actions here, I'm happy to explain that for you, as well.

      Delete
    8. BTW, McLatchie, when you come back you really need to address this:

      Billy wrote:

      Folk may be interested in this. McLatchie is now going about saying I didn't know how to use the database. This guy is far along the path to the darkside


      Do you have any explanation for this blatant lie you are spreading regarding someone who actually educated you on how to use the database?

      Delete
    9. "I lost interest in this discussion long ago. It has no relevance to any argument I currently defend"

      A couple of points here:

      1: the database says there is no supporting evidence. It really does, and Fiona has clearly pointed this out to you. Who do you think you are convincing here?

      2: The issue is now that you are lying about my understanding of the database!

      I can only echo Diogenes with resp[ect to what you actually said in your own quote. You are being dishonest again, and I am happy to have this exposed in as many places as possible

      Delete
    10. @lutesuite

      So you're back, McLatchie, to make more comments after what you yet again promised would be your "last comment."


      "Just the place for a Snark!" the Bellman cried,
      As he landed his crew with care;
      Supporting each man on the top of the tide
      By a finger entwined in his hair.
      "Just the place for a Snark! I have said it twice:
      That alone should encourage the crew.
      Just the place for a Snark! I have said it thrice:
      What I tell you three times is true."

      Delete
    11. @ Billy

      1: the database says there is no supporting evidence. It really does, and Fiona has clearly pointed this out to you. Who do you think you are convincing here?

      If I may, since we're hardly likely to get an honest answer from Habitual Liar for Jesus Jonathan McLatchie: He's not trying to convince anyone here. He just has to convince his fellow sycophantic IDiots at ENV (where no comments are allowed), few if any of whom will be privy to the present discussion. And what he is trying to convince them of is that his embarassing gaffe was not the result of his own laziness in failing to confirm whether GULOP was even transcribed, or his own incompetence in not knowing how to use the database that could have provided him with that information. Rather, he wants to create the impression that his error was not his fault, but that of the database which he claims is misleading and inaccurate. IOW, he want them to continue to believe he is an honest and competent scientist, and not an ignorant, incompetent, Habitual Liar for Jesus.

      Close to the mark, McLatchie?

      Delete
    12. Absolutely lutesuite.
      It's a turn of phrase that he'll understand to mean pretty much as you described :-)

      Delete
    13. Why did I bother Reading MacLatchie's link? Let me quote the bit after his chrry pick "Biochemists have long wondered: if immutability
      and universality were early properties (i.e. the genetic code was a ‘frozen accident’
      [3]), then how could natural selection encourage error minimization?
      If selection for an error-minimizing genetic code predated immutability and
      universality, then why is the standard code less than optimal?"

      This is a side issue to him trying to re-write what was said, but it's fun to point out that a quote mine does not support what he says it does - even if it is not what he is being taken to task over.

      Also notice the word's I've made bold in MacLachie's quote:

      "The genetic code, the mapping of nucleic acid codons to amino acids via a set of tRNA and aminoacylation machinery, is near-universal and near-immutable. In addition, the code is also near-optimal in terms of error minimization, i.e. tRNAs recognizing similar codons may be mistaken for each other during translation, yet these mistakes often have no negative impact on translation because similar codons map to identical amino acids or ones with similar physiochemical properties."

      Of course, whe have already shown there are lots of exceptions to this, and substituting with similar aminoacids can severely affect function.

      He is also citing folk citing other work and not the evidence itself - effectively quotemining an argument from authority out or context.

      Anyway, let's not let him off the hook for his other crimes

      Delete
    14. Mclatchie is quote mining. He leaves out the part that says the code is suboptimal:

      http://rsif.royalsocietypublishing.org/content/10/88/20130614

      "Biochemists have long wondered: If immutability and universality were early properties (i.e. the genetic code was a “frozen accident” [3]), then how could natural selection encourage error-minimization? If selection for an error minimizing genetic code predated immutability and universality, then why is the standard code less than optimal?"

      The authors further clarify:

      "Numerous hypotheses have been proposed to reconcile this apparent paradox [3][4][5][6].
      It has been hypothesized that neutral evolution, for instance through proto-tRNA duplication (also termed “expansion”), could account for the code’s near optimality (though not necessarily its universality) without the need for selection [6][7]. Other models have suggested that the code’s progression might be explained entirely by selection for the best combination of genetic code and genome in a greedy fashion; however, these models are prone to premature freezing, particularly if the genome evolves rapidly [5][8]. Here we introduce an evolutionary model based on information-asymmetric games, which allow for a rich combination of both neutral evolution and selection, leading in combination to the suboptimal yet stable genetic code described above."

