Wednesday, January 18, 2017

Pyruvate dehydrogenase astonishes Ann Gauger

Ann Gauger was reading a cell paper the other day [Digging Deep in Biology: "Things Get Even More Complicated When You Look Closer"]. The subject was the localization of citric acid cycle enzymes and pyruvate dehydrogenase (PDH). She did a little digging and this is what astonished her ...

... so I looked up pyruvate dehydrogenase and found to my astonishment that it is not one enzyme but an enormous complex of three different enzymatic activities clustered together on a cube-shaped core of 24 units, or alternatively a dodecahedral core of 60 units. The enzymes work together to turn pyruvate into acetyl CoA in a three-step process, handing off to each other as the reaction proceeds.
Theme
Pyruvate Dehydrogenase
Ann Gauger has a B.S. in biology and a Ph.D. in developmental biology (1989). I can understand how she might have forgotten details about biochemistry and metabolism but I'm sure that at one point she was taught correctly. The idea that she would be "astonished" at the structure and function of pyruvate dehydrogenase is itself astonishing. It's described in all the biochemistry textbooks. You may have forgotten what you learned but surely a memory jog doesn't count as "astonishment"?

Ann Gauger is an Intelligent Design Creationist who thinks that God created Adam and Eve. From her perspective, the most astonishing thing about her discovery is not that this is common knowledge among today's undergraduates but that she can spin it into support for her creationist views.
Let me emphasize: this is a core enzymatic activity. The TCA cycle is important to the process by which cells make ATP, the energy currency of the cell. PDH is the link that connects glycolysis, the breakdown of sugars, to the TCA cycle. Without it cells would obtain much less energy from the breakdown of sugars. But it is also essential for embryonic development past the two- to four-cell stage (in mice and humans, and presumably other mammals).

It's also essential for bacteria like E. coli, where it has a similar structure and three-step reaction. This is an ancient enzyme complex, yet of great sophistication.

How could early cells have assembled such a structure, bringing together separate enzyme activities to work cooperatively? Getting enzymes to assemble into multi-subunit structures is non-trivial, requiring multiple side-chain interactions and three-dimensional fit. Even further, the genes encoding these enzymatic activities of the PDH complex are clustered together into a single operon in E. coli. They are neighbors, side-by-side in E. coli's genome, and co-expressed. Of course, that's how an intelligent designer would do it. What's the use of part of a complex? Make the enzymes together and assemble them into a factory to turn pyruvate into acetyl CoA -- it's much more efficient.
She tells us in the update on her post that she checked a biochemistry textbook after writing this so at least she's done a bit of after-the-fact checking. But normally a scientist does a bit more research before advancing a claim as radical as the one she advances; namely, that there's no evolutionary explanation for pyruvate dehydrogenase.

Let's look at another textbook to see if there are any clues that might have helped her.1
A similar pyruvate dehydrogenase complex is present in many species of bacteria although some, such as gram-negative bacteria, have a smaller version where there are only 24 E2 enzymes in the core. In these bacteria, the core enzymes are arranged as a cube with one trimer at each of the eight vertices. The E2 subunits of the two different bacterial enzymes and the eukaryotic mitochondrial and chloroplast versions are all closely related. However, the gram-negative bacterial enzymes contain E1 enzymes that are unrelated to the eukaryotic versions.

Pyruvate dehydrogenase is a member of a family of multienzyme complexes known as the 2-oxo acid dehydrogenase family. (Pyruvate is the smallest 2-oxo organic acid.) We will encounter two other 2-oxo (or α-keto) acid dehydrogenases that closely resemble pyruvate dehydrogenase in structure and function. One is a citric acid cycle enzyme, α-ketoglutarate dehydrogenase (Section 13.3#4), and the other is branched chain α-keto acid dehydrogenase, used in amino acid metabolism (Section 17.10E). All members of the family catalyze essentially irreversible reactions in which an organic acid is oxidized to CO2 and a coenzyme A derivative is formed.

The reverse reactions are catalyzed in some bacteria by entirely different enzymes. These reactions form part of a pathway for fixing carbon dioxide in anaerobic bacteria. Some bacteria and some anaerobic eukaryotes convert pyruvate to acetyl CoA and CO2 using pyruvate:ferredoxin 2-oxidoreductase, an enzyme that is unrelated to pyruvate dehydrogenase.
She could have learned several things by reading my undergraduate textbook.

1. More simple versions of this enzyme exist in bacteria suggesting strongly that the complex version in mammals evolved from a simpler version and there may be even more simple versions in other bacteria.

2. Separate E1 subunits may have evolving several times independently. A little digging in the scientific literature would have uncovered more information about their evolution.

3. There are two other related enzymes in most cells. A simple google search would have uncovered a post I wrote ten years ago [Pyruvate Dehydrogenase Evolution]. I explained that the available evidence (sequence comparisons, etc.) suggest strongly that the common form of modern pyruvate dehydrogenase evolved from a primitive version of branched chain α-keto acid dehydrogenase, a key enzyme in amino acid biosynthesis.

4. Some bacteria have a different enzyme that catalyzes the same reaction: pyruvate:ferredoxin 2-oxidoreductase. This suggests that the earliest cells probably used this enzyme and the modern version of pyruvate dehydrogenase evolved later. (There's plenty of evidence supporting the idea that ferredoxin enzymes were the first oxidation-reduction enzymes.)

I'm not saying we have definitive proof of a stepwise evolutionary pathway to the first complex form of branched chain α-keto acid dehydrogenase and from there to the complex modern version of pyruvate dehydrogenase. These scenarios are speculative, but they are plausible. The fact that we have plausible, naturalistic, explanations for the evolution of pyruvate dehydrogenase means that we have no need of Ann Gauger's god(s).

But here's the more important point. She could have easily uncovered all this information by herself in just a few hours (at most). Why do Intelligent Design Creationists always assume that a gap in their own knowledge means that nobody knows anything about the subject?

And why do they always go on to fill these gaps with god(s)?



1. Moran, L.A., Horton, H.R., Scrimgeour, K.G., and Perry, M.D. (2012) Principles of Biochemistry 5th ed., Pearson Education Inc. © Pearson/Prentice Hall

92 comments :

  1. ID creationists have an incentive to know nothing.

    Step 1. I don't know about this. Therefore, no scientist in the world knows about this.

    Step 2. Since no scientists knows about this, God did this.

    Step 3. That's it.

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    1. They have a much bigger incentive - they believe steadfastly not-getting-it will be Rewarded. Surviving ridicule and cognitive dissonance are all part of The Test. There is little point (beyond entertainment) in trying to change minds, when all you can offer to balance the scales is a certain intellectually satisfying consistency.

      Delete
  2. “She could have learned several things by reading my undergraduate textbook.”

    Would she have learned anything that would address her question? You can’t respond to ‘how’ questions with ‘what’ answers.

    “How could early cells have assembled such a structure, bringing together separate enzyme activities to work cooperatively?”

    Do the textbooks offer realistic mechanisms for bringing separate enzymes together and making them work cooperatively? Saying something evolved from a primitive version, and declaring plausibility isn’t adequate.

