# The Return of the Probability Argument

**URL:** <https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745>\
**Category:** Conversation\
**Tags:** Science\
**Created:** [December 12, 2020, 8:58pm UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745 "2020-12-12T20:58:25Z")\
**Posts on this page:** 20\
**Page:** 1

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**Author:** ![ProfBravus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/profbravus/32/9712_2.png) [@ProfBravus](https://discourse.peacefulscience.org/u/ProfBravus)\
**Post date:** [December 12, 2020, 8:58pm UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/1 "2020-12-12T20:58:25Z")

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(except that, here on Peaceful Science, it never went away)

> **[The return of the probability argument](https://freethoughtblogs.com/pharyngula/2020/12/11/the-return-of-the-probability-argument/)**
>
> We should have known. We’ve heard it for so long. Creationists love the Argument from Big Numbers — if we chain together a whole series of improbabilities and multiply them, we can get …

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [December 12, 2020, 9:25pm UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/2 "2020-12-12T21:25:24Z")

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The article does not characterize the argument properly. A version of the probability argument convinced me that Darwin’s original claim 'universal common descent" was not viable.

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**Author:** ![Timothy\_Horton](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/timothy_horton/32/9410_2.png) [@Timothy\_Horton](https://discourse.peacefulscience.org/u/Timothy_Horton)\
**Post date:** [December 12, 2020, 10:00pm UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/4 "2020-12-12T22:00:58Z")

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> [@colewd](#):
>
> The article does not characterize the argument properly. A version of the probability argument convinced me that Darwin’s original claim 'universal common descent" was not viable.

Please _do_ relate to us the proper probability argument which disproves UCD. Provide your calculations and don’t forget to justify any assumptions you may make.

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [December 12, 2020, 10:47pm UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/5 "2020-12-12T22:47:37Z")

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Time for bingo? Key words tornado, junkyard, 747, 150 amino acids, number of atoms in the universe. Not sure what else.

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**Author:** ![Witchdoc](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/witchdoc/32/10610_2.png) [@Witchdoc](https://discourse.peacefulscience.org/u/Witchdoc)\
**Post date:** [December 13, 2020, 12:16am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/6 "2020-12-13T00:16:17Z")

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So if it convinced you, presumably you understand their argument and should be able to present the argument to us.

What _is_ the probability argument that convinced you?

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [December 13, 2020, 12:52am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/7 "2020-12-13T00:52:56Z")

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> [@Witchdoc](#):
>
> What _is_ the probability argument that convinced you?

It was initially an argument actually against ID advocate Doug Axe by @Art.

> **[Axe (2004) and the evolution of enzyme function](https://pandasthumb.org/archives/2007/01/92-second-st-fa.html)**

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**Author:** ![Witchdoc](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/witchdoc/32/10610_2.png) [@Witchdoc](https://discourse.peacefulscience.org/u/Witchdoc)\
**Post date:** [December 13, 2020, 1:35am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/8 "2020-12-13T01:35:44Z")

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Go on.

Can you explain the argument and what about Axe’s argument that convinced you?

Since you are convinced by it, you should be able to enunciate to us the argument.

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**Author:** ![dsterncardinale](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/dsterncardinale/32/9144_2.png) [@dsterncardinale](https://discourse.peacefulscience.org/u/dsterncardinale)\
**Post date:** [December 13, 2020, 1:36am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/9 "2020-12-13T01:36:17Z")

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_The_ problem with Axe (2004): Sought a _specific_ target protein, calculated it’s likelihood, and extrapolated that to _all_ proteins.

The assumptions embedded in that are…wow. For starters, assumed there is one way, and one way _only_, to accomplish some biochemical process. Assumed there is no selection for intermediate states. Assumed no recombination.

That stuff alone is sufficient to invalidate his work. It just isn’t relevant to how evolutionary processes work in reality.

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**Author:** ![CrisprCAS9](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/crisprcas9/32/9145_2.png) [@CrisprCAS9](https://discourse.peacefulscience.org/u/CrisprCAS9)\
**Post date:** [December 13, 2020, 2:32am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/10 "2020-12-13T02:32:44Z")

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> [@colewd](#):
>
> A version of the probability argument convinced me that Darwin’s original claim 'universal common descent" was not viable.

