Wednesday, December 1, 2010

Back to School Part VIII

We continue to examine the work of authors George Johnson and Jonathan Losos in their biology textbook, The Living World ((Fifth Edition, McGraw Hill, 2008). In their chapter on evolution and natural selection, these accomplished evolutionists begin by (1) misrepresenting the relationship between microevolution and macroevolution and biological variation here, (2) making a non scientific, metaphysical, truth claim that just happens to mandate the truth of evolution here, (3) making the grossly false statement that the fossils themselves are a factual observation that macroevolution has occurred here and here, (4) making a series of misrepresentations by carefully selecting the evidence to provide to the student and protecting it with circular reasoning here, (5) misrepresenting the molecular evidence here, (6) presenting the student with a blatantly false history of evolutionary theory here, (7) introducing the usual if-and-only-if evolutionary reasoning here, and (8) repeating the centuries old religious argument that bad design proves evolution here.

Johnson and Losos’ next move is to make the erroneous, yet typical, argument that evolution is not improbable by manipulating statistics. The old joke that there are lies, damn lies, and then there are statistics is fully exemplified in the evolutionist’s pretzel logic. Here is what they write, first presenting an argument that evolution is improbable and then responding to it:

Proteins are too improbable. “Hemoglobin has 141 amino acids. The probability that the first one would be leucine is 1/20, and that all 141 would be the ones they are by chance is (1/20)^141, an impossibly rare event.” You cannot use probability to argue backward. The probability that a student in a classroom has a particular birthday is 1/365; arguing this way, the probability that everyone in a class of 50 would have the birthdays they do is (1/365)^50, and yet there the class sits. [302]

Those who are unfamiliar with the evolution genre don’t realize how badly evolution has damaged science. Here we have an example. Remember that Johnson and Losos are professors at leading universities (Washington University and Harvard University, respectively). And remember that the text was reviewed by a small army of evolutionists.

Yet this silly argument that Johnson and Losos present cannot even fool young biology students. Their analogy is, of course, ludicrous. The amino acid sequence folds up into a phenomenal molecular machine whereas a list of birthdays is, well, a list of birthdays.

And what does this molecular blueprint produce? The hemoglobin blood protein carries carbon dioxide to the lungs where it is exposed to inhaled air across a gas-permeable membrane. Here the blood and air trade oxygen for carbon dioxide and the replenished blood is drawn back to the heart to begin another cycle.

Hemoglobin is a complex of four similar proteins attached together. When the blood passes by the lungs it picks up oxygen molecules from the air. But the blood can hold only so much oxygen—while it gains oxygen atoms from the air it also loses oxygen atoms to the air. Hemoglobin solves this problem. It binds the oxygen so it cannot escape back to the air. The result is the blood can carry much more oxygen.

When the blood then moves on to the various parts of the body the hemoglobin molecules unload the oxygen where needed. But time is of the essence and as hemoglobin loads and unloads oxygen it must do so quickly. Consider a dump truck carrying a load of dirt. The truck would be practically worthless if it couldn’t tilt up its box to quickly dump the dirt. Likewise, as the hemoglobin passes by the lung there is little time to load its complement of oxygen, and as it passes by an oxygen-starved muscle there is little time to unload the oxygen.

Hemoglobin speeds things up via small, clever changes in its structure. Small conformational changes in this amazing protein make hemoglobin a quick oxygen loader and unloader.

Amazingly evolutionists think hemoglobin’s special amino acid sequence encoding for this machine is no different than any random list, such a list of birthdays. To be sensible Johnson’s and Losos’ analogy would need the list of birthdays to provide something fantastic, such as the answers to the biology class final exam.

And how special is hemoglobin’s amino acid sequence? It is a research question, but what science is telling us is that not very many different sequences encode for proteins such as hemoglobin. Of the 20^141 (a 1 with more than 180 zeros trailing it) total number of sequences, those that lead to a functional hemoglobin protein—or any functional protein for that matter—is tiny. Intermediates are hard to come by, and most proteins are much longer than hemoglobin. The odds of evolution finding these wonders involve numbers with hundreds of zeros—literally astronomical long shots.

The evolutionist’s analogy between protein sequences and random lists signifying nothing, such as a list of birthdays, is absurd. It is another example of evolution’s undermining of science. Religion drives science, and it matters.

