# Side Comments on Kondrashov’s Paradox

**URL:** <https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842>\
**Category:** Side Conversation\
**Tags:** Comments\
**Created:** [May 26, 2026, 8:42pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842 "2026-05-26T20:42:06Z")\
**Posts on this page:** 20\
**Page:** 6

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**Author:** ![Gisteron](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/gisteron/32/15845_2.png) [@Gisteron](https://discourse.peacefulscience.org/u/Gisteron)\
**Post date:** [May 30, 2026, 11:56am UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/101 "2026-05-30T11:56:07Z")

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> [@UncensoredPilgrims](#):
>
> From the Science Direct writeup: …

Oh. So not from the actual article, then.

> [@UncensoredPilgrims](#):
>
> Is this something you genuinely trust?

Can’t speak for Rumraket, but I sure do not. Press releases about scientific literature are not in their own right scientific literature. What ever trust is due the latter in no way translates to the former.

> [@UncensoredPilgrims](#):
>
> But it gets wierder.
> 
> > the team calculated that more than 99% of amino acid substitutions should be adaptive. Gene evolution should also happen much faster than scientists actually observe in nature.
> 
> What is this trash?

Not the actual publication presented for our consideration is what this is. What’s your point?

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**Author:** ![Paul\_King](https://avatars.discourse-cdn.com/v4/letter/p/5f8ce5/32.png) [@Paul\_King](https://discourse.peacefulscience.org/u/Paul_King)\
**Post date:** [May 30, 2026, 11:57am UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/102 "2026-05-30T11:57:00Z")

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[Deep mutational scanning](https://pmc.ncbi.nlm.nih.gov/articles/PMC4410700/) does not use AI. Indeed the brief description given - “In deep mutational scanning, scientists create many mutations in a gene or region of the genome and then measure how those changes affect the organism” should have told you that.

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**Author:** ![Tim](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/tim/32/9381_2.png) [@Tim](https://discourse.peacefulscience.org/u/Tim)\
**Post date:** [May 30, 2026, 11:58am UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/103 "2026-05-30T11:58:11Z")

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> [@UncensoredPilgrims](#):
>
> > A mutation that boosts fitness today may reduce fitness tomorrow. As a result, evolution can be filled with beneficial changes that never become permanent.
> 
> Okay … so evolution is impossible then. Environments change too quickly for anything to be helpful long enough to spread to fixation.

So we can add the English language to phenotypic traits, and the difference between theory and simulation on one hand, and empirical evidence on the other, as things Paul doesn’t understand.

The article indicates that the environment _ **“may”** _ change, not that it _will_. It does not mean that “evolution is impossible”, it merely means that, in an uncertain world (and thus uncertain environment), its effects are never completely certain.

It may rain tomorrow – but that doesn’t mean that I can never get my washing dry.

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**Author:** ![UncensoredPilgrims](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/uncensoredpilgrims/32/24034_2.png) [@UncensoredPilgrims](https://discourse.peacefulscience.org/u/UncensoredPilgrims)\
**Post date:** [May 30, 2026, 12:02pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/104 "2026-05-30T12:02:09Z")

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From the paper you just linked:

> For other proteins with complex functions (e.g. signaling proteins), large-scale mutagenesis data will need to be combined with an integrative computational model.

Yeah, I’m still getting the strong impression this is talking about AI.

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**Author:** ![UncensoredPilgrims](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/uncensoredpilgrims/32/24034_2.png) [@UncensoredPilgrims](https://discourse.peacefulscience.org/u/UncensoredPilgrims)\
**Post date:** [May 30, 2026, 12:03pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/105 "2026-05-30T12:03:01Z")

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> [@Gisteron](#):
>
> Not the actual publication presented for our consideration is what this is. What’s your point?

Either the science writer is lying about what is in the paper, or somewhere in the paper they make the ridiculous claim that 99% of amino acid substitutions are beneficial.

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**Author:** ![Tim](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/tim/32/9381_2.png) [@Tim](https://discourse.peacefulscience.org/u/Tim)\
**Post date:** [May 30, 2026, 12:15pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/106 "2026-05-30T12:15:24Z")

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Not only “not the actual publication”, but a fragment deceptively quoted out of context.

