# Hunter: Finally, the Details of How Proteins Evolve

**URL:** <https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714>\
**Category:** Conversation\
**Tags:** Science\
**Created:** [February 21, 2019, 6:26pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714 "2019-02-21T18:26:15Z")\
**Posts on this page:** 20\
**Page:** 4

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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:** [February 24, 2019, 12:44am UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/67 "2019-02-24T00:44:15Z")

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> [@Cornelius\_Hunter](#):
>
> Please read these:

LOL! I point out you often dodge questions by linking back to your own blog to repeat the claim. So what do you do? **Post four links back to your own blog to repeat the claim**. 😄

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [February 24, 2019, 1:24am UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/68 "2019-02-24T01:24:17Z")

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@Cornelius_Hunter, that last post was spam. Please do not do that again.

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**Author:** ![Cornelius\_Hunter](https://avatars.discourse-cdn.com/v4/letter/c/e495f1/32.png) [@Cornelius\_Hunter](https://discourse.peacefulscience.org/u/Cornelius_Hunter)\
**Post date:** [February 24, 2019, 2:52am UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/69 "2019-02-24T02:52:20Z")

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> [@Rumraket](#):
>
> If this is supposed to constitute an analogy to this current situation you’re going to have to explain how.

The fact that all outcomes are equiprobable does not save the theory. The majority of outcomes don’t help, making for a big entropy barrier. But Epicureanism has bred and fueled this erroneous argument that it doesn’t matter because all outcomes are equiprobable, which I explain at the links which were banned. Metaphysics is driving the theory–no one would make this argument otherwise.

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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:** [February 24, 2019, 3:26am UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/70 "2019-02-24T03:26:43Z")

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What is Mr. Hunter talking about above?

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**Author:** ![Patrick](https://avatars.discourse-cdn.com/v4/letter/p/b2d939/32.png) [@Patrick](https://discourse.peacefulscience.org/u/Patrick)\
**Post date:** [February 24, 2019, 3:30am UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/71 "2019-02-24T03:30:59Z")

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> [@Cornelius\_Hunter](#):
>
> The fact that all outcomes are equiprobable does not save the theory. The majority of outcomes don’t help, making for a **big entropy barrier.** But **Epicureanism** has bred and fueled this erroneous argument that it doesn’t matter because all outcomes are equiprobable, which I explain at the links which were banned. **Metaphysics** is driving the theory–no one would make this argument otherwise.

Please translate or explain what the above is talking about. Thanks

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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:** [February 24, 2019, 3:31am UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/72 "2019-02-24T03:31:45Z")

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> [@Cornelius\_Hunter](#):
>
> The fact that all outcomes are equiprobable does not save the theory.

All outcomes aren’t equiprobable. The selection feedback part of the evolutionary process favor those solutions which give their possessors a better chance at reproducing than their neighbors. I know you’ve had your false claim corrected probably close to a hundred times over the years but you keep right on making it.

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**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [February 24, 2019, 10:51pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/73 "2019-02-24T22:51:45Z")

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> [@Cornelius\_Hunter](#):
>
> The fact that all outcomes are equiprobable does not save the theory.

But they aren’t equiprobable. Rather they just look equiprobable after the fact, so because there are many possible outcomes, any one of them looks unlikely.

> The majority of outcomes don’t help

Don’t help with what? Are you talking about the fact that most mutations are neutral or deleterious?

> making for a big entropy barrier.

Entropy barrier?

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**Author:** ![Cornelius\_Hunter](https://avatars.discourse-cdn.com/v4/letter/c/e495f1/32.png) [@Cornelius\_Hunter](https://discourse.peacefulscience.org/u/Cornelius_Hunter)\
**Post date:** [February 25, 2019, 6:11am UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/74 "2019-02-25T06:11:24Z")

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> [@Rumraket](#):
>
> But they aren’t equiprobable. Rather they just look equiprobable after the fact, so because there are many possible outcomes, any one of them looks unlikely.