      Additionally, Mclatchie is trying to state that substitution by similar amino acids is not a problem:

      "I stand by what I said. Phenylalanine, like leucine, is both hydrophobic and non-polar, which means that it can often substitute for leucine without affecting protein structure and function. You can also change the C in the 5' position to an A or a G, which alters the codon to specify isoleucine and valine respectively, which also have physical and chemical properties similar to leucine."

      But such substitutions can change protein function/activity as these papers show:

      http://www.nrcresearchpress.com/doi/abs/10.1139/g02-080?journalCode=gen#.UkK214bI1VQ
      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC51992/
      http://jvi.asm.org/content/74/2/892.abstract
      http://www.ncbi.nlm.nih.gov/pubmed/11389142
      http://www.malariajournal.com/content/5/1/56
      http://www.ncbi.nlm.nih.gov/pubmed/7538206
      http://www.ncbi.nlm.nih.gov/pubmed/8916927

      Thus, Mclatchie's claim that the code is exquisitely fine tuned (see: http://www.evolutionnews.org/2011/11/the_finely_tuned_genetic_code052611.html) is unfounded to say the least.

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    15. There's one other minor detail, as well. I don't have access to the full paper, but it seems from the abstract they hypothesize a mechanism by which the code could have arisen thru evolutionary processes.

      If so, that paper does not exactly support McLatchie's hypothesis of "goddidit".

      Delete
  5. The whole truth.
    Well me first. I asked first and its about the thread topic and the general forum topic or science and origins and creationism(s).
    Can you tell me what the scientific molecular evidence is that demonstrates modern conclusions about using molecular facts of today can extrapolate back to the past and draw conclusions??
    I don't mean a good hunch but SCIENTIFIC evidence worthy to persuade creationists who are told SCIENCE is being done about evolutionary conclusions.??

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    Replies
    1. I should google to check my facts but since the argument is pointless I won't bother, but as I recall there are ways for physicists to check whether the basic parameter values of their theories have changed over the roughly 14 billion years of this universe (especially their ratio, the alpha constant) and the conclusion is that they have not, with a very small error tolerance. More basically, they see stars forming now in the interstellar dust and the most reasonable hypothesis is that the existing stars formed the same way. The same is true for molecular evolution. This is not a basic flaw in methodology, it is a reasoning method that has worked well.

      Of course, there will always be some gaps for a god to hide in. Without a continuous data record throughout all of time, a god could have snuck in somewhere and fabricated misleading evidence or changed all the rules for a while and then changed them back.

      However, suppose you are on the jury of a murder trial. The accused was found standing over the dead body of an enemy with a smoking gun in his hand. There is one bullet missing from the gun and there is a bullet in the dead man's heart which came from the gun. A paraffin test shows that the accused fired the gun. The defense lawyer says your methodology of extrapolating back to the death is flawed. Physics could have changed between then and now. Advanced aliens could have forced the gun's trigger to squeeze by telekinesis. Do you let the accused go free? This is what you are asking molecular biologists to do.

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    2. byers said:

      "I don't mean a good hunch but SCIENTIFIC evidence worthy to persuade creationists who are told SCIENCE is being done about evolutionary conclusions.??"

      That the scientific evidence doesn't persuade you and other creationists just shows that creationists choose to believe fairy tales over reality. Your willful ignorance and distortions regarding scientific methods and evidence is certainly worthy to persuade rational people that you are just plain nuts.

      You constantly assert that scientists do not use scientific methods and evidence, and especially biological methods and evidence, to study biological evolution. You're wrong. WAY wrong. Many thousands of previous and ongoing scientific studies show just how wrong you are.

      Since scientific, biological methods and evidence matters so much to you, robert, let's see your scientific, biological methods and evidence that supports or better yet verifies anything in the bible. For instance, let's see your scientific, biological methods and evidence that supports or better yet verifies that goats and sheep produce striped and/or spotted offspring by mating while looking at striped sticks.

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    3. Or that locusts use four legs for walking.

      http://jeb.biologists.org/content/58/1/45.full.pdf

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    4. Yeah, it's not the first time he's been caught quote mining, and it wont be the last. I particularly love the one that he copied directly from Harun Yahya mentioned here.

      Delete
  6. http://www.sciencemag.org/content/341/6152/1344.1.full
    Review in Science . Seems FREE!

    ReplyDelete
  7. What IS surprising is that a passage like this demonstrates that the book was not reviewed by anyone who is knowledgeable about the field.

    How could they have gotten anyone truly knowledgeable who (1) would want to review the book in order to help prepare it for publication, and (2) would have left enough of the text post-review to publish?

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