Hunter: Finally, the Details of How Proteins Evolve

Agreement is not the goal. Understanding is the goal. If you move us forward this way, many of us would be thrilled.

@Chris_Falter I hope you can help us too.

Yes it is. It actually is. This kind of microsattelite DNA is established as very prone to duplication, so much so that it often varies from parents to offspring.

Additionally, the fact of it’s significant variability in length between closely related fish species just lends additional support to this phenomenon.

Also, this is just one piece of the evidence. This evidence is for how the repeat sequence grew in size between different species. The evidence for the ORF’s origin in non-coding DNA is the phylogeny of similar sequences in closely related fish species, and it’s increasing dissimilarity with distance of relatedness.

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If this isn’t evidence for the historical emergence of a de novo protein from non-coding DNA, then what the hell would such evidence even have to look like?

What should closely related species DNA actually look like on that hypothesis, if not something like this?

Can you even answer such questions, or are you just stuck in “I don’t know what it would look like but I just know this isn’t it”?

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Just as a forensic scientist’s inferences from observed data (DNA on the gun handle, gunpowder on the hands, proximity to the crime scene in time and space) to an unobserved event (the defendant committed the crime) are theory-laden.

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You are missing the point. You are arguing from evolution. The paper doesn’t do that. Instead, it makes a much broader, more important, claim, and that is the point. Quote:

The paper goes on to make more of these claims. As for your argument from evolution, you offer supporting reasons for it. Fine, but that is a different claim, with its own problems. Regarding AFGP, it leads to teleology and enormous serendipity, as displayed in the paper. For example, it states that AFGP is an example of “evolutionary ingenuity.”

In the press release Cheng admits that AFGP evolution “occurred as a result of a series of seemingly improbable, serendipitous events.” For “not just any random DNA sequence can produce a viable protein.” Furthermore, in addition to the gene itself, “several other serendipitous events occurred.” The DNA was “edited in just the right way,” and “somehow, the gene also obtained the proper control sequence that would allow the new gene to be transcribed into RNA.”

Serendipity/Just-So is prevalent in evolutionary thinking. It is a monumental problem.

Now you are walking back the claim. Sure all of that is “evidence,” of course. It is also a meaningless claim.

That doesn’t make sense. Testing hypotheses about past events giving rise to observed data is always about finding patterns more consistent with the hypothesis, and less consistent with others. If you want to call that “arguing from evolution” then it isn’t clear to me that “arguing from evolution” is any sort of a problem.

Yes, what is the problem here? That description makes good logical sense. Repetitive microsattelite DNA is the sort of thing known to be prone to duplication, which is further corroborated by the fact that similar loci in closely related species show variable length of these repeats.

I’m sure you understand the concept of a metaphor.

In the press release Cheng admits that AFGP evolution “occurred as a result of a series of seemingly improbable, serendipitous events.” For “not just any random DNA sequence can produce a viable protein.”

I’m left wondering so what? You’re not explaining how that is a problem, or even that it is a problem?

Furthermore, in addition to the gene itself, “several other serendipitous events occurred.” The DNA was “edited in just the right way,” and “somehow, the gene also obtained the proper control sequence that would allow the new gene to be transcribed into RNA.”

And?

Serendipity/Just-So is prevalent in evolutionary thinking. It is a monumental problem.

So you say, but it’s not clear to me what the problem even is. You seem to have said what amounts to “this particular chain of events looks now, after the fact, as an unlikely combination”. But wouldn’t that be true for ANY conjunction of serial stochastic events?

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We see the same in geology and astronomy of course. Observed data or phenomena are explained by invoking certain theories about forces in the present also operating in the past. The distribution of elements in the Earth’s crust and mantle, the geological features on the surface, the prevalence of Earthquakes in particular areas and so on, are exlained by invoking various physical theories about plate tectonics.