Here is what the writer actually said:

> They found that more than 1% of the amino acid changing mutations they examined were beneficial. That may sound small, but in evolutionary theory it is enormous. If that many mutations are helpful, the team calculated that more than 99% of amino acid substitutions should be adaptive. Gene evolution should also happen much faster than scientists actually observe in nature.
> 
> That mismatch forced the researchers to rethink one of their assumptions. The problem, they concluded, may be that environments do not stay still.

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**Author:** ![Paul\_King](https://avatars.discourse-cdn.com/v4/letter/p/5f8ce5/32.png) [@Paul\_King](https://discourse.peacefulscience.org/u/Paul_King)\
**Post date:** [May 30, 2026, 12:20pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/107 "2026-05-30T12:20:35Z")

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> [@UncensoredPilgrims](#):
>
> Yeah, I’m still getting the strong impression this is talking about AI.

Did you notice that the paper dates from 2014? Or that the statement you quote applies to only some proteins? Did you bother to check if the computational tools actually mentioned in the paper are AI? Noting that they will - naturally - be older than the paper?

Your impression is what you want to see.

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**Author:** ![UncensoredPilgrims](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/uncensoredpilgrims/32/24034_2.png) [@UncensoredPilgrims](https://discourse.peacefulscience.org/u/UncensoredPilgrims)\
**Post date:** [May 30, 2026, 12:21pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/109 "2026-05-30T12:21:44Z")

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> [@Paul\_King](#):
>
> Did you notice that the paper dates from 2014?

Machine learning is not so new that it didn’t exist in 2014, it just wasn’t mainstream yet. And in any case, we’re talking about a paper from 2025.

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**Author:** ![UncensoredPilgrims](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/uncensoredpilgrims/32/24034_2.png) [@UncensoredPilgrims](https://discourse.peacefulscience.org/u/UncensoredPilgrims)\
**Post date:** [May 30, 2026, 12:24pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/110 "2026-05-30T12:24:05Z")

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I just realized my mistake. The writer said “amino acid substitutions”, not “mutations”. My bad.

I still think it’s wrong, and it’s a denial of neutral theory obviously. Based on what exactly we can’t be sure.

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**Author:** ![Paul\_King](https://avatars.discourse-cdn.com/v4/letter/p/5f8ce5/32.png) [@Paul\_King](https://discourse.peacefulscience.org/u/Paul_King)\
**Post date:** [May 30, 2026, 12:27pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/111 "2026-05-30T12:27:10Z")

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The explosion in machine learning is relatively new - and of course the 2014 date is the most relevant to the method itself. Skimming things, looking for excuses to jump to convenient conclusions is no way to get to the truth.

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**Author:** ![UncensoredPilgrims](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/uncensoredpilgrims/32/24034_2.png) [@UncensoredPilgrims](https://discourse.peacefulscience.org/u/UncensoredPilgrims)\
**Post date:** [May 30, 2026, 12:32pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/112 "2026-05-30T12:32:20Z")

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> [@Paul\_King](#):
>
> Skimming things, looking for excuses to jump to convenient conclusions is no way to get to the truth.

You guys are not trying to get to the truth, that much is obvious. Looking for convenient ways to make rhetorical attacks on me and anyone that would dare to question evolution – that’s no way to get to the truth either.

Suffice it to say I don’t think mainstream population genetics needs to fear this paper is going to be overturning neutral theory any time soon, but maybe ICR would get a kick out of this seemingly affirming their CET model, but then claiming the environment changes so quickly that it basically cannot be tracked.

It’s funny when you apply critical thinking to these kinds of pseudoscientific claims. At the same time we are supposed to believe that environments are so ridiculously active and dynamic that what is beneficial today may be deleterious tomorrow, but at the same time they are so static that we can see millions upon millions of years of almost complete evolutionary stasis. Crazy.

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**Author:** ![Paul\_King](https://avatars.discourse-cdn.com/v4/letter/p/5f8ce5/32.png) [@Paul\_King](https://discourse.peacefulscience.org/u/Paul_King)\
**Post date:** [May 30, 2026, 12:38pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/113 "2026-05-30T12:38:38Z")

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> [@UncensoredPilgrims](#):
>
> You guys are not trying to get to the truth, that much is obvious. Looking for convenient ways to make rhetorical attacks on me and anyone that would dare to question evolution – that’s no way to get to the truth either.

Catching you making obvious errors, indulging in clear misrepresentations and jumping to erroneous conclusions are rather more significant than “mere rhetorical attacks”. And your getting angry when you are caught only compounds the issue.