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    1. "Do the textbooks offer realistic mechanisms for bringing separate enzymes together and making them work cooperatively? "

      Yes they do. But much more importantly, even if they did not, the next step isn't "There must have been a GOD that did it" and then declare the matter settled. The next step is let's try to find out.

      "Saying something evolved from a primitive version, and declaring plausibility isn’t adequate. "

      Adequate for what? For an answer that gives you the illusion of certainty that you have found the TheTruth(tm)? Saying "GOD did that" is adequate then? Does that really convince you? Do you really find that to be a settling answer?

      What do gods need pyruvate dehydrogenases for anyway? It seems to me gods can make life entirely without material stuff like atoms, fields and molecules. Isn't your god supposed to have made a spiritual dimension for immaterial souls? How do those work? Supposedly the immaterial soul doesn't need pyruvate dehydrogenase, right? So in what way is the material components and structures of natural physical entities, the products of immaterial and supernatural gods?

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    2. txpiper,
      Viewing natural complexes in the same way as man-made machines is a big mistake creationists often make. Man-made machines are mechanical, they don’t assemble by themselves without help from their designers. But natural complexes are chemicals that come together all by themselves through physical and chemical interactions. And they don’t need any intervention by an external agency to do that.

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    3. "natural complexes are chemicals that come together all by themselves through physical and chemical interactions"

      I think you are standing on the actual bedrock of evolutionary theory with that.

      Delete
    4. Txpiper: "Saying something evolved from a primitive version, and declaring plausibility isn’t adequate."

      That's not what Larry did, but, why is saying something was created by a designer and declaring certainty adequate?

      Delete
    5. It's one of the chief handicaps creationists operate under, that they are unable understand metaphor and analogy. So if a scientist writes that DNA can be thought of as a "code", they conclude that DNA is literally a code, written by an intelligent being.

      This is not surprising, since creationists are almost invariably also religious fundamentalists, who read scripture as being literally true, rather than interpreting it as metaphor and allegory. It'd be interesting to determine if this mental deficiency is a cause or effect of their religious belief.

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    6. who read scripture as being literally true, rather than interpreting it as metaphor and allegory

      'Cause Jesus never spoke in parables, right?

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    7. TX, if pyruvate dehydrogenase evolved (it did) we'd expect that simpler forms of it exist, and that it might show evidence of having evolved from simpler enzymes. As Dr. Moran writes, those predictions are accurate.

      Even you, who are determined not to understand evidence for evolution, understand this. Therefore, you jump immediately to a request for more details, insisting that if scientists don't have all of them, this evidence for evolution can simply be erased.

      (I don't know if scientists know more about this or not, but I personally don't.)

      TX, honest scientists don't erase this evidence. You shouldn't either.

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    8. bwilson295,

      “we'd expect that simpler forms of it exist, and that it might show evidence of having evolved from simpler enzymes”

      The ‘simpler’ part is not a point well made in this post.
      -
      “Therefore, you jump immediately to a request for more details”

      No, I asked about “realistic mechanisms for bringing separate enzymes together and making them work cooperatively”, because none were proposed.

      I could have asked how three genes were linked together to form the operon Gauger mentions, or how cows jumped over the moon.

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    9. Txpiper has changed the subject and moved the goalposts. The original thesis was the invalidity of Gauger's nonsense. Txpiper doesn't dispute the silliness of what Gauger wrote. But he's got new goalposts. OK then, we accept your surrender on Gauger's claims.

      On to the new goalposts. What's so hard about bringing enzymes together and making them work cooperatively? As an example, there's HIV viroporin, which recently evolved the ability to bind to itself in a multimer complex that channels through a membrane.

      Although creationists wax rhapsodic about the "perfect" fit on proteins for each other, it doesn't take many mutations to form a protein-protein interface. For one thing, protein outer surfaces are a delicate balance of hydrophobic and hydrophilic amino acids. Flip one or two -phobic amino acids to -philic, and you've got an oil patch that wants to stick to the oil patches of its fellow protein molecules. If this change happens to protein A's gene then all copies of protein A get the oil patch.

      And they do stick, molecular biologists know this from experience-- sometimes sad experience because it often happens by accident in the lab when they don't want to change the multimeric state of their target protein.

      Certain repetitive structures like to fit together, like beta sheets. But there's an additional mechanism to facilitate the evolution of protein-protein interfaces: domain swapping. Suppose a protein domain has an alpha helix (let's say) on its outside. It must fit into an alpha-helix shaped hole, assuming there are no gaps in the hydrophobic core of the domain. But protein molecules are floppy and vibrate in solution. One change of an amino acid facing into the core can destabilize it a little, so now that alpha helix flops around a bit and spends part of its time not fitting into its hole. If another protein of the same type comes along, they both have the same problem, a flopping alpha helix and a hole that fits it. So copy A's alpha helix can fit into the helix-shaped hole on copy B, and copy B's alpha helix can fit into the helix-shaped hole on copy A. Bango, instant binding of two protein molecules. This has been observed, so it's not hypothetical.

      I could go on. The point is, Michael Behe says crazy stuff about how you need X number of *simultaneous* mutations to make a protein-protein interface. This is absurd and contrary to observation and experience. We know it sometimes takes very few amino acid changes to make a protein-protein interface, esp. when a protein binds with copies of itself.

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    10. Diogenes,

      "As an example, there's HIV viroporin, which recently evolved the ability to bind to itself in a multimer complex that channels through a membrane.”

      When did this evolution occur?
      -
      “Bango, instant binding of two protein molecules. This has been observed, so it's not hypothetical.”

      But two protein molecules bangoed together means you have two protein molecules bangoed together. It does not mean that you have a functional molecular machine, like the one Gauger is talking about.
      -
      “Michael Behe says crazy stuff about how you need X number of *simultaneous* mutations to make a protein-protein interface.”

      I would suppose that Behe is talking about protein-protein interactions, which are a far cry from interfaces. The Wikipedia entry about PPI’s says this:

      “Proteins rarely act alone as their functions tend to be regulated. Many molecular processes within a cell are carried out by molecular machines that are built from a large number of protein components organized by their PPIs. These interactions make up the so-called interactomics of the organism, while aberrant PPIs are the basis of multiple aggregation-related diseases, such as Creutzfeldt–Jakob, Alzheimer's disease, and may lead to cancer.”

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    11. or how cows jumped over the moon

      If God exists, science tells us about His creation. Why do you wish to remain ignorant to its awesome beauty? Do you really find a tale of a Creator blowing on a handful of dust more inspiring than science finding we are made from the insides of exploding stars?

      In the last paragraph of Origin, Darwin spoke of beauty and grandeur. It is there if you allow the scales to fall from your eyes.

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    12. Txpiper,

      The Vpu viroporin was widely discussed in a 2007 online controversy between Michael Behe and a grad student, ERV, aka Abbie Smith. Behe lost.

      When I link to these things, I wish you would read them. This repetition is exhausting.