50 comments:

  1. Cornelius Hunter:

    "And remember that the text was reviewed by a small army of evolutionists."
    ====

    Not surprising since it's the religious hierarchy in any organization/group who controls the approved academic cirriculum to establish a comfortable following which hopefully ensures the dogma's entrenched future.

    Hence the correct term here should be "Peer Approved". But again, this shouldn't surprise anyone.
    -----

    Cornelius Hunter:

    "Yet this silly argument that Johnson and Losos present cannot even fool young biology students."
    =====

    Hmmmmmmmmmm, I'm not so sure. When I toured many of the universities and even community colleges around the state of California in the 1990s, I found very few students interested in actual deep thinking and study. At least for the average spoiled American bred brat, being a campus party animal was first on the agenda, for which I'm sure many of the present contributors here can attest to. However there were a few who took it seriously, but the majority not.

    The one acception were the Asian students who always had their noses in a book before, between and after classes when the natives used free time for screwing around. Though for most of those Asians kids, the number one focus was almost always attributing real success with how much money you'd be making later on. Guess there are pros & cons to every culture. Still I saw some African American students (with terrible backgrounds) who worked hard and struggled out of a passion for the joy of learning and a deep and sincere interest in what they were learning and that was satisying to see. Unfortunately such academic highlights as these are rarely magnified and held up as examples.

    So it's hard to say what the modern student actually thinks anymore, especially since the internet distractions are far more intense than they were back then.

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  3. Cornelius Hunter: Of the 20^141 (a 1 with more than 180 zeros trailing it) total number of sequences, those that lead to a functional hemoglobin protein—or any functional protein for that matter—is tiny.

    Keefe & Szostak, Functional proteins from a random-sequence library, Nature 2001: The frequency of occurrence of functional proteins in random-sequence libraries appears to be similar to that observed for equivalent RNA libraries {roughly 1 in 10^11}.

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  4. DNA sequencing supports a long evolutionary history for hemoglobins. There are hemoglobins in bactera, nematodes, plants and fungi, as well as in insects and vertebrates*. So, what we have today in human hemoglobin did not have to arise de novo, by the random assortment of amino acids. Instead, as the theory of evolution would predict, what we have today seems to have been produced over eons of time by stepwise changes.

    This supports the textbook authors' quoted proposition:

    You cannot use probability to argue backward.
    ------
    *See: R C Hardison, A brief history of hemoglobins: plant, animal, protist, and bacteria.

    Proc Natl Acad Sci U S A. 1996 June 11; 93(12): 5675–5679

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  5. "Of the 20^141 (a 1 with more than 180 zeros trailing it) total number of sequences, those that lead to a functional hemoglobin protein—or any functional protein for that matter—is tiny."

    And here is the teapot:

    for the darwinist, everything is just fine as long as they can believe the number of functional sequences to be just so small that any won't be found in the laboratory, but still big enough, so that 10^40 living organisms would be just enough to find plenty of them.

    Of course it wouldn't be a problem for the darwinist if some complex protein would be found from a random sequence library, but certainly the current lack of empirical support doesn't seem to disturb them.

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  6. Do you consider that the difference in the sequence of hemoglobin between human and chimp cannot be explained by natural mechanisms?

    If not, why?

    At which moment during evolution you consider that the sequence of hemoglobin changed so much that it could not be explained by natural mechanisms?

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  7. Cornelius Hunter said...

    And how special is hemoglobin’s amino acid sequence? It is a research question, but what science is telling us is that not very many different sequences encode for proteins such as hemoglobin. Of the 20^141 (a 1 with more than 180 zeros trailing it) total number of sequences, those that lead to a functional hemoglobin protein—or any functional protein for that matter—is tiny. Intermediates are hard to come by, and most proteins are much longer than hemoglobin. The odds of evolution finding these wonders involve numbers with hundreds of zeros—literally astronomical long shots.


    We'll add probability theory to the long list of things CH writes about but is incompetent in.

    The 1 in 20^141 number is only valid in the case of all 141 being present at the start and then spontaneous assembling. No competent scientist thinks or says that is the case.

    Pay attention Cornelius, this is important:

    You can't calculate the probability of a long term iterative process by taking a one-time snapshot of the results. You have to take into account the history and the mechanisms of the process to even make an educated guess.