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**Author:** ![Gisteron](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/gisteron/32/15845_2.png) [@Gisteron](https://discourse.peacefulscience.org/u/Gisteron)\
**Post date:** [May 30, 2026, 12:46pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/114 "2026-05-30T12:46:52Z")

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> [@UncensoredPilgrims](#):
>
> > [@Gisteron](#):
> >
> > Not the actual publication presented for our consideration is what this is. What’s your point?
> 
> Either the science writer is lying about what is in the paper, or somewhere in the paper they make the ridiculous claim that 99% of amino acid substitutions are beneficial.

With all due respect, my experience with creationists quoting PopSci articles (or anything else, for that matter) equipped me with little trust of their accuracy of such representations. That being said, press authors being lay persons, I would sooner expect them to make a mistake summarizing the research, and have no qualms about pointing out their errors, if it so matters to the discussion. We are discussing the paper, however, not what people who are not here said about it in other texts. In that context, I think it rather odd that you would choose to quote those words instead of the paper.

> [@UncensoredPilgrims](#):
>
> You guys are not trying to get to the truth, that much is obvious. Looking for convenient ways to make rhetorical attacks on me and anyone that would dare to question evolution – that’s no way to get to the truth either.

You were not questioning evolution, though. The genetic entropy argument openly permits that evolution happens, and argues that in such a case life, or at least currently living lineages, must be young. _At most_ it is against an argument against most common ancestry, if we’ll say that it takes a while for species to diverge. It is not an argument, at any rate, against the idea that evolution in general happens.

> [@UncensoredPilgrims](#):
>
> At the same time we are supposed to believe that environments are so ridiculously active and dynamic that what is beneficial today may be deleterious tomorrow, but at the same time they are so static that we can see millions upon millions of years of almost complete evolutionary stasis. Crazy.

What’s your objection? Some environments change quickly, some stay the same for long periods of time. Some environments settle after being turbulent, others become very chaotic after a time of relative stasis. Nature doesn’t care how easy or convenient it is for us to describe. It is messy. It is complicated. There is nothing crazy about acknowledging it and trying to model what ever parts we can the best way we can. If anything, it’s crazy to deny the facts as they are merely because no quick little phrase can fully characterize them all.

And on that note I shall remind you again that the age of the earth – you know, the thing you are _actually_ arguing against – is known by studying things far simpler than entire ecospheres. So as interesting as complicated problems are, pointing at how far they are from entirely solved, or how much of an effort it would be to understand what solutions there are to them (much more than would be to just “nuh-uh” at all of it), will do nothing to erase the rather complete answers to much simpler questions that beyond any doubt disprove the conclusion you are building towards.

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**Author:** ![AnEvolvedPrimate](https://avatars.discourse-cdn.com/v4/letter/a/a183cd/32.png) [@AnEvolvedPrimate](https://discourse.peacefulscience.org/u/AnEvolvedPrimate)\
**Post date:** [May 30, 2026, 12:57pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/115 "2026-05-30T12:57:09Z")

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> [@Gisteron](#):
>
> And on that note I shall remind you again that the age of the earth – you know, the thing you are _actually_ arguing against – is known by studying things far simpler than entire ecospheres.

And it’s worth noting that underpinning all of this is an apologetics arugment. Paul is not arguing in favor of a young Earth because it furthers our understanding of the natural world. It’s simply about reinforcing a particular theistic belief system.

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**Author:** ![UncensoredPilgrims](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/uncensoredpilgrims/32/24034_2.png) [@UncensoredPilgrims](https://discourse.peacefulscience.org/u/UncensoredPilgrims)\
**Post date:** [May 30, 2026, 1:04pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/116 "2026-05-30T13:04:41Z")

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> [@Paul\_King](#):
>
> Catching you making obvious errors, indulging in clear misrepresentations and jumping to erroneous conclusions are rather more significant than “mere rhetorical attacks”. And your getting angry when you are caught only compounds the issue.

Sigh. This is why it’s pointless to engage here. I made the “obvious error” of temporarily misreading “substitution” as “mutation”, then correcting myself.

As far as “jumping to erroneous conclusions” goes, it remains to be seen what methodology was actually employed in that paper, since I cannot access it. And I think it’s more accurate to call what I said about their use of AI as a “suspicion” not a “conclusion”.

My biggest mistake is one that I have committed more than a few times, which was to act as if any truly honest and mutually-respectful dialog was possible in this setting.