      Abbie Smith answered your question. The mutations occurred since HIV diverged from SIV: "Vpu is, in fact, a new gene.1 Of the five major phylogenetic groups of SIV, Vpu is only found in one group– Chimpanzee SIV (SIVcpz) and its descendants – including HIV-1. It is absent in all of the other major lineages (Sooty Mangabey, African Green Monkey, Sykes Monkey, and L’Hoest Monkey). This means that Vpu is in HIV-1 but not HIV-2.2

      Ah, Michael Behe, you might try to talk your way around Vpu now (though you were evidently unaware of its existence moments ago) by insisting that it is not *new* new. “Sure it’s new in chimpanzees, but its not *new* in HIV-1!” Sorry, you’ll find no escape with that limp-wristed, ad hoc parry. SIVcpz Vpu and HIV-1 Vpu act in different ways, biochemically, which is predictable enough when you do something as simple as comparing amino acid sequences. For instance, if you compare a laboratory strain gag to SIVcpz gag, you get a similarity of ~75%.3 Not too shabby. On the other hand, if you compare the subunit portion of env (the gene I use to create phylogenetic trees because it’s the most variable between viruses) you get an AA similarity of only ~59.5%.

      The amino acid similarity between HIV-1 Subtype B Vpu and SIVcpz Vpu is ~37%. Ah but that study was published in 1990. Perhaps things are different now? I found the AA sequence of NL4-3 (lab standard Subtype B) and several recently entered SIV cpz sequences at the Los Alamos National Laboratory HIV Sequence Database4 – I got the same numbers. Highest was ~39% AA sequence similarity.

      Turns out a LOT of evolution has been going on in HIV-1 since it was transferred to humans 50-60 years ago."


      ERV vs. Michael Behe, Behe loses

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    13. Txpiper: "But two protein molecules bangoed together means you have two protein molecules bangoed together. It does not mean that you have a functional molecular machine, like the one Gauger is talking about."

      I gave you an example of a functioning molecular machine, Vpu viroporin.

      Moreover, the anti-evolution position starts from the *assumption* that by default, any protein-protein interface is incredibly improbable to evolve. Michael Behe stated this explicitly. Behe was wrong. ID proponents said the evolution of protein-protein interactions is astronomically unlikely, and they've been proven wrong again and again.

      You seek to change the subject to a claim, "Well, but a protein-protein interaction is not sufficient to make a machine!" The argument is not about sufficiency. It's about probability. The ID authorities like Gauger and Behe claimed astronomical improbability, and have been proven wrong over and over.

      (Begin digression:

      For my colleagues who are Aurors (expert debaters of creationists), I will point out that this is one of a class of creationist counter-arguments, which I call the 'necessity-sufficiency straw-man'. E.g. Txpiper wishes to change the subject again, from 'super improbability' to 'lack of sufficiency.' The creationist first makes false claims about necessity, and is proven wrong, so he changes the subject to claims about sufficiency. The necessity-sufficiency straw-man works like this:

      1. Creationist: (opens with claim about a missing, necessary element) For evolution to be true, there MUST BE new species appearing! But we have NEVER observed a new species! It's necessary and we've NEVER seen it! NOT EVEN ONE NEW SPECIES!

      2. Scientist: Here are new species: culiex pipiens. Monkey flower. Triticale. etc.

      3. Creationst: (switches to sufficiency) OH! So you're saying that just because two mosquitoes have sex and make a slightly different mosquito, that proves that pond scum can transform into a beautiful baby! WELL IT'S NOT THAT EASY, BUSTER!

      End digression.)

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  3. "And why do they always go on to fill these gaps with god(s)?"

    It's in their job description. :)

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  4. I don't think it takes much to astonish Ann Gauger. If I remember correctly, she was astonished to find that this team might actually have been right about the fact that we do still have fragments of a gene for egg yolk in our genome.

    Of course even with her astonishment at the evidence, she still managed to remain somewhat in denial. It can be difficult to cast aside young earth creationism when you have so much invested in it 😂

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    1. Is Gauger a YEC? I didn't know that.

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    2. Maybe I went too far calling her a YEC. I know she gets very defensive about evidence for common descent, so she may just be an Old Earth Creationist, common descent denier.

      But this is just my suspicion given that in the past she has responded very defensively to clear evidence for common descent.

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    3. In her BIO-Complexity paper, she attacked population genetics and defended Adam and Eve, even specifying that the original pair of humans could have come recently from the Middle East, and she treated all conventional time frames as speculative and based on assumptions. Whether or not she is YEC, her writing is contrived to contain nothing whatsoever that could challenge YEC.

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  5. > Why do Intelligent Design Creationists always assume that a gap in their own knowledge means that nobody knows anything about the subject?

    The above is not true.

    I wish Larry and others would stop stereotyping.

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  6. @txpiper,

    you ask lots of questions, but propose nothing in return. As always, IDiots such as yourself, perch condescendingly on your pedestal, and seek to undermine the scientific process, not by contributing or explaining...but by sowing doubt. It's a regressive tendency of your nature.

    I have no problem with your skepticism - it can be a healthy exercise.

    But let's turn the discussion, for once, to your brand of science:

    Where did all of these enzymes come from? Were you there?
    When/how did life originate? Please provide evidence.
    If god played a role, how did god do it? Again, cite your reasoning.
    What have you done, personally, to contribute to the science of biochemistry, development, and apparent evolution of life on Earth?

    As I see it, you aren't qualified by your level of education, scientific contributions, or content of your discussion, to be taken seriously. Just a troll.

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    1. Terminus Est,

      “Where did all of these enzymes come from?”

      I’ve posed that question many times. Is this the first time you’ve ever asked it?

      I’m a creationist, so you pretty much know my answer. I didn’t notice any of the other commenters responding to your inquiry, but maybe they’ll answer if it is you asking it.

      Delete
    2. txpiper,

      No, I don't pretty much know your answer. There are all flavors of creationists. Was each species poofed into existence with all its enzymes in place, or was there some sort of evolution within "kinds"? What's a "kind", by the way?

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    3. The bigger problem is that creationists actually think "God did it, with magic" is an answer.

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    4. lutesuite, that is the central problem. Its a hollow bubble with no internal detail or mechanism. The sort of empty platitude that so completely satisfies the religious mind.

      I wonder if a politician uttered empty platitudes whether that would work as favorably on the mind of a religious person...oh, right... never mind.

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    5. John Harshman,

      “No, I don't pretty much know your answer. There are all flavors of creationists.”

      If you know of a flavor that thinks enzymes are the result of nothing but natural processes, they probably aren’t actually creationists.
      -
      “Was each species poofed into existence with all its enzymes in place”

      My flavor thinks so, substituting ‘kinds’ for ‘species’, and ‘spoke’ for ‘poofed’.
      -
      “…was there some sort of evolution within “kinds”?"

      Of course, though we would limit it to adaptation.
      -
      “What's a "kind", by the way?”

      Have you ever been to a dog show?

      Would you like to take a stab at Terminus Est’s question about where enzymes come from?


      Delete
    6. Would you like to answer my question about what a "kind" is? You seem to be waffling. You think there's evolution within kinds, which are not species, but you seem to be telling me that either dogs are a kind or different dog breeds are kinds. I suspect you aren't interested in clarity.

      Enzymes mostly come from previous enzymes through gene duplication, domain-shuffling, and such. Phylogenetic analysis can help discover that sort of thing, but unfortunately I suspect you don't believe in phylogeny.

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    7. John Harshman,

      “Would you like to answer my question about what a "kind" is? You seem to be waffling.”