    Suppose you walk into a room where you are told people are playing poker. You see me holding a royal straight flush. What is the probability of that? Being CH you quickly calculate the odds I was dealt that in one hand as 649,739 to 1. But what if I was playing draw poker and had 3 discards and redraws? Now the odds aren't so bad. What if the rules of the game allowed for me to discard and draw indefinitely until I was satisfied? Due to the power of cumulative selection, now the probability is approaching 1.

    You can't calculate the probability of a long term iterative process by taking a one-time snapshot of the results.

    But I'll bet this goes right over CH's head just like all the other technical things he misunderstands.

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  8. Thornton, how would you select the 3 discards?

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  9. 20^141 (a 1 with more than 180 zeros trailing it)

    umm, no: that is a number with 183 digits, of which only the last 141 are zeros. And the first digit is a 2...

    Of course it is bigger than a 1 with 180 zeros trailing it, but not every big number consists from only zeros and a lonely 1!

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  11. Besides that the 20^141 critiques something other than evolution, how did Hunter arrive at this number?

    This calculation would say 141 residues are REQUIRED for hemoglobin? Are you sure Dr. Hunter? Is the empirical data in your favor?

    So, which sequence from what species did Hunter choose? I guess human, so which of the human hemoglobin variants did he choose? Oh, and which of the 1500 or so functional polymorphs was selected? I bet my hemoglobin isn't the same as yours!

    Besides that, biochemists know of so many heme-binding globins of diverse sequence, some with truncations at either end, or in the middle. So lets take a 15% identity over 100 residues, and apply your calculation. I get (20^15=3X10^19)* for the globin fold. This ignores the symmetry of globin, suggesting it is a product of gene duplication and fusion of a smaller functional unit, that might only obligately require 7 residues (20^7=1X10^9). Considering there are an estimated 5 million trillion trillion (5 with 30 zeros) bacteria on earth (and lets keep this number for pre-O2 earth), with a conservative mutation rate of 10^-10 per base per generation, you want to tell me this is impossible? Add a few His, and you've got heme binding.

    I thought Hunter had a Ph.D. related to protein folding, yet he's never read the classic Ala-scan papers showing how many residues it take to make a fold? No familiarity with computational Ala-scans? No sense that there the heme-binding globins are an enormous family with incredible plasticity?

    No familiarity with the selection of heme binders from four-helix bundle libraries, or random peptide libraries?

    And for goodness sake, I still can't believe he made the tornado in a junkyard calculation.

    * dispensing with the 1 over for X convenience.

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  12. A quick bit of Googling reveals lots of interesting research into the evolution of proteins. From here for example:

    We report x-ray crystal structures of a resurrected ancestral protein—the ∼450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. “Permissive” mutations—substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes—played a major role in determining GR's evolutionary trajectory.

    The take home message is that proteins have evolutionary histories. They don't just pop into existence, but evolve new functions gradually over time (I know, I know, it's all metaphysics!).

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  13. "The take home message is that proteins have evolutionary histories. They don't just pop into existence, but evolve new functions gradually over time."

    It is a particularly odd feature of the creationist mindset to hold up a modern structure, proclaim it must have been created at once at impossible odds, and declare evolution dead!

    Take the massive protein Titin. 33,000 amino acids. 20^33,000? Or do we know it is built up of small IgG and Fibronectin repeats, themselves built up of smaller motifs (greek key beta sheets)?

    So what is the cFSCI (or whatever) of a simple motif, say the Walker A nucleotide binding motif: GXXXXGK(T/S)?

    And why is it nature shows such tinkering, and modular building? Why are domains constrained to only a few hundred amino acids? Why aren't there any novel protein folds in humans (or even multicellular life, as far as I know?) Why the abundance of repeat proteins? Was the designer constrained, or just not creative? Evolution embraces and explains the constraints on molecular evolution, while design grasps at straws.

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  14. 'Unique' ORFan Genes Challenge Common Descent - Paul Nelson - video - short version
    http://vimeo.com/17135166

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  15. Zach:"Keefe & Szostak, Functional proteins from a random-sequence library, Nature 2001: The frequency of occurrence of functional proteins in random-sequence libraries appears to be similar to that observed for equivalent RNA libraries {roughly 1 in 10^11}."

    Then, similarities between proteins or genes are not prove of Common Descent, as each similar protein could start from similar proteins of the library and the follow convergent evolution.