Right. Don’t get hung up on “equiprobable.” They are equiprobable for examples such as coin tossing, which is a common example. But the problem doesn’t hinge on that. The argument to which you appealed (which is not uncommonly used by evolutionists), that unlikely events are OK because all possible events are unlikely, doesn’t save the theory. I posted four links which explain the science in more detail, but Swamidass said it was spam. You can see the landscaper story which illustrates the problem.

> [@Rumraket](#):
>
> Entropy barrier?

Yes, the origin of the biosphere is an enormous entropy problem (i.e., reduction). The same is true for biological structures on a smaller scale, such as genes. You are advocating a theory that calls for this.

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**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [February 25, 2019, 11:47am UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/75 "2019-02-25T11:47:09Z")

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> [@Cornelius\_Hunter](#):
>
> Right. Don’t get hung up on “equiprobable.” They are equiprobable for examples such as coin tossing, which is a common example. But the problem doesn’t hinge on that. The argument to which you appealed (which is not uncommonly used by evolutionists), that unlikely events are OK because all possible events are unlikely, doesn’t save the theory. I posted four links which explain the science in more detail, but Swamidass said it was spam. You can see the landscaper story which illustrates the problem.

I really don’t see what the problem is here. Pick sufficiently long series of neutral and beneficial mutations and compound the probability, and you’ll get some absurdly small number. **Yet it happened.**

In one of the lineages in the LTEE over 600 mutations have been fixed. What are the odds of those 600 mutations? Many of them are neutral, some of them are adaptive. Some of the adaptive ones were dependent on earlier neutral ones.

What is this kind of after-the-fact apparent improbability of some event supposed to tell us? You say this is a problem, but how? You don’t explain how, you just declare it a problem.

> [@Cornelius\_Hunter](#):
>
> Yes, the origin of the biosphere is an enormous entropy problem (i.e., reduction). The same is true for biological structures on a smaller scale, such as genes. You are advocating a theory that calls for this.

It’s ironic that you did a blog post on a paper that explains _how_ a protein coding gene arose, and now you’re calling that a problem because you can calculate that the particular changes that led to this protein would compound to a small probability out all the other ways mutations could have happened but didn’t.

This kind of evidence should actually cause you to question your own view that there is some sort of problem. Why do we have this kind of evidence in the first place if that which you imagine to be a big problem is one?

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**Author:** ![Cornelius\_Hunter](https://avatars.discourse-cdn.com/v4/letter/c/e495f1/32.png) [@Cornelius\_Hunter](https://discourse.peacefulscience.org/u/Cornelius_Hunter)\
**Post date:** [February 25, 2019, 2:03pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/76 "2019-02-25T14:03:33Z")

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> [@Rumraket](#):
>
> I really don’t see what the problem is here. Pick sufficiently long series of neutral and beneficial mutations and compound the probability, and you’ll get some absurdly small number. **Yet it happened.**

Yes, yes, precisely. This is the evolution argument. It underwrites anti-realism, as anything can evolve because small probabilities have now been rationalized.

> [@Rumraket](#):
>
> What is the kind of after-the-fact apparently improbability of some event supposed to tell us? You say this is a problem, but how? You don’t explain how, you just declare it a problem.

Actually I did explain it with the landscaper story, but the judge saw no problem in what was a pretty obvious problem. There will always be Epicureans. I also provided 4 links with more scientific detail (but Swamidass said it was spam). Here’s another explanation. You walk into your co-worker’s office, and “CONSTANTINOPLE” is spelled out in Scrabble letters on his desk. “What luck,” he exclaims, “can you believe this?” You look at it and after about 1 second realize he is playing a trick on you. He didn’t just throw down those letters randomly, he carefully arranged them.

Most configurations are junk. The chances of getting a useful configuration is small. Saying that “well, it doesn’t matter because all configurations are unlikely” is a way of getting around the scientific problem. You would never say that in the “CONSTANTINOPLE” example, because evolution is not at stake. When evolution is not at stake you can see the truth.