      Not really. Dogs are a kind. Cats are a kind. Bovines are kind. Bats are a kind. Bears are a kind. If you are aware of any crossovers or intermediates, feel free to list those.

      There are lots of unanswered questions, but I don’t think the basic concept is that hard to recognize or understand.
      -
      “You think there's evolution within kinds, which are not species”

      No, the data shows that there is amazing variation and adaptability within kinds. The definition of “species” is malleable.
      -
      “but you seem to be telling me that either dogs are a kind or different dog breeds are kinds.”

      No, wolves, dogs, coyotes, and perhaps foxes, are the descendants of an original kind. The genetic profile of the original was obviously packed with versatility. I understand that this is foreign and unpleasant for you, but the idea that random DNA replication accidents add variation is equally absurd to me. I think in accordance with a record, and you are working with an idea.
      -
      “I suspect you aren't interested in clarity.”

      Well, that’s really dumb, John.
      -
      “Enzymes mostly come from previous enzymes through gene duplication, domain-shuffling, and such.”

      The community breathed a sigh of relief when Ohno’s ideas about gene dupes floated to the top. As Larry has noted, de novo genes are rare. It is much easier to imagine genes being duplicated (as if they are like perforated postage stamps) and altered by fortuitous replication errors, than it is to expect something as fabulous as a novel, functional gene being accidentally generated from scratch.

      That said, there are all kinds of critical enzymes that do not lend themselves to duplication, domain-shuffling, and such, for their origins. You know that as well as I do. At some point, either raw accidents, or some evolutionary mechanism, assembled things like replication enzymes. I don’t think you can offer the evolutionary mechanism, and I don’t believe in marvelous accidents. Call me incredulous.
      -
      “Phylogenetic analysis can help discover that sort of thing, but unfortunately I suspect you don't believe in phylogeny.”

      As proof of common ancestry, no, I do not.

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    8. Not really. Dogs are a kind. Cats are a kind. Bovines are kind. Bats are a kind. Bears are a kind.

      Cool. So, since all "kinds" were created individually by God at once, then there must be pre-Cambrian fossils of dogs, cats and bears. Rabbits, to, I surmise. I'd be most interested in seeing the examples of these fossils that have been excavated by creationist paleontologists.

      If you are aware of any crossovers or intermediates, feel free to list those.

      Ah, yes. There are not Dog-o-bears, nor Cat-o-rabbits, just as there are no Crock-o-ducks. My fellow atheists, txpiper is just burying us with his superior understanding of evolutionary theory!

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    9. As Larry has noted, de novo genes are rare.

      Yes. Isn't strange, since you believe all genes are poofed into existence by a god who can create anything from nothing? A theological conundrum, to be sure.

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    10. Correction:

      "Isn't strange" should read "Isn't that strange..."

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    11. I think in accordance with a record, and you are working with an idea.

      Yep, that book is *much* more reliable than stupid old fossils and genetics.

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    12. I suspect you aren't interested in clarity.

      I feel that is too harsh. I suspect incapacity rather than intent.

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    13. then there must be pre-Cambrian fossils of dogs, cats and bears. Rabbits, too, I surmise. I'd be most interested in seeing the examples of these fossils that have been excavated by creationist paleontologists

      [Insert made-up "flood geology" answer here.]

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    14. Tx:
      " If you are aware of any crossovers or intermediates, feel free to list those. "

      This is a nice example...
      Not a spider, not a scorpion... do tell which kind are we talking about here?

      Want to try to explain the platypus?. A mammal, which lays eggs. And is poisonous.

      Hyena? Do tell, which kind is this?

      Rabbits?

      And I'd very much like to see the pre-cambrian rabbit which should be found in the fossil record if your version of ID were true.

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    15. Judmarc:
      "[Insert made-up "flood geology" answer here.]"

      Nah, Tx hides his true creationist identity. Because he knows if he admits to one of the many flavor of creationism, he would have to explain why only his version of creationism is the true one. And why supporters of other versions of creationism are doing their utmost best to exterminate each other.

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    16. "It is much easier to imagine genes being duplicated . . . and altered by fortuitous replication errors"

      In my isozyme work, I saw the work of duplicated genes. This isn't something we need to imagine. Some of the duplicated genes were the same as the originals with occasional variants. Some were different from the original in all individuals in the study.

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    17. Dogs are a kind. Cats are a kind. Bovines are kind. Bats are a kind. Bears are a kind. If you are aware of any crossovers or intermediates, feel free to list those.
      When you say "dog", what do you mean? Are you referring to Canis familiaris, all of Canis, all of Canidae, Canoidea, or what? Are bovines a separate kind from other taxa in Bovidae? Most importantly, how do you know that any of this is true? I'm not sure what you mean by "crossovers or intermediates". If you refer to hybrids, there's no reason to expect hybridization of taxa long-separated. If you refer to intermediate morphologies, those can be found in the fossil record. I note you think dogs and bears are separate kinds, and there's a pretty good record of intermediates there.

      There are lots of unanswered questions, but I don’t think the basic concept is that hard to recognize or understand.

      That's because you haven't thought about it very hard. I retract my claim that you are uninterested in clarity. You are just uninterested in facts and incapable of clarity.

      (Me:)“You think there's evolution within kinds, which are not species”

      No, the data shows that there is amazing variation and adaptability within kinds. The definition of “species” is malleable.


      See, that was so unclear as to be useless. Are you saying that kinds could all be considered single species? Under what definition of species?

      No, wolves, dogs, coyotes, and perhaps foxes, are the descendants of an original kind. The genetic profile of the original was obviously packed with versatility. I understand that this is foreign and unpleasant for you, but the idea that random DNA replication accidents add variation is equally absurd to me. I think in accordance with a record, and you are working with an idea.

      No, I'm working in accord with evidence. Phylogenetic analysis shows us that all canids, including foxes, belong to the same kind. But of course it also shows us that all mammals belong to the same kind too. There's just nowhere you can draw a line. If you disagree, tell me where and how.

      Call me incredulous.

      I'd rather call you credulous, as you are willing to believe anything as long as it fits your prior beliefs.

      (Me:)“Phylogenetic analysis can help discover that sort of thing, but unfortunately I suspect you don't believe in phylogeny.”

      As proof of common ancestry, no, I do not.


      Why not? How do you account for the data otherwise? (Note: "common design" is not an explanation.)

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    18. "Accounting for the data" is a concept entirely alien to creationists. Any three year old can point at animals and say "Doggy! Kitty! Bunny!", which is all baraminology amounts to. One would expect biologists to aspire to something a bit more rigorous, and which accounts for all organisms, including the ones that went extinct. AFAIK, there has yet to be a creationist who has so much as attempted to categorize every known species into "kinds".

      I can't remember if this was txpiper or one of his fellow creationist imbeciles, but no matter: He was claiming that the nested hierarchy was a mere human artifact and reflected nothing in reality. So I challenged him to demonstrate this by creating a thorough classification of motor vehicles that formed such a hierarchy and which addressed all the relevant questions e.g. Is a Ford SUV more closely related to a General Motors SUV, or to a Ford compact hatchback? How did Takata airbags appear simultaneously in the "lineages" of multiple models, from multiple manufacturers? Etc. As you might expect, all I received in response was silence.