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  16. Zachriel:

    ===
    Keefe & Szostak, Functional proteins from a random-sequence library, Nature 2001: The frequency of occurrence of functional proteins in random-sequence libraries appears to be similar to that observed for equivalent RNA libraries {roughly 1 in 10^11}.
    ===

    No, 10^12, but who's counting. What matters is that Keefe & Szostak screened for ATP binding. Comparing that to hemoglobin function would be like comparing a tricycle to a jet plane.





    Pedant:

    ======
    DNA sequencing supports a long evolutionary history for hemoglobins. There are hemoglobins in bactera, nematodes, plants and fungi, as well as in insects and vertebrates*. So, what we have today in human hemoglobin did not have to arise de novo, by the random assortment of amino acids. Instead, as the theory of evolution would predict, what we have today seems to have been produced over eons of time by stepwise changes.

    This supports the textbook authors' quoted proposition:

    You cannot use probability to argue backward.
    ------
    *See: R C Hardison, A brief history of hemoglobins: plant, animal, protist, and bacteria.

    Proc Natl Acad Sci U S A. 1996 June 11; 93(12): 5675–5679
    ======

    It is astonishing how evolutionists will twist science. This would be like comparing a line of jet aircraft that have only minor differences, and concluding they therefore evolved via "stepwise changes."




    Charles:

    ====
    Do you consider that the difference in the sequence of hemoglobin between human and chimp cannot be explained by natural mechanisms?
    ===

    No, I know of nothing that cannot be explained by natural mechanisms. Just look at the evolution literature for endless examples of heroic mechanisms that can do just about anything.

    ===
    At which moment during evolution you consider that the sequence of hemoglobin changed so much that it could not be explained by natural mechanisms?
    ===

    Again, the creation of a globin chain (~140 amino acid residues), or any other protein for that matter, or anything else at all for that matter, can easily be explained by evolutionists. Humanity has an astonishing myth-making capability.

    If you're asking at which moment during evolution is the origin of a globin chain unlikely, that would be from the very first moment until you have the first complete, functional, globin chain. Of course we can go beyond that--the silliness doesn't end there. But that's a good starting point. Evolution is not motivated by science.





    RobertC:

    ===
    Besides that the 20^141 critiques something other than evolution, how did Hunter arrive at this number?
    ===

    Math. 20^141 = the number of different possible combinations when you have 20 types of items taken 141 times (with replacement of course).




    Norm Olsen:


    ===
    The take home message is that proteins have evolutionary histories. They don't just pop into existence, but evolve new functions gradually over time (I know, I know, it's all metaphysics!).
    ===

    See response to Pedant above.




    RobertC:

    ===
    It is a particularly odd feature of the creationist mindset to hold up a modern structure, proclaim it must have been created at once at impossible odds, and declare evolution dead!
    ===

    Beyond unscientific speculation we have no idea how these modern structures arose, but so what? We all know they must have. Those silly creationists again ... So long as we have such convenient foils--who we can blame for everything--then we can continue telling ourselves lies.

    Folks, the key to maintaining an absurdity is first to have an enemy.

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  17. Cornelius states:"The odds of evolution finding these wonders involve numbers with hundreds of zeros—literally astronomical long shots."

    Yet, this is at odds with his later claim, that "[b]eyond unscientific speculation we have no idea how these modern structures arose."

    It follows that the first statement must fall into the category of 'unscientific speculation'.

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  18. ===
    RobertC: Besides that the 20^141 critiques something other than evolution, how did Hunter arrive at this number?
    ===

    CH: . 20^141 = the number of different possible combinations when you have 20 types of items taken 141 times (with replacement of course).
    ++++++++++
    No crap.
    Thanks for reading only the first line of my post. I think it is indicative of how you choose to approach this blog, the literature and comprehension in general! Care to respond to the rest of the post?

    +++++++
    " What matters is that Keefe & Szostak screened for ATP binding. Comparing that to hemoglobin function would be like comparing a tricycle to a jet plane."

    ATP=Tricycle, Heme=Jet plane? How, in complexity? Lol. Biochem 101? Here you again ignore the actual argument made again. No one is saying an ATP binder is ATP synthase, or a Heme binder is hemoglobin. They are saying small functional bits are easily evolved. Then follow gene duplication, recombination and divergence, which are observed and historically tractable (to an extent).

    This renders the 'poof' calculation meaningless.

    "Beyond unscientific speculation we have no idea how these modern structures arose" should be corrected to "beyond increasingly well evidenced and testable hypotheses......" Cornelius just wants to make sure you ignore the motifs and domains, the signatures of evolution, and go 'gee whiz' those structures look real complex!