Looking at the distribution of matter in the solar system into planets, asteroids, and comets, their locations in relation to each other and their observed trajectories are explained as a consequence of physical forces like gravity having operated for billions of years into shaping the observed patterns. This can be extended to basically the entire cosmos. Globular clusters, trails of dust and gas, galaxies and entire clusters of them are also explained by invoking these forces.

The past gave rise to the present conditions through the physical forces acting on the “initial conditions” in effect at the time.

IDcreationists seem to have a hard time fathoming that this exact same elementary concept is how evolutionary biologists explain presently observed patterns in genetics and anatomy by invoking observed mechanisms such as mutation, drift, and natural selection having operated in the past given the conditions at the time. There really is no in principle difference here.

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How would one test the scenario in question?

Here’s the problem (the same problem occurs throughout this entire story, actually). Why include the adverb “fortuitously” in this sub-hypothesis?

“A putative translocation event in the last common ancestor of AFGP-bearing gadids moved the hitherto unexpressed AFGP precursor to a new genomic location that fortuitously contained a TATA motif thereby enabled transcription.”

Well, OK. Serial stochastic chains occur. That’s what Markov processes are.

But “fortuitously,” and similar language that occurs in the press release, which George noted – e.g., “serendipitous” – suggests that we are being asked to accept the occurrence of a long string of very low probability events, which the authors themselves acknowledge are unlikely, and flag as such with appropriate modifiers.

Testability?

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What a strange question.

How would one test a scenario for how some mountain range, or a particular mountain formed?

The basic scientific principle about explaining observed patterns that arose in the past essentially take this form: If X happened we should expect to find Y. Finding or not finding Y is the test. That’s the only way to do it.

Here’s the problem (the same problem occurs throughout this entire story, actually). Why include the adverb “fortuitously” in this sub-hypothesis?

How is that a problem at all?

“A putative translocation event in the last common ancestor of AFGP-bearing gadids moved the hitherto unexpressed AFGP precursor to a new genomic location that fortuitously contained a TATA motif thereby enabled transcription.”

That’s what happened to the citrate transporter gene in the LTEE. A locus was duplicated into another part of the genome and it just so happened to end up under control of a promoter that was active under aerobic conditions, and the translocated gene just so happened to be a citrate transporter that could take up citrate, which just so happened to be present in the growth medium.

Stuff like this happens.

Well, OK. Serial stochastic chains occur. That’s what Markov processes are.

But “fortuitously,” and similar language that occurs in the press release, which George noted – e.g., “serendipitous” – suggests that we are being asked to accept the occurrence of a long string of very low probability events, which the authors themselves acknowledge are unlikely, and flag as such with appropriate modifiers.

What’s the probability of your particular set of mutations? What’s the probability of your parent’s particular set of mutations? What’s the probability of their parents sets of mutations? Compound those probabilities back in time 10.000 generations.

Testability?

Are we to re-create planetary orbits too, and regrow forests, rivers, glaciers, mountains, and tectonic plates? How did the world happen up so arranged as to give rise to the exact structure we recognize as the Mt Everest? To think of all the ways the combination of erosion and plate tectonics had to play out in minute detail to explain the precise location of every atom that makes up the Mt Everest. That event very likely only happened once in the entire history of the observable universe, and likely won’t repeat again before it undergoes heat-death.

How do we “test” the theory of the origin of the Mt Everest? Try to think of how you would have to create, for example, a computer simulation and let erosional forces and plate tectonics produce an exact replica of the Mt Everest down to the atomic scale.

Some of you seem to be demanding something absurd from science about explaining past events, and I doubt you hold that same level of evidence for any other beliefs you have. Are you a creationist? How would you test creationist claims about how this gene originated?

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I’ll take that as the long form of “this scenario can’t be tested – it’s a narrative, not a testable hypothesis.”

Which was George’s original point, in his blog post.