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    19. John Harshman,

      When you say "dog", what do you mean? Are you referring to Canis familiaris, all of Canis, all of Canidae, Canoidea, or what?

      Kinds don’t precisely match any taxon. I would suppose that kinds are between family and genus, but I really don’t care. Is your life enriched by phylogenetics? Are you disturbed when morphology and gene sequencing produce different cladograms?

      Why are you so edgy about imprecise crap like this, and have no interest whatever about the origin of critical enzymes? I thought you worked in accord with evidence?

      Delete
    20. Tx,
      I'd say this response summs up your interest in the subject(s) at hand on this blog:
      "I really don’t care."

      Anyway, you move the goalposts to "the origin of critical enzymes".
      Do tell, Tx, what *exact* words did your designer of choice speak when he decided to make pyruvate dehydrogenase?

      Delete
    21. Kinds don’t precisely match any taxon. I would suppose that kinds are between family and genus, but I really don’t care.

      That's actually helpful, so thanks. So the level of "kinds" would be analogous to a sub-family. It would not involve there being a clade such as Canidae. Grouping all canids together would just be arbitrary and reflect nothing about the lineal relationship between them. An example of a "kind" would be the grouping that includes wolves, coyotes, and domestic dogs, whereas foxes would constitute a separate "kind". The division would be as depicted in the illustrated cladogram here:

      https://en.wikipedia.org/wiki/Canidae#Phylogenetic_relationships

      The conclusion to be drawn from this is that there is no ancestral relationship whatsoever between, say, the grey wolf and the red fox. They would be no more closely related to one another than either would be to, say, a grizzly bear, or a chickadee, or a moth, or a banana plant.

      That's quite an interesting and testable hypothesis. Now, I know you say you "really don't care" about such questions, but surely the creationist scientists you admire are not so lacking in curiosity. These scientists don't write papers in which their conclusion is "Don't know, don't care", do they? So perhaps you could share come of the research creation scientists have done to support your claim. Is there really evidence, based on morphology and molecular genetics, that the grey wolf and the red fox are no more closely related to one another than either is to a mushroom? Please share this evidence with us, txpiper.

      Delete
    22. "Is there really evidence, based on morphology and molecular genetics, that the grey wolf and the red fox are no more closely related to one another..."

      Maybe 'no more' is a good way to put it. The grey wolf has 78 chromosomes, while the red fox has only 34*.

      https://en.wikipedia.org/wiki/List_of_organisms_by_chromosome_count

      Delete
    23. Are you disturbed when morphology and gene sequencing produce different cladograms?

      No, happy to get a correct answer, knowing that gene sequencing is a more accurate method (just as DNA evidence in court is considered more accurate than a physical description - do you think DNA evidence is accurate, and if so, why?).

      Overall the morphological and genetic cladograms are very similar, showing morphological similarity and the third and fourth reinforcing scientific threads of geology (stratigraphy) and nuclear physics (carbon dating) worked extremely well together.

      Please do tell us about the ludicrous flood geology and "new" (and completely unevidenced) nuclear physics creationist excuse-makers have trotted out as counter-explanations for these other reinforcing threads.

      Delete
    24. @ txpiper:

      Maybe 'no more' is a good way to put it. The grey wolf has 78 chromosomes, while the red fox has only 34*.

      TBH, I have no idea how many chromosomes exist in fungal genomes. But your answer suggests that, if a fungus possessed 34 chromosomes, it would be considered by creationists to belong to the same "kind" as the red fox. That, to me, is a rather bizarre conclusion. But, then, I'm not a creationist.
      '

      Delete
    25. In fact, if we look at that reference you provided, we see that the gray wolf not only has the same number of chromosomes as jackals, dingoes and coyotes. Chickens, doves, and the African pitcher plant also have 78 chromosomes. So does that mean all of them are of the same "kind" according to creationism? Please explain. I'm finding creationist biology very confusing.

      Delete
    26. txpiper,

      Yeah, I know you aren't interested. Creationists are never interested in science except for the little bits they can cherry-pick to misconstrue as evidence for their preconceived views. I notice you didn't answer my question about how you know what you know, as well as failing to answer what any kinds are, even the "dog" kind.

      Your sole foray into data was chromosome counts, but I bet you wouldn't stick to even that if challenged. Is it in fact your change that chromosome number is completely fixed and cannot change at all?

      Delete
    27. TX: at this link you'll find photos and drawings of a duplicated gene, and pictures of its effect. No need to read, just scroll down to the picture.

      https://whyevolutionistrue.wordpress.com/2017/01/24/alfred-sturtevant-a-hero-of-genetics/

      Duplicated genes are not imaginary.

      Delete
    28. “I have no idea how many chromosomes exist in fungal genomes. But your answer suggests that, if a fungus possessed 34 chromosomes, it would be considered by creationists to belong to the same "kind" as the red fox.”

      Well, you did peruse the Wikipedia link. You could have looked up yeast. But your previous question was “Is there really evidence, based on morphology and molecular genetics, that the grey wolf and the red fox are no more closely related to one another than either is to a mushroom?” I thought chromosome count answered the ‘molecular genetics’ part. I didn’t consider that you might stall out on the morphology.

      ===

      John Harshman,

      “I notice you didn't answer my question about how you know what you know, as well as failing to answer what any kinds are”

      Well yeah, but you asked “Under what definition of species?”, so you don’t sound surefooted about what those are either. Nor should you. Taxonomy is not a science of discovery. It is a classification method. Some flexibility is necessary.
      -
      “even the "dog" kind.”

      I would use chromosome count and being able to interbreed as a reasonable metric. That doesn’t hold up for including foxes, but I’ve read about supposed dog-fox hybrids.

      So, still no interest in how enzymes evolved, huh? I can’t say I blame you. You have no reason to be surefooted about that either.

      ===

      judmarc,

      “Please do tell us about the ludicrous flood geology”

      Why don’t you start that discussion with a conventional explanation for coal seams 200 feet thick?

      Delete
    29. bwilson295,

      I’ve read all kinds of stuff about duplicate genes. I know that there is such a thing. That isn’t really the issue.

      ===

      John Harshman,

      Sorry. I neglected to answer your last question.

      “Is it in fact your change that chromosome number is completely fixed and cannot change at all?”

      Of course not.

      Delete
    30. txpiper,

      So if chromosome number can change, why does a difference in chromosome number tell you that two species are different kinds?

      And please don't lecture a systematist on species definitions. You don't know what you're talking about, clearly. I do.

      Delete
    31. @ txpiper:

      I thought chromosome count answered the ‘molecular genetics’ part.

      It doesn't. Unless you consider this man with 44 chromosomes a different "kind" from other humans.

      Delete
    32. So if chromosome number can change, why does a difference in chromosome number tell you that two species are different kinds?

      Head shot. Fortunately for txpiper, his head is empty, so it does no harm.

      Delete
    33. TX wrote, "I’ve read all kinds of stuff about duplicate genes. I know that there is such a thing. That isn’t really the issue."

      And yet earlier he wrote, "It is much easier to imagine [italicised] genes being duplicated (as if they are like perforated postage stamps) and altered by fortuitous replication errors, than it is to expect . . . a novel, functional gene being accidentally generated from scratch."