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  19. Cornelius, note also that in the paper I cited above, the researchers identified the specific sequence of mutations required to get from one protein to another. This is the kind of detail that IDists/creationists are always shouting for.

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  20. A truly pathetic OP. Smearing once again Johnson & Logos and repeating the beyond silly tornado in the junkyard fallacy.

    On top of that, ignoring nearly all of RobertC's well-informed rebuttal.

    All lingering doubt I had about Cornelius' dishonesty has been thoroughly trampled in this thread.

    And as usual Cornelius offers no alternative to evolution with more explanatory power. No wonder he's stuck at a biblical propaganda institute with zero impact on science.

    Bah.

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  21. Blas: Then, similarities between proteins or genes are not prove of Common Descent, as each similar protein could start from similar proteins of the library and the follow convergent evolution.

    Not just a similarity, but a nested hierarchy.

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  22. Cornelius Hunter: Of the 20^141 (a 1 with more than 180 zeros trailing it) total number of sequences, those that lead to a functional hemoglobin protein—or any functional protein for that matter—is tiny.

    Zachriel: Keefe & Szostak

    Cornelius Hunter: What matters is that Keefe & Szostak screened for ATP binding. Comparing that to hemoglobin function would be like comparing a tricycle to a jet plane.

    Did you forget? Your claim concerned "any functional protein". In any case, more complex molecules are posited to have evolved from primitive versions, so the calculation is irrelevant.

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  23. Zach:"Not just a similarity, but a nested hierarchy."

    But also nested hierarchy could be produced by a poliphyletic tree of life. So Common Descent is just an explanation unless you have other overhelming proofs

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  24. "So Common Descent is just an explanation "

    Just an explanation means a lot in science, when it is unfalsified and most parsimonious.

    Take the globin family, as one example. We could say all the independent polyphlya arose/were created with the same fold to deal with heme binding (despite that others will and have been demonstrated to do quite nicely). Moreover, their individual proteins are related in sequence in a manner that gives the exact appearance of common ancestry--descent with modification--down to the conservation of flanking phage insertions in prokaryotes, or intron/exon boundries in Eukaryotes.

    We could say these things, but why?

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  25. troy:

    ===
    A truly pathetic OP. Smearing once again Johnson & Logos and repeating the beyond silly tornado in the junkyard fallacy.
    ===

    Even with a clear, obvious logical fallacy as Johnson & Losos make here, evolutionists will not back down an inch. I explained that the globin sequence and a random list of birthdays are not analogous. If I am wrong, then evolutionists can simply explain why and I'll edit or retract the OP.

    ===
    On top of that, ignoring nearly all of RobertC's well-informed rebuttal.

    All lingering doubt I had about Cornelius' dishonesty has been thoroughly trampled in this thread.
    ===

    I didn't see a "well-informed" rebuttal. But we need not argue. Since you are a life science professor, this should be simple. Please just explain to us how the first globin chain evolved. There must have been a series of intermediates, correct? How long was the first one? one residue? two? 5, 10? What was the function? How was it that evolution produced an ever longer chain? What new functionalities emerged? About how many different intermediates were there? If multiple residues were added at a time, how was that done?

    Or did the globin arise from gene duplication and mutation? If so, how was it that evolution constructed a world where such a creation machine just happened to arise? And what was the series of proteins that finally culminated in the globin? I can think of a couple of examples, but the mutations required are again extremely low probability. And where did all this start? What was the first protein that started this domino effect, and how did it arise?

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  26. I loved the Szostak study because it shows how rare something as simple as even getting one stable chemical bond can be. Imagine how the chances plummet when it actually has to convert energy into motions that are significant in the context of its particular cellular environment?

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  28. RobertC:

    ===
    So lets take a 15% identity over 100 residues, and apply your calculation. I get (20^15=3X10^19)
    ===

    No, this is an evolutionary corruption of science. 15% identity does not mean 85% of the residues can be anything and 15% need to be a particular residue. Your 10^19 value is too liberal. We don't have hard numbers, but the science is indicating there is not a great deal of flexibility in protein sequences. Yes, you can have as little as 15% (or less) sequence identity and still have the same fold and function, but that does *not* mean the other 85% of the sequence is unrestricted.