> [@Rumraket](#):
>
> It’s ironic that you did a blog post on a paper that explains _how_ a protein coding gene arose, and now you’re calling that a problem because you can calculate that the particular changes that led to this protein would compound to a small probability out all the other ways mutations could have happened but didn’t.
> 
> This kind of evidence should actually cause you to question your own view that there is some sort of problem.

Actually it should not cause me to question my view that there is a problem. The fact that an explanation has been provided does not mean that explanation is true, or compelling. It is the assumption that evolution is true that is underwriting the explanation. In fact even the evolutionists, in a rare admission, say the explanation is unlikely and involves a lot of serendipity. If you free yourself of Epicureanism you can see the problem.

> [@Rumraket](#):
>
> Why do we have this kind of evidence in the first place if that which you imagine to be a big problem is one?

Good question, but our inability at this time to understand all things about biology is not evidence for evolution. Nor is it evidence that a problem is not actually a problem. In fact, this question you are asking is highly underdetermined at this time. IOW, what you are saying here is that either (i) I supply you with explanations for everything biology, or (ii) it evolved.

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**Author:** ![pnelson](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/pnelson/32/876_2.png) [@pnelson](https://discourse.peacefulscience.org/u/pnelson)\
**Post date:** [February 25, 2019, 2:38pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/77 "2019-02-25T14:38:49Z")

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George’s point (in the post immediately above) can be seen most vividly in origin-of-life (OOL) research.

OOL researchers face daunting small probabilities: the formation of RNA from its chemical constituents, the isolation of that RNA in a vesicle, the establishment of metabolic pathways in the same vesicle, and so on. Their research goal, therefore, is find natural pathways from chemistry to a living cell whose probabilities are as close to 1.0 as possible, **so they don’t have to rely on luck** (“serendipity”). Francis Crick wrote eloquently about this “don’t lean on luck” problem in his classic _Life Itself_ (1981). Chance is always available, of course. Some damn thing happened, and go figure, here we are. Whooda thunkit.

George said:

“The fact that an explanation has been provided does not mean that explanation is true, or compelling.”

_Exactement._ This is precisely what I was getting at with my questions, above, about testability. Why should I think the long chain of highly serendipitous events invoked in the antifreeze gene origin story is _true_?

The answer cannot be, “Well, we told you a story using lucky events, so that’s enough.” That may suffice for an Epicurean, but it should not satisfy anyone else.

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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:** [February 25, 2019, 2:58pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/78 "2019-02-25T14:58:02Z")

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> [@Cornelius\_Hunter](#):
>
> Most configurations are junk. The chances of getting a useful configuration is small. Saying that “well, it doesn’t matter because all configurations are unlikely” is a way of getting around the scientific problem. You would never say that in the “CONSTANTINOPLE” example, because evolution is not at stake. When evolution is not at stake you can see the truth.

LOL! After all these years you’re still pushing the silly Creationist canard the genetic sequences we see today had to happen by **pure chance** instead of the long-term iterative feedback process we know produced them from simpler precursors.

Tell us CH, have you ever convinced a single person with that lame argument? One a reasonably bright Jr. High School student can see through?

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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:** [February 25, 2019, 2:58pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/79 "2019-02-25T14:58:15Z")

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> [@pnelson](#):
>
> Why should I think the long chain of highly serendipitous events invoked in the antifreeze gene origin story is _true_ ?

The problem with this line of reasoning is that nothing about the origination of antifreeze genes has been shown to be highly (or even possibly) improbable, such that a “long chain of highly serendipitous events” is needed or involved. And, as indicated somewhere in the preceding, the process is eminently testable, in that hypotheses concerning mechanism can be proposed, tested, and evaluated.

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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:** [February 25, 2019, 3:02pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/80 "2019-02-25T15:02:16Z")

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> [@pnelson](#):
>
> _Exactement._ This is precisely what I was getting at with my questions, above, about testability. Why should I think the long chain of highly serendipitous events invoked in the antifreeze gene origin story is _true_ ?