      1. No doubt genes that arise from duplicated, modified genes are much more common than genes generated from scratch -- this is true.

      2. Genes can be duplicated, as TX agrees.

      3. In a pair of duplicated genes, one often becomes modified, does things a little or a lot differently -- evidence from my isozyme work, among many, many other sources.

      So . . . why that statement with the emphasized *imagine*? As if duplicated and modified genes weren't real and can't be explanations for a lot of the genetic diversity we see?

      Delete
    34. txpiper no doubt imagines that once a gene is duplicated, Baby Jesus personally tends to it to make sure it doesn't mutate enough to create a new function. Otherwise, one "kind" would inevitably split into two "kinds", and his religion forbids that.

      Delete
    35. Why don’t you start that discussion with a conventional explanation for coal seams 200 feet thick?

      HAHAHAHAHA! Now *that's* entertainment! All the same ridiculous tactics on display: All of science must be wrong because of an interesting issue in one branch of one science (in this case the paleogeology of coal formation), where "Creation science" liberally takes citations and quotes out of context to try to score points amongst the credulous uninformed.

      Here's your answer, from the very first paper cited in the very first Creation science flood geology article I looked at on the topic:

      "The most likely factor is regional paleogeography. Drainage from the Wind River Basin to the Powder River Basin throughout most of the early Tertiary greatly increased the volume of water flowing through the basin along the basin-axis trunk streams. Greater amounts of water favored accumulation and preservation of peat and the formation of thicker and more widespread coal deposits than in adjacent basins that were climatically and tectonically similar but lacked a major extrabasinal water source."

      Whoops, guess all of nuclear physics, geology, paleontology and genetics are *not* wrong based on some thick coal deposits in Wyoming.

      But I asked *you* for *support* for flood geology and new nuclear physics, and all you've given me is an article that tries to turn an interesting actual geological topic into a major problem that doesn't exist. That isn't *support* for ludicrous flood geology or some weird version of nuclear physics. Don't you know what *support* means? Where's your evidence?

      Delete
    36. John Harshman,

      “So if chromosome number can change…”

      How do you think chromosome numbers change? Are they more likely to be gained or lost?
      -
      “why does a difference in chromosome number tell you that two species are different kinds?”

      It doesn’t. I told you above that I would think that kinds would fall between family and genus. That would mean that species and subspecies are not different kinds. For chromosome counts, horses have 64, donkeys 62, zebras 32-46 (depending on species). All the same genus, all the same family. All obviously the same kind.
      -
      “And please don't lecture a systematist on species definitions.”

      If a systematist cannot pin down a single definition for what a species is, it is because there is some amount of arbitrariness involved. I’m sure you know what the ICZN is, and why there is such a thing. Sometimes, things are reclassified. The organisms are what they are. It is the system that has to be adjusted.

      But I would still think a systematist would know all about the origin of enzymes, or at least the ideas about where they came from. Why the reluctance to answer Terminus Est’s question?

      Delete
    37. judmarc,

      Well, shoot. I was hoping you’d use a USGS report or something like that. Why would you go to a creation site for an answer?

      You didn’t link to the paper you quoted from, so I couldn’t tell what they are trying to explain when it says “The most likely factor…”.

      The Powder River coal deposits are quite large. Here is a picture of one of the mines:

      https://www.usgs.gov/media/images/coal-mine-powder-river-basin

      Your quote says “Drainage from the Wind River Basin to the Powder River Basin throughout most of the early Tertiary greatly increased the volume of water flowing through the basin along the basin-axis trunk streams. Greater amounts of water favored accumulation and preservation of peat”

      They estimate the ratio of peat to formed coal to be 3-7:1. So a 100 foot thick coal seam would represent what would have been a 300-700 foot thick layer of peat. Just the Black Thunder mine has exposed more than 40 square miles of coal beds. I don’t think ‘water flowing through the basin’ adequately explains the accumulation of that much concentrated plant matter. But I’m sure you do.

      Delete
    38. Terminus Est asked you about the origin of enzymes, not John Harshman.

      And no, although systematists know something about enzymes, we don't know everything about them.

      Delete
    39. Txpiper,

      You persist in being so obtuse that one wonders if you have any clue about what you read or write.

      How do you think chromosome numbers change? Are they more likely to be gained or lost?

      Usually they change either by polypoidy, fission, or fusion. I can't say that either gain or loss is more common, but note that in fission and fusion no genetic material is actually either gained or lost, just repackaged. As in, for example, the fusion that resulted in humans having one more chromosome than chimps.

      (Me:)“why does a difference in chromosome number tell you that two species are different kinds?”

      It doesn’t.


      And yet when asked how you knew that foxes and dogs were different kinds, you pointed exclusively to chromosome number. Do you even remember what you say from one moment to the next?

      I told you above that I would think that kinds would fall between family and genus. That would mean that species and subspecies are not different kinds. For chromosome counts, horses have 64, donkeys 62, zebras 32-46 (depending on species). All the same genus, all the same family. All obviously the same kind.

      Why "obviously"? How do you tell if two species belong to the same kind?
      If a systematist cannot pin down a single definition for what a species is, it is because there is some amount of arbitrariness involved.

      Indeed there is, and of course it's because speciation happens, and speciation isn't instantaneous, so there are all degrees of intermediacy. What does this have to do with "kinds"?

      I’m sure you know what the ICZN is, and why there is such a thing.

      I do. But I don't think you do. It has nothing to do with the subject.

      Why the reluctance to answer Terminus Est’s question?

      Two reasons:

      1) Not my job.

      2) I did answer it. Remember the bit about gene duplication, etc.?

      Delete
    40. bwilson295,

      I overlooked this. My apologies.

      “So . . . why that statement with the emphasized *imagine*? As if duplicated and modified genes weren't real and can't be explanations for a lot of the genetic diversity we see?”

      I wasn’t saying that similar genes are imaginary. What I was emphasizing is the way they are appraised. Gene duplication is an easier thing to imagine than de novo genes. I think GD is a panacea. As I mentioned, I’ve read many articles and papers, and they usually just repeat the same thing. Here is an interesting example:

      ”Gene duplication provides opportunities to explore this forbidden evolutionary space more widely by generating duplicates of a gene that can ‘wander’ more freely, on condition that between them they continue to supply the original function.”

      ”What Is the Evidence for the Importance of Gene Duplication?”

      ”The primary evidence that duplication has played a vital role in the evolution of new gene functions is the widespread existence of gene families.”
      http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0020206

      That is not evidence of the duplicate-and-modify narrative. That is looking at something and making an assumption. Gene families would mean as many accidental duplication events as there are family members, and more accidental further refinements. I don’t believe things like happen accidentally.

      -

      “Terminus Est asked you about the origin of enzymes, not John Harshman.”

      Yes, and he knew my answer when he asked. I’m a creationist. I believe things were created fully functional and integrated. Terminus Est does not. He believes, along with most of the people here, that things like replication enzymes and ribosome ‘evolved’. I can’t say I blame any of you for not wanting to talk about things like that. With gene duplication, at least you’ve got a starting point.

      Delete
    41. John Harshman,

      "1) Not my job."

      Nobody wants that job.

      "2) I did answer it. Remember the bit about gene duplication, etc.?"