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  29. In order for on protein to evolve into another, how many amino acids do you have to change? And will the intemediaries serve some function?
    Don't these question have to be addressed?

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  30. Nat - did you read the paper Norm linked to?

    There are indeed attempts to do precisely these things. At a certain point the people on your side of the fence really need to provide some positive evidence for their positions too, rather than pointing to gaps in knowledge.

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  32. "Your 10^19 value is too liberal."

    I'd argue it is too conservative, demanding that because the globin fold became used in evolution for this purpose, it had to be the globin fold. Four helix bundles, an OB fold. etc., could have perhaps done the trick. Contingency. Who knows, but arguing probability from 1 result without knowing all possibilities or pathways is silly.

    Nevertheless, it sets a lower bound for globins, taking only the conserved residues. Scanning mutagenesis and computational approaches puts it somewhere in the 30% alterable range, instead of 15%. Nevertheless, we've lost something like 160 zeros in between.

    At any rate, it is better thought out than the dishonesty your 20^140 is, where you assume EVERY residue is absolutely fixed, unable to be lost or changed without function. How can a physical biochemist argue all residues in a protein are essential for function, and unalterable, when there are classic mutagenesis studies, and the residues aren't even conserved among humans?? Seriously, you led with absolute dishonesty!

    The real point is that these calculations ignore potential evolutionary pathways-such as the formation of the globin fold from duplication of a precursor. I say potential, since the relics of the actual pathways of ancient fold formation are likely lost to history. We can suggest mechanisms, recapitulate them in the lab, but we probably won't know for certain what the actual historical mechanism was.

    You know this, but of course go on a JoeG like petulant rant demanding details that are not known, and will not be known.

    Or perhaps you and natchuster actually want to learn, in which case:

    Suggested mechanisms include those presented in "Evolution After Gene Duplication" Chapter 7.

    For more recent gene emergence, and tractable studies on the emergence of genes, see: "THE ORIGIN OF NEW GENES: GLIMPSES FROM THE YOUNG AND OLD" NATURE REVIEW NATURE REVIEWS GENETICS (4 )| NOVEMBER 2003

    Or a few empirical study of the evolution and conversion of folds can be found here: fold:http://www.pnas.org/content/105/8/2759.long

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  33. By the way, design does not escape from the demand for detail. It is a misguided assumption, not a mechanism. How and when was the first globin gene designed? How long was the first one? one residue? two? 5, 10? What was the function it was designed for? When were new functionalities designed? About how many different intermediates did the designer employ? Why did the designer employ apparent intermediates? Why stick strictly with the globin fold? Why alter residues in a manner that exactly correlates with evolutionists' ideas on phylogeny, giving the appearance of a nested hierarchy, conserving even introns, flanking phages, etc.? Why were humans designed with 1500 different hemoglobins, including deleterious ones?

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  34. Hey look, it's Gary the cowardly little lap dog doing his weekly drive-by, right on schedule!

    Yip yip yip yip yip yip! goes the mean little puppy!

    Gary-puppy, are you ever going to show us that disproof of ToE by equations from statistical mechanics you claimed to have? People are going to think you were lying about it.

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  35. Blas: But also nested hierarchy could be produced by a poliphyletic tree of life. So Common Descent is just an explanation unless you have other overhelming proofs

    No, you wouldn't expect a nested hierarchy from polyphyly. You might expect convergence, but differences, if any, would not tend to form a nested hierarchy. If there were several distinct origins, then you would see disconnected trees, or a forest.

    John: Imagine how the chances plummet when it actually has to convert energy into motions that are significant in the context of its particular cellular environment

    It's called evolution. Citing the Szostak study just answered Cornelius Hunter's specific claim.

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  36. Paul:

    ===
    Cornelius says:"I explained that the globin sequence and a random list of birthdays are not analogous."

    In saying this, you have missed the authors' point, which is a general one about probabilities of specified versus non-specified events (probably the very reason they chose birthdays), and not about how birthdays and peptides compare.
    ===

    No, I'm not the one missing the point. Let me try another explanation. Imagine finding a list of apparently random numbers. You later find out that it is actually a list of all of the answers, in order, to the biology final exam. You tell me about it, and I explain that this is just a coincidence, and not at all a surprise because, after all, those particular numbers on the list are of exactly equal probability as any other set of numbers that might have been on the list. I assure you there was no cheating, that list was indeed just a set of unrelated numbers that *happened* to match the answers on the exam.