Some narratives are true; others are not. Very hard to say in this case, because we are banking on the very lucky role(s) of several unrelated dice. The point George was making is this scenario gives us no independent grounds for thinking it is true, other than the alternative is creationism. Since the alternative is magic (for most biologists), low standards of testability apply. This has been a standing weakness of evolutionary theory since Darwin.

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Lotteries are designed to be unpredictable. That’s how they work.

Are you saying that evolutionary narratives are designed to be untestable? Or just that such untestability happens to be a logical consequence of their narrative structure?

We can and have tested the mechanisms which produce the results. We don’t have to recreate the specific results. Seriously, do you actually use this dumb rhetorical argument anywhere?

I will disagree. The experiment - transfer, duplication, activation of genes - is ongoing, and can be studied computationally and in real time. Specifically, in plants, there ha been a large-scale movement of genes from organelles to nuclear genomes. This is an ancient process, but one that is occurring today, and one that can be studied in real time. The basic bottom line from all of this is that the activation of new genes isn’t (in geological or evolutionary timescales) a particularly improbable event. This includes the recruitment or de novo origination of organellar localization information.

To be sure, more work needs to be done. But the notions that these processes are beyond the reach of direct experimentation, and that they are fantastically improbable, are wrong.

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Evolution also doesn’t have any pre-specified results. That’s how it works.

How would a geologist test the idea plate tectonic collisions caused the Himalayas to rise? We can measure plate tectonic movement (in mm per year), calculate the forces involved, find additional physical evidence the process did indeed cause the mountains to rise over the last 50 MY or so. Because we can’t actually recreate the same mountain ourselves is that evidence space aliens built Everest and K2?

I realize Creationism relies on empty rhetoric in lieu of scientific evidence but wow, you’re really hitting the bottom of the barrel with the “evolution is untestable” nonsense.

You are restating my point in different words. The entire narrative – what you call “the specific results” – is untestable.

Unhappiness with the overwhelmingly narrative logical structure of evolutionary explanation, in the late 1970s, led many younger investigators out of neo-Darwinism. Joel Cracraft, for instance, complained loudly:

The critical factor in the scientific study of any phenomenon is that explanatory hypotheses should be susceptible to criticism, that explanations should be evaluated by empirical tests of some sort. As far as I can see, statements of the type that “phenotype x is an adaptation, evolved via the agency of natural selection” are thoroughly untestable. The necessary data needed to refute such an assertion cannot be gathered, and we are more or less forced to accept it as an article of faith rather than as a scientific statement.

J. Cracraft, “The Use of Functional and Adaptive Criteria in Phylogenetic Systematics,” American Zoologist 21 (1981):21-36; p. 32. [Nota bene: Cracraft told me a couple of years ago, in a conversation at the American Museum in NYC, that he is less confident about this criticism of neo-D today.]

Now, maybe Art is right – testability is still available – but that’s not what folks earlier in this thread were saying. We don’t need no stinkin’ tests.

“Testing” is most certainly possible. This is a good place to start learning more. Enjoy.

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Thanks, Art. I have that paper (very interesting work). I don’t think it applies directly to the antifreeze gene origins scenario, however.

Gotta run, thanks to all.

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This body of work speaks directly to the idea that promoter capture is in some way fantastically improbable. Which may be, IMO, an important aspect of antifreeze gene origins.

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Oh my.

Wow.

Wow again. I can’t find the slightest hint of that in anything @Timothy_Horton stated. Am I missing something?

Even though I’ve seen the “evolution is untestable” trope in countless forums, I’m very surprised to see it applied in this particular context.

I heartily commend Dr. Nelson for being so forthright in sharing this anecdote of updated information. Truly. Such willingness to put everything on the table is much appreciated and contributes even more of value to this very interesting discussion. Thank you for that.

No matter how much we may all disagree on various matters, I greatly respect the willingness to engage in peaceful and forthright constructive dialogue.

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I would say that parts of the narrative are testable and due to the limits of science and the laws of physics, not all of it directly testable. It seems you neglect the possibility that science is limited.

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