      Yes, and that did qualify as a 'bit'.

      Delete
    42. txpiper,

      I will merely note that you attempt no coherent defense of your views.

      Delete
    43. Well, shoot. I was hoping you’d use a USGS report or something like that. Why would you go to a creation site for an answer?

      It was a USGS paper, Tx. Sorry to disappoint(?) you. It was cited in an article at a creation site that tried to cite/quote mine parts of it incorrectly as support for the creation science view that big coal seams are utterly inexplicable, therefore all of science is wrong. (Geiger counters don't work, that sort of thing, because that's what would have to be true for creation science to be correct.) The USGS paper just does what a lot of papers do, which is survey the former work in the field and analyze it in view of what is known at the time the paper is written. The author comes to the quite reasonable and utterly non-miraculous conclusion I quoted at the end of the paper, which of course is completely opposite to the proposition for which the creation science website referenced it.

      The reason I had to look at a creation science site in the first place is because that was the first place I thought of going to check out loony theories about thick coal seams being impossible. After all, I don't recall the CEO of Peabody Powder River Mining all over the news shrieking "Our coal mine is an impossible miracle from God!" Betcha their geologists don't believe that either. So no, for anything that bonkers, I had to check out a creation science site. And of course in the very first paper (the USGS paper) cited in the very first article I looked at on the very first creation science site I went to, I found the very reasonable scientific conclusion I quoted to you.

      Now that I've cleared up your misimpression, I just know you're going to regale me with *support* for flood geology and creationist nuclear physics like I asked, right, Tx? Tx??

      (By the way, *after* you provide the support I've been politely requesting, I'm curious about something else: Why does your God demand you remain ignorant of His creation? It seems to me you'd be right there with the scientists who want to know Him *through* His creation. But perhaps that's just me, and the awesomeness and beauty of the universe as revealed by scientific research strikes you as more of a threat to your beliefs than a path to your Creator?)

      Delete
    44. Gene families would mean as many accidental duplication events as there are family members, and more accidental further refinements. I don’t believe things like happen accidentally.

      Some cancers are caused by partial gene duplication events, including some pediatric tumors and leukemias. So I guess your God wants babies to die in pain?

      Delete
  7. The enzyme complexes that are mentioned may be a product of constructive neutral evolution, as described by Larry a while ago: http://sandwalk.blogspot.com/2015/09/constructive-neutral-evolution-cne.html
    Surely A. Gauger was in a position to at least consider this, since I am pretty sure she checks this site.

    ReplyDelete
    Replies
    1. This comment has been removed by the author.

      Delete
    2. “ http://sandwalk.blogspot.com/2015/09/constructive-neutral-evolution-cne.html “

      “Imagine an enzyme "A" that catalyzes a biochemical reaction as a single polypeptide chain. This enzyme binds protein "B" by accident in one particular species. That is, there is an interaction between A and B through fortuitous mutations on the surface of the two proteins.”

      “Over time, enzyme A might acquire additional mutations such that if the subunits were now separated the enzyme would no longer function (red dots). These mutations would be deleterious if there was no A + B complex but in the presence of such a complex the mutations are neutral and they could spread in the population by random genetic drift. Now protein B is necessary to suppress these new mutations making the heterodimer (A + B) irreducibly complex.”

      Further mutations might make the interaction more essential and make the two subunits more dependent on one another.”

      So,

      “All that's required is that evolutionary biologists propose a reasonable explanation making it possible for such structures to evolve naturally in a world where gods play no role in evolution. That has been done. The idea that irreducibly complex structures are impossible to evolve has been falsified.

      No, it has not been falsified. I’m sorry, but that’s not reasonable or realistic at all. That explanation invokes very unlikely events. You could propose that Elvis is doing two shows a day on Saturn with this rationale. It is all conjecture, speculation and appeal to sequential miracles.

      But, this is how science is done these days. Just use your imagination.

      Delete
    3. Here's how Michael Behe describes his view in Darwin's Black Box (p. 39). As you read his description, note that his entire argument is based on the supposition that an irreducibly complex system cannot be the product of naturalistic evolution. It's impossible, according to Behe, so the only alternative is god(s) did it.

      In order to refute the logic of that claim, all you have to do is show there are perfectly reasonable ways to achieve an irreducibly complex system with no need of god(s). Such systems can evolve in ways perfectly consistent with modern evolutionary theory. These refutations have the same standing in logic as the claims of impossibility by IDiots.

      By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of these parts causes the system to effectively cease functioning. An irreducibly complex system CANNOT [my emphasis, LAM] be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to act on.

      Delete
    4. There's also the problem that the statement, "An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system..." has not been substantiated, not by Behe or anyone else. It is merely asserted. So no refutation of his claim was even necessary in the first place. That examples of functional precursors were readily found in the extant literature was icing on the cake, in terms of refuting his claims.

      Delete
    5. "By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of these parts causes the system to effectively cease functioning."

      Perhaps Behe should have made his definition a little more exclusive. "Perfectly reasonable ways" would be more elusive if the system was the critical elements of eyes/sight/vision.

      Delete
    6. "Perfectly reasonable ways" would be more elusive if the system was the critical elements of eyes/sight/vision.

      You do know the "critical elements of eyes/sight/vision" are arranged fundamentally differently in different animals, right? So there is provably not one irreducibly complex way to make an eye.

      Do you think God just liked to switch up designs for fun?

      Delete
    7. Larry
      "Here's how Michael Behe describes his view in Darwin's Black Box (p. 39). As you read his description, note that his entire argument is based on the supposition that an irreducibly complex system cannot be the product of naturalistic evolution. It's impossible, according to Behe, so the only alternative is god(s) did it. "

      This is a straw man argument. You are doing the same thing you accuse the ID guys of. The argument is evidence of design not the designer.

      Delete
    8. This is a straw man argument. You are doing the same thing you accuse the ID guys of. The argument is evidence of design not the designer.

      Actually, it isn't if you follow the argument logically. If we are designed by a non-divine advanced civilization, then all you have done is move the location of the discussion - in other words, who designed *them*? So you simply get into a who-designed-the-designers infinite series, where the very first designers were either created by some supernatural/divine entity, or evolved themselves, and thus evolution is true.

      So that's the issue, Bill, evolution versus the divine, no matter whether you want to locate it on Earth or elsewhere.

      Delete
    9. @ Bill Cole:

      If you were capable of understanding Larry's argument, you would have noticed that your objection is irrelevant. Larry addresses and refutes Behe's argument for "design", without addressing the identity of the alleged "designer."

      At the same time, Larry is also calling out the IDiots for their disingenuous claims they believe this "design" could result from anything else other than God. I lie which you see fit to repeat her.

      Delete
    10. But hey, Bill, if you really believe "design" can exist without implying the existence of a "designer", then join the club of which Richard Dawkins is a member. He call his non-designer "Tthe Blind Watchmaker".

      Delete
    11. LS
      "But hey, Bill, if you really believe "design" can exist without implying the existence of a "designer", then join the club of which Richard Dawkins is a member. He call his non-designer "The Blind Watchmaker"."

      Certainly a candidate.

      I am interested if you guys can make a case without straw man and ad hominem arguments. If not you are going to eventually lose this battle.