    You would immediately realize something is fishy. You'd probably figure it out that I was, in fact, the cheater and am now just trying to hide my tracks. You'd realize this because, while I may in fact be correct that the list was a set of unrelated numbers, I was most definitely incorrect that this is obvious. It is not at all obvious, and my explanation that it is simply raises questions about my motives.

    We can argue about whether it is a fact, or even just likely, that evolution would just happen to create thousands and thousands of proteins with sequences that occupy narrow subspaces in the astronomical sequence space. It is an argument that evolutionists do not fare well in, but they can try.

    But there is no rational argument about the evolutionary claim that the protein sequences are no different than any list of random numbers.



    ===
    You fail to make this distinction yourself when you state "[t]he odds of evolution finding these wonders involve numbers with hundreds of zeros—literally astronomical long shots", a further demonstration that you have not followed the point the authors are making. What is the basis for this estimation?
    ===

    I assume you are asking me what is the basis for the estimate that the odds are long of evolution finding protein sequences. The basis is primarily two findings. First, that proteins are not robust to a large number of random changes. There are many changes one can make to a protein sequence and have it still work, but these many changes are tiny in comparison to the entire sequence space. So just luckily hitting on a globin sequence, let along thousands of other proteins, is out of the question. Second, that there do not exist many intermediates for a typical protein, such as a globin. You don't find a sequence of ever growing sequences providing some needed function, leading finally to the full globin protein. These two findings together do not bode well for evolutionary explanations.

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  37. Cornelius,
    "Amazingly evolutionists think hemoglobin’s special amino acid sequence encoding for this machine is no different than any random list, such a list of birthdays. To be sensible Johnson’s and Losos’ analogy would need the list of birthdays to provide something fantastic, such as the answers to the biology class final exam."

    By assuming that the list of birthdays has no function you are excluding all the other functions of that list that have not been identified or even conceived yet. Hence you are making a metaphysical claim. Religion drives anti-science rhetoric and it matters.

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  38. Cornelius Hunter said...

    No, I'm not the one missing the point. Let me try another explanation. Imagine finding a list of apparently random numbers. You later find out that it is actually a list of all of the answers, in order, to the biology final exam. You tell me about it, and I explain that this is just a coincidence, and not at all a surprise because, after all, those particular numbers on the list are of exactly equal probability as any other set of numbers that might have been on the list. I assure you there was no cheating, that list was indeed just a set of unrelated numbers that *happened* to match the answers on the exam.


    So show us your big list of proteins that *happens* to matche the ones we see in nature now. Demonstrate that the proteins we see now are the only possible ones that will support life.

    I assume you are asking me what is the basis for the estimate that the odds are long of evolution finding protein sequences. The basis is primarily two findings. First, that proteins are not robust to a large number of random changes. There are many changes one can make to a protein sequence and have it still work, but these many changes are tiny in comparison to the entire sequence space. So just luckily hitting on a globin sequence, let along thousands of other proteins, is out of the question.

    As expected, you are too confused/dim/dishonest to understand basic probability theory. You're still pushing the sad old canard that the proteins had to spontaneously assemble instead of being the end result of a long iterative selection-filtered process. Pathetic.

    Second, that there do not exist many intermediates for a typical protein, such as a globin. You don't find a sequence of ever growing sequences providing some needed function, leading finally to the full globin protein.

    How many of your great-great-great-great grandparents are still alive CH? Why would you expect all the intermediate forms that existed millions of years ago to still be present?

    I guess it's lucky your salary doesn't require you to do any actual scientific work. You'd be living in a cardboard box under the bridge.

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  39. Cornelius says:"I assume you are asking me what is the basis for the estimate that the odds are long of evolution finding protein sequences."

    From my subsequent paragraph, it was quite clear that I asked that in light of another point that you made in this thread - namely that we only have unscientific speculation as to the origins of modern proteins.

    Despite this, you claim a broad but semi-quantitative probability for "evolution" to have created these proteins. Your own words in this thread says this cannot be done!

    "These two findings together do not bode well for evolutionary explanations. "

    And yet, not 'boding well' does not constitute the basis for a quantitative claim, so you didn't even answer the part of my post that you addressed.