Is today National “Repeat Creationist Canard It Happened Just By Luck” Day? 🙄

How would you test the idea the Grand Canyon was formed by erosion and not just “a long chain of highly serendipitous events” which happened to carve a huge hole in the ground? Are you going to attack modern Geology too with your silly strawman reasoning?

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**Author:** ![pnelson](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/pnelson/32/876_2.png) [@pnelson](https://discourse.peacefulscience.org/u/pnelson)\
**Post date:** [February 25, 2019, 3:05pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/81 "2019-02-25T15:05:20Z")

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> [@Art](#):
>
> The problem with this line of reasoning is that nothing about the origination of antifreeze genes has been shown to be highly (or even possibly) improbable, such that a “long chain of highly serendipitous events” is needed or involved.

The lead author on the study apparently disagrees:

“Its development in these fishes that make their living in icy Arctic waters occurred as a result of a series of seemingly improbable, serendipitous events,” Cheng said.

Read more at: [Study of Arctic fishes reveals the birth of a gene—from 'junk'](https://phys.org/news/2019-02-arctic-fishes-reveals-birth-genefrom.html#jCp)

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<div class="post-metadata">

**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:** [February 25, 2019, 3:07pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/82 "2019-02-25T15:07:53Z")

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> [@pnelson](#):
>
> “Its development in these fishes that make their living in icy Arctic waters occurred as a result of a series of seemingly improbable, serendipitous events,” Cheng said.

As we have seen in this discussion, Dr. Cheng is wrong. Especially about the expectations regarding recruitment of gene expression signals.

Or perhaps, @Paul_Nelson , you are telling us that it is Bock who is wrong. Maybe you can relate some of the experimental data that supports this assertion. Not quotes, but pointers to data…

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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:** [February 25, 2019, 3:08pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/83 "2019-02-25T15:08:01Z")

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> [@pnelson](#):
>
> “Its development in these fishes that make their living in icy Arctic waters occurred as a result of a series of **seemingly** improbable, serendipitous events,” Cheng said.

Note the key word **seemingly.**

I know the DI is pretty desperate for any poo they can fling at evolutionary theory but are these really the best you and Hunter can come up with?

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**Author:** ![pnelson](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/pnelson/32/876_2.png) [@pnelson](https://discourse.peacefulscience.org/u/pnelson)\
**Post date:** [February 25, 2019, 3:17pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/84 "2019-02-25T15:17:09Z")

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> [@Art](#):
>
> you are telling us that it is Bock who is wrong

No – you cited Bock 2017 as relevant. Since we both have the paper in question, please provide the data in Bock which you see as bearing on the antifreeze gene story, and I’ll take a look at it.

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<div class="post-metadata">

**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:** [February 25, 2019, 3:18pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/85 "2019-02-25T15:18:25Z")

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> [@Art](#):
>
> As we have seen in this discussion, Dr. Cheng is wrong. Especially about the expectations regarding recruitment of gene expression signals.

Dr. Cheng wasn’t wrong, that was just a bit of hyperbole by her used as a framing sentence. The money shot is her final quote:

“After years of study, we finally understand the birth of the codfish [antifreeze](https://phys.org/tags/antifreeze/) gene,” Cheng said. “This paper explains how the [antifreeze protein](https://phys.org/tags/antifreeze+protein/) in the northern codfish evolved. And it’s an even more fascinating mechanism than the Antarctic version, which involved a pre-existing gene.”

Of course the good Dr. Nelson forgot to include that sentence while he was quote-mining.

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<div class="post-metadata">

**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:** [February 25, 2019, 3:20pm UTC](https://discourse.peacefulscience.org/t/hunter-finally-the-details-of-how-proteins-evolve/4714/86 "2019-02-25T15:20:53Z")

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> [@pnelson](#):
>
> No – you cited Bock 2017 as relevant. Since we both have the paper in question, please provide the data in Bock which you see as bearing on the antifreeze gene story, and I’ll take a look at it.

Second full paragraph on p. 7, I believe. And reference 104.

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