      Delete
    12. Lose which battle? The battle to persuade Bill Cole to accept evolution? That battle is a lost cause until Bill Cole decides to understand the evidence presented to him, and acquires the ability to think rationally.

      Delete
    13. LS
      "Lose which battle? The battle to persuade Bill Cole to accept evolution? That battle is a lost cause until Bill Cole decides to understand the evidence presented to him, and acquires the ability to think rationally."

      Let me repeat for the last time.

      I am interested if you guys can make a case without straw man and ad hominem arguments. If not you are going to eventually lose this battle.

      Delete
    14. "We guys" can, and have been, for over a century and a half. We wonder when you guys are going to open your eyes and remove your fingers from your ears.

      Delete
    15. without straw man

      Hi Bill - I explained just above why that wasn't a straw man argument. Did you follow? Just saying we were designed isn't good enough. Somewhere back at the end of any chain of designers must be some supernatural (because eternal, for starters) entity to create the first non-supernatural designers; or, alternatively, the designers evolved. If the designers evolved, you haven't overthrown evolution, just changed the time and place it happened. So yes, it really must come down logically to supernatural creation or evolution.

      Thus anyone who claims evolution didn't occur *must* have an eternal supernatural being as the original cause of life. So people who point that out aren't attacking a straw man, they're pointing out a logical necessity of the anti-evolution argument.

      Delete
    16. There's also the fact that I explained why Larry's argument was not a strawman, but a direct response to the argument as enunciated by Behe. Larry even quoted Behe's words directly.

      Bill ignores all that, and claims that all he sees are "straw man and ad hominem arguments." For how many years has he been discussing evolution here, at The Skeptical Zone, and who knows where else? And he seriously tries to claim that no one has ever provided anything but straw men and ad homs? All he does in so doing is confirm his intellectual dishonesty, and that he is either unwilling or incapable of engaging in a discussion in good faith.

      A typical creationist, IOW.

      Delete
    17. I would say to some extent atypical, in that he does actually accede to some arguments sometimes (e.g., about Behe getting his rear end handed to him regarding the supposed irreducible complexity of the blood clotting cascade during cross examination at the Dover trial). Whether such small realizations will eventually lead to the larger one that none of these anti-evolution arguments rests on solid ground, and there really is a world of evidence supporting evolution, is anyone's guess.

      Delete
  8. Larry, you have not responded to my inquiry at Facebook, so i ask you here:

    Laurence Moran wrote:
    The breakdown of glucose (glycolysis) uses some of the same enzymes used in gluconeogenesis except they catalyze the reverse reaction. (All enzymes catalyze reactions in both directions.) Thus, some of the enzymes required for glyolysis were already present making it easier for the glycolytic pathway to evolve millions of years after the gluconeogenesis pathway arose.

    You cannot get around the fact which i mentioned already: Whatever first pathway you replace glycolysis with, it has to be a complex multi-step process , requiring a number of enzymes and regulation. And you will ALWAYS be confronted with the initial problem exposed : it takes energy to make energy. If Gluconeogenesis came before or not, does not change anything in that fundamental problem.

    Following paper makes the same assertion:
    Evolution of the coordinate regulation of glycolytic enzyme genes by hypoxia
    The first glycolytic enzymes in the Archean period probably contributed mainly anabolic, gluconeogenic functions (Conway, 1992; Romano and Conway, 1996; Selig et al., 1997), with catabolic functions being acquired subsequently as kinases appeared to use ATP, ADP or pyrophosphate as phosphate shuttles (Romano and Conway, 1996).
    http://jeb.biologists.org/content/206/17/2911

    They just assert catabolic functions were being acquired subsequently . How ?! 3 enzymes had to be replaced to generate a reverse function.

    Many papers mention glycolysis as one of the most conserved and fundamental metabolic pathways.

    Monroe Strickberger, Evolution, page 13:
    "Anaerobic glycolysis, the breakdown of glucose in the absence of oxygen, is perhaps the most elemental metabolic pathway, and all living creatures share various sections of this pathway.This universality seems to depend on the fact that all existing organisms derive their free energy from the chemical breakdown of such monosaccharides."

    Origins of Life on the Earth and in the Cosmos pg. 194
    "Glycolysis is the most ubiquitous pathway in all energy metabolism, occurring in almost every living cell."

    The Origin and Evolution of Cells
    "In the initially anaerobic atmosphere of Earth, the first energy-generating reactions presumably involved the breakdown of organic molecules in the absence of oxygen. These reactions are likely to have been a form of present-day glycolysis—the anaerobic breakdown of glucose to lactic acid, with the net energy gain of two molecules of ATP."
    https://www.ncbi.nlm.nih.gov/books/NBK9841/

    ReplyDelete
  9. Your explanation does not take into consideration that :

    at three points, all outside the metabolic pools, do we find reactions in gluconeogenesis that use different enzymes:

    https://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/gluconeo.htm
    (1) the conversion of pyruvate to phosphoenolpyruvate (PEP),
    (2) the conversion of fructose-1,6-bisphosphate to fructose-6-phosphate, and
    (3) the conversion of hexose phosphate to storage polysaccharide or hexose phosphate to glucose.


    Clearly, if cells are to conduct these reactions in the reverse direction, the three reactions must have a different ATP-to- ADP Stoichiometry and accordingly different enzymes are required.

    Gluconeogenesis (GNG) is a metabolic pathway that results in the generation of glucose from the breakdown of proteins ,these substrates include glucogenic amino acids (although not ketogenic amino acids); from breakdown of lipids (such as triglycerides), they include glycerol (although not fatty acids); and from other steps in metabolism they include pyruvate and lactate.

    Questions:
    If Gluconeogenesis came first, where did the atp and all other essential products to make enzymes come from to make the enzymes in the gluconeogenesis pathway ?
    Prior Glycolysis took over, what other pathway would supposedly have been in place to produce the same substrates as Glycolysis ?
    What was in your view the precursos of gluconeogenesis?
    Why would Gluconeogenesis be a less chicken egg - catch 22 problem ? Its complexity is basically the same as of Glycolysis.
    If the problem of Glycolysis first was the fact that no Glucose was readily available on early earth, what makes you think, the above mentioned substrates to feed gluconeogenesis were less a problem ?
    Does Gluconeogenesis not depend on mitochondria, the cytoplasm, and the cell membrane amongst other molecules ?
    Had pyruvate carboxylase and acetyl-CoA not have to be present for gluconeogenesis to start ?
    How did the transition from the 3 enzymes used in Gluconeogenesis to Glycolysis occur, and upon what selective pressures ?
    Why would there have been a transition from a supposed precursor system to Glycolysis ?

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  10. I take a chance and offer this quote from Reinventing The Sacred where the author, Stuart A. Kauffman argues

    My own theory of collectively autocatalytic sets suggests that their formation is highly probable. The theory can now be teseted. If correct, the routes to molecular reproduction may be much easier than we have imagined and constitute a form of fully emergent, spontaneous self-organization of a chemical-reaction system. Such emergence would not be reducible to physices. And life, in the sense of molecular reproduction, would be expected, not incredibly improbable. If so, our view of life changes radically. Not only does life not need special intervention by a Creator God, it is a natural, emergent expression of the routine creativity of the universe.

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