One assumes, since these arguments are based on proteins, that you fully accept then the common descent of all animal life? Ignoring, of course, the fact that the probability arguments are all flawed to the point of absurdity.

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [December 13, 2020, 3:15am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/11 "2020-12-13T03:15:26Z")

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> [@Witchdoc](#):
>
> Can you explain the argument and what about Axe’s argument that convinced you?

It was not Axe’s argument. It was his experiment that showed the possibility given certain conditions that specific protein function is sequence dependent and in some cases highly sequence dependent.

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**Author:** ![CrisprCAS9](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/crisprcas9/32/9145_2.png) [@CrisprCAS9](https://discourse.peacefulscience.org/u/CrisprCAS9)\
**Post date:** [December 13, 2020, 3:25am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/12 "2020-12-13T03:25:38Z")

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> [@colewd](#):
>
> that specific protein function is sequence dependent

Except that all of his assumptions were wrong, and his conclusion was wrong. By ~70 orders of magnitude.

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**Author:** ![Art](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/art/32/3805_2.png) [@Art](https://discourse.peacefulscience.org/u/Art)\
**Post date:** [December 13, 2020, 3:50am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/13 "2020-12-13T03:50:26Z")

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> [@colewd](#):
>
> It was his experiment that showed the possibility given certain conditions that specific protein function is sequence dependent and in some cases highly sequence dependent.

Axe did no such experiment.

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [December 13, 2020, 4:00am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/14 "2020-12-13T04:00:53Z")

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> [@Art](#):
>
> Axe did no such experiment.

I did not make a claim about his methods. Here is your claim which you reviewed with Doug.

> “Axe (2004) has performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and corrects for several sources of possible estimation error inherent in them. On the basis of these experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that perform a specified function via any folded structure to (b) the whole set of possible amino acids sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 10^77. Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 10^77.”

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<div class="post-metadata">

**Author:** ![ProfBravus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/profbravus/32/9712_2.png) [@ProfBravus](https://discourse.peacefulscience.org/u/ProfBravus)\
**Post date:** [December 13, 2020, 4:21am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/15 "2020-12-13T04:21:03Z")

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I don’t know enough in the field to interpret it, but did read that paper. Here’s a direct link for anyone keen to do likewise: [https://www.sciencedirect.com/science/article/pii/S0022283604007624?casa\_token=I1Hf0uk7pSMAAAAA:SiJLUqWGQ32ihUTFDCsj9p\_Zh5S0oGui5vdLYoUN2xkPdO8\_unFJJiZSUH5o3yc2PhENNq6fCQ](https://www.sciencedirect.com/science/article/pii/S0022283604007624?casa_token=I1Hf0uk7pSMAAAAA:SiJLUqWGQ32ihUTFDCsj9p_Zh5S0oGui5vdLYoUN2xkPdO8_unFJJiZSUH5o3yc2PhENNq6fCQ)

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**Author:** ![Witchdoc](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/witchdoc/32/10610_2.png) [@Witchdoc](https://discourse.peacefulscience.org/u/Witchdoc)\
**Post date:** [December 13, 2020, 4:29am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/16 "2020-12-13T04:29:27Z")

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Okay.

So can you explain to me how his experiment demonstrates 1 in 10^77.

For our 1 in 1x10^9 figure, it is very easy to see how we reached it.  
Phage display of 2-3 billion different antibodies demonstrated 5 have beta lactamase ability.

Did Axe make 10^100 proteins, and figure out 10^23 of those showed beta lactamase ability, or something along these lines??

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [December 13, 2020, 4:48am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/17 "2020-12-13T04:48:52Z")

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> [@Witchdoc](#):
>
> For our 1 in 1x10^9 figure, it is very easy to see how we reached it.  
> Phage display of 2-3 billion different antibodies demonstrated 5 have beta lactamase ability.

Let’s assume for arguments sake that your 10^9 is right in certain applications. How do you account for the origin of ATP synthase given these odds for a single 100AA protein?

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**Author:** ![Witchdoc](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/witchdoc/32/10610_2.png) [@Witchdoc](https://discourse.peacefulscience.org/u/Witchdoc)\
**Post date:** [December 13, 2020, 4:53am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/18 "2020-12-13T04:53:02Z")

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Did you just chuck out a red herring?