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**Author:** ![Tim](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/tim/32/9381_2.png) [@Tim](https://discourse.peacefulscience.org/u/Tim)\
**Post date:** [May 30, 2026, 1:33pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/117 "2026-05-30T13:33:24Z")

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> [@UncensoredPilgrims](#):
>
> My biggest mistake is one that I have committed more than a few times, which was to act as if any truly honest and mutually-respectful dialog was possible in this setting.

I would suggest that it is impossible in any setting that contains an apologist.

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**Author:** ![RonSewell](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/ronsewell/32/6194_2.png) [@RonSewell](https://discourse.peacefulscience.org/u/RonSewell)\
**Post date:** [May 30, 2026, 1:53pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/118 "2026-05-30T13:53:18Z")

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> [@Gisteron](#):
>
> Some environments change quickly, some stay the same for long periods of time. Some environments settle after being turbulent, others become very chaotic after a time of relative stasis. Nature doesn’t care how easy or convenient it is for us to describe. It is messy. It is complicated.

Environments eventually do change of course, but even while they are stable, there is generally variation and gradients in the existing zone which may exert differing selective pressures on the same trait, and might even present new niches to exploit. Rock pocket mice are a studied example, but variation in environment is typical. Fish with antifreeze in blood have an advantage in neighboring cold water over kindred species without, which would serve no purpose in warmer water. So I agree, ecologies are messier and more complicated than petri dishes.

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**Author:** ![Paul\_King](https://avatars.discourse-cdn.com/v4/letter/p/5f8ce5/32.png) [@Paul\_King](https://discourse.peacefulscience.org/u/Paul_King)\
**Post date:** [May 30, 2026, 2:21pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/119 "2026-05-30T14:21:21Z")

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> [@UncensoredPilgrims](#):
>
> Sigh. This is why it’s pointless to engage here. I made the “obvious error” of temporarily misreading “substitution” as “mutation”, then correcting myself.

I wasn’t referring to that. I was thinking of your obvious error in denying the importance of traits to selection, of writing them off as merely subjective human judgements.

> [@UncensoredPilgrims](#):
>
> As far as “jumping to erroneous conclusions” goes, it remains to be seen what methodology was actually employed in that paper, since I cannot access it. And I think it’s more accurate to call what I said about their use of AI as a “suspicion” not a “conclusion”.

A suspicion that turned out to be unjustified by any actual evidence you found. But of course I can add:

> [@UncensoredPilgrims](#):
>
> At the same time we are supposed to believe that environments are so ridiculously active and dynamic that what is beneficial today may be deleterious tomorrow, but at the same time they are so static that we can see millions upon millions of years of almost complete evolutionary stasis. Crazy.

The idea that the environment can vary and that beneficial mutations can become deleterious - or vice versa - is hardly new. Indeed, sexual selection can change a deleterious trait into a beneficial one.. The idea that the environment might be variable in some respects yet stable in others seems to be obviously true, not obviously false as you would have it.

And you don’t even mention that your claimed proof that population geneticists treated their models as gospel - and Hancock’s supposed agreement - was based on a statement that said nothing of the sort.

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**Author:** ![Giltil](https://avatars.discourse-cdn.com/v4/letter/g/5f8ce5/32.png) [@Giltil](https://discourse.peacefulscience.org/u/Giltil)\
**Post date:** [May 30, 2026, 3:19pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/120 "2026-05-30T15:19:05Z")

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> [@John\_Harshman](#):
>
> Whether current population genetics theories are correct is not relevant to that central issue

It is, for according to GE analysis, either deep time is wrong or current population genetics theories are wrong. So if deep time is true, then current population genetics theories are wrong (according to GE analysis).

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<div class="post-metadata">

**Author:** ![Giltil](https://avatars.discourse-cdn.com/v4/letter/g/5f8ce5/32.png) [@Giltil](https://discourse.peacefulscience.org/u/Giltil)\
**Post date:** [May 30, 2026, 3:32pm UTC](https://discourse.peacefulscience.org/t/side-comments-on-kondrashov-s-paradox/17842/121 "2026-05-30T15:32:04Z")

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> [@RonSewell](#):
>
> Evolution and deep time is a _ **conclusion** _ of extensive evidence broader and deeper than any individual simulation model

That depends on what you mean by evolution. If you mean evolution as a blind, unpurposeful materialistic process, then your claim is wrong.

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