    Cornelius also says:"Let me try another explanation. Imagine finding a list of apparently random numbers. You later find out that it is actually a list of all of the answers, in order, to the biology final exam. You tell me about it, and I explain that this is just a coincidence, and not at all a surprise because, after all, those particular numbers on the list are of exactly equal probability as any other set of numbers that might have been on the list. I assure you there was no cheating, that list was indeed just a set of unrelated numbers that *happened* to match the answers on the exam."

    So you answer what you claim to be a bad analogy with a far worse analogy? In this analogy you commit the very same fallacy you made earlier.

    In a biology exam where the answer is a set of numbers (lets say a multichoice test, where the options are numbered) there is a prespecified and exact set of answers. In a protein - in biology itself - there is absolutely no such thing and that is the difference between your 'cheating' example and the 'birthday' example. You've used a series of very similar, flawed examples that continue to demonstrate that you are attacking a strawman.

    You repeat the fallacy by stating "[w]e can argue about whether it is a fact, or even just likely, that evolution would just happen to create thousands and thousands of proteins with sequences that occupy narrow subspaces in the astronomical sequence space. It is an argument that evolutionists do not fare well in, but they can try." The point you consistently fail to consider is that 'evolution' didn't have to go down the path it has. You are talking about these events as necessities ("So just luckily hitting on a globin sequence, let along thousands of other proteins, is out of the question"). They are demonstrably not necessities because life existed before them. You are taking contingencies and turning them into explicitly prespecified necessities.

    You would be better off addressing the paper that Norm cited and I re-linked to for Natschuster. There, the evolutionary sequence is reconstructed, intermediates and functions examined i.e. effectively what you claim above doesn't happen.

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  40. First, that proteins are not robust to a large number of random changes. There are many changes one can make to a protein sequence and have it still work, but these many changes are tiny in comparison to the entire sequence space.

    For the record, either Cornelius knows nothing about the statistical data on the relationship between structure and sequence similarity (a lot more literature about it) or 80% is not a large number for him... or he lied, but let's not consider that.

    Yes, sequence space is ginormous, but structure space is a lot smaller, so proteins can change aa sequence a lot and still preserve much of their structure.

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  41. nanobot74 - LOL, that was superb!

    I wonder if Cornelius will actually address your point, or will he simply ignore it, as he usually does when people point out the blindly flaws in his logic?

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  42. I see Cornelius has put up a new post, so that'll be the last of him here, most likely, once again leaving his numerous errors and fallacies unaddressed.

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  43. Yes Paul, the Gish Gallop strikes again.

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  44. I'm starting to think Biola imposes a monthly quota of stupid anti-science articles on CH, so he's just posting to keep his job. It would explain the zero research he does and almost zero though he puts into this drivel.

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  45. @Thorton

    I'm not so sure about that. Less prolific creationist writers manage to do just as little research as CH.

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  46. Zach:"No, you wouldn't expect a nested hierarchy from polyphyly. You might expect convergence, but differences, if any, would not tend to form a nested hierarchy."

    No, what you can say is polyphyly would not NECESSARILLY tend to form a nested hierarchy"

    "If there were several distinct origins, then you would see disconnected trees, or a forest."

    And it is what we see in the nature, because the junction are drawed by darwinist assuming the common ancestor.

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  47. Blas: No, what you can say is polyphyly would not NECESSARILLY tend to form a nested hierarchy

    with organic beings we should bear in mind that the form of each depends on an infinitude of complex relations, namely on the variations which have arisen, these being due to causes far too intricate to be followed out--on the nature of the variations which have been preserved or selected, and this depends on the surrounding physical conditions, and in a still higher degree on the surrounding organisms with which each being has come into competition--and lastly, on inheritance (in itself a fluctuating element) from innumerable progenitors, all of which have had their forms determined through equally complex relations. It is incredible that the descendants of two organisms, which had originally differed in a marked manner, should ever afterwards converge so closely as to lead to a near approach to identity throughout their whole organisation. If this had occurred, we should meet with the same form, independently of genetic connection, recurring in widely separated geological formations; and the balance of evidence is opposed to any such an admission. — Darwin 1872.

    You really need to try and keep up on the scientific literature.

    Blas: And it is what we see in the nature, because the junction are drawed by darwinist assuming the common ancestor.

    You seem to have lost track of your own claim, which doesn't concern any particular phylogeny.

    Blas: But also nested hierarchy could be produced by a poliphyletic tree of life. So Common Descent is just an explanation unless you have other overhelming proofs.

    No. A single nested hierarchy is not expected from polyphyly.

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