But let’s humor you for a sec.

The current idea for how it evolved is that it is thought to have come about from two functionally independent subunits which became associated and mutated to gain a new function.

There is another thread where a paper by Thornton et al demonstrates that the mutations causing association of proteins is favorable from a natural selection point of view, making them more mutable without loss of function, and able to have synergistic beneficial mutations.

> [@A hydrophobic ratchet entrenches molecular complexes](https://discourse.peacefulscience.org/t/a-hydrophobic-ratchet-entrenches-molecular-complexes/12726/2):
>
> Fascinating. Seems like an excellent example of constructive neutral evolution. Using structural bioinformatics, we show that a universal mutational propensity drives sites that are buried in multimeric interfaces to accumulate hydrophobic substitutions to levels that are not tolerated in monomers. Even more fascinating is the idea of an intrinsic mutational bias towards this kind of gratuitous complexity.

The two subunits thought to have associated and gained new functionality together was the combination of V-ATPase with a DNA helicase.

> **[ATP synthase](https://en.m.wikipedia.org/wiki/ATP_synthase)**
>
> ATP synthase is a protein that catalyzes the formation of the energy storage molecule adenosine triphosphate (ATP) using adenosine diphosphate (ADP) and inorganic phosphate (Pi). ATP synthase is a molecular machine. The overall reaction catalyzed by ATP synthase is:
> ATP synthase lies across a cellular membrane and forms an aperture that protons can cross from areas of high concentration to areas of low concentration, imparting energy for the synthesis of ATP. This electrochemical gradient is gen...

It is supposed that glycolysis first produced ATP, then oxidative phosphorylation and ATP synthase evolved afterwards to make use of waste products of glycolysis to increase efficiency.

That all said and done, I am not ashamed to admit that whether or not abiogenesis is true, if it did occur, we may not know or ever know how it happened.

_Abiogenesis is not a prerequisite for evolution to be true._

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**Author:** ![Art](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/art/32/3805_2.png) [@Art](https://discourse.peacefulscience.org/u/Art)\
**Post date:** [December 13, 2020, 5:10am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/19 "2020-12-13T05:10:32Z")

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> [@colewd](#):
>
> Here is your claim which you reviewed with Doug.
> 
> > “Axe (2004) has performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and corrects for several sources of possible estimation error inherent in them. On the basis of these experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that perform a specified function via any folded structure to (b) the whole set of possible amino acids sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 10^77. Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 10^77.”

Sorry @colewd but this excerpt doesn’t match your description. If you got from this that “ his experiment that showed the possibility given certain conditions that specific protein function is sequence dependent and in some cases highly sequence dependent.”, then I believe you are misunderstanding Axe’s work. You may want to reconsider your position, given that you have not properly grasped the argument that brought you there.

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [December 13, 2020, 5:43am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/20 "2020-12-13T05:43:23Z")

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> [@Art](#):
>
> Sorry @colewd but this excerpt doesn’t match your description. If you got from this that “ his experiment that showed the possibility given certain conditions that specific protein function is sequence dependent and in some cases highly sequence dependent.”, then I believe you are misunderstanding Axe’s work. You may want to reconsider your position, given that you have not properly grasped the argument that brought you there.

I don’t see a problem with my statement and I believe you are misinterpreting it. It is certainly as I intended it supported by your claims in the paper of various probabilities given different experimental methods. If there are probabilities of function dependent on sequence then by definition the protein is sequence dependent. That does not mean only one sequence will perform the function.

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [December 13, 2020, 5:47am UTC](https://discourse.peacefulscience.org/t/the-return-of-the-probability-argument/12745/21 "2020-12-13T05:47:37Z")

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> [@Witchdoc](#):
>
> That all said and done, I am not ashamed to admit that whether or not abiogenesis is true, if it did occur, we may not know or ever know how it happened.
> 
> _Abiogenesis is not a prerequisite for evolution to be true._

I understand and if ATP synthase was required for first life then this point is valid, I however only am showing that the low end probability estimates are problematic for protein complexes with multiple proteins and long AA chains. These appear through long time scales and new animal origin events

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