Leisola: Cited to Attack Darwin Devolves, Study Devolves on Close Inspection

@Wayne_Rossiter, the article includes this quote:

But biologist Wayne Rossiter emailed with a note about the 2012 Näsvall paper. “For those who weren’t aware, the 2012 study mentioned in the review (reference 11) was… debunked by Matti Leisola (and his co-author Jonathan Witt) in his wonderful book, Heretic: One Scientist’s Journey from Darwin to Design . It’s a must have for anyone’s ID library.”

Are you saying that the ENV article is citing you incorrectly here?

This is not a drive by on you. I’m here to engage. As for using your name, we just found out that that ENV may have inappropriately used your name. Fo this reason, I’ve changed the title now to Leisola, who’s book is quoted.

It isn’t a tarring you, just asking for conversation. I’m sorry it appears that ENV inappropriately used your name. Here are other examples of threads started with someones name:

  1. Ken Keathley: Notes from Dabar and a Baptist's Hope
  2. Clinton Ohlers: Two Parables on Divine Action
  3. Randal Rauser: Is the Atheist My Neighbor?

This is just how we work.Yes, it is peaceful too. It isn’t meant to put you down, but to include you in the conversation. I can see your frustration though, especially if ENV used your name with permission. If this is the case, I hope you can contact them to fix remove your name from the original article.

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Correction, I did share an email with someone (apparently the author of the ENV post) saying that Leisola had dealt with this 2012 paper.

The point is that this paper is supposed to show gene duplication and adaptation. I never rejected that notion. You used it as an example against Behe, but it’s a rotten one (perhaps my paper would’ve been better!). Leisola is correct. There was no demonstration of “Real-Time Evolution of New Genes by Innovation, Amplification,” only divergence. They artificially made copies of a gene they engineered, and gave it a second (limited) function, so as to cause divergence by selection for function. It’s a terrible example. One I would’ve never used in your Science review.

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Good to know! That is why we ask these questions. So it was appropriate to tag this with your name in the first place. I hope that ENV had permission to include your name in that article.

We do not understand why this rebuttal is valid. Even the editor’s note from ENV seems to disagree with you.

Can you explain to us why this is “rotten”? We can discuss your paper next if you are interested (but I don’t want this to mushroom unless you want it).

We understand it as an excellent example. It is a system engineered to test a specific evolutionary mechanism. The @AGauger study was misunderstood by Leisola, and she said as much here: https://discourse.peacefulscience.org/t/gauger-realtime-evolution-by-innovation-amplification-and-diversification/4828 . So, when you have time, I hope you can come explain why you think it is not a valid study to cite.

@Art and @Nlents, what do you make of this?

Ann didn’t feel that her work demonstrate any refutation of the Nasvall paper. That wasn’t its intent. I didn’t quote that from the book (the ENV author did). The refutation is in the actual methods Nasvall et al. used, and what the paper claims. I’ve explained the problem above. For this reason, it’s a terrible example of gene duplication/adaption/divergence, but you used it again Behe, as if he should’ve dealt with it (among the thousands of other possible papers you could’ve used). It’s simply whack-a-mole tactics. Roll through some rolodex of examples, and then complain that someone hasn’t addressed all of them. Ken Miller is notorious for that crap. Don’t be like that.

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Very helpful clarification. Thank you @Wayne_Rossiter. That is our point, my point it seems. @Agauger did not think her paper refutes Nasvall, but Leisola did. Perhaps you agree with Leisola, and disagree with @Agauger, because you did point the ENV author to this excerpt.

By which I think you mean:

So, do you disagree or agree with Behe’s response to this?

His objection is that it is an engineered system, therefore it is an example of intelligent design. That is also what @Agauger thinks too. Are you agreeing with them in that reasoning or disagreeing? I’m asking to tease out what you really mean here.

From what we meant to explain from that article, it is an excellent citation. I’m not sure you why you think is not a valid citation yet. It is a system engineered to test a specific mechanism of evolution, and finds that this mechanism is very effective. The fact it is engineered, does not some how make its findings about the evolutionary mechanism irrelevant.

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Sorry but I don’t agree with this portrayal.

They didn’t “artificially” make copies of it, the bacteria made copies of it. The way you describe it seems to imply the researchers literally made and inserted extra copies of the gene to synthetically mimic the process of duplication. But that’s not what they did. They placed the gene in a location on a plasmid more-prone-than-“normal” to duplication. But that duplication is done in bacteria, by the bacteria, not artificially by the researchers.

You couldn’t say that placing the gene in a genetic location with a higher-than-average rate of duplication for the genome is to “artificially make copies” of it, as all they did would have affected the rate of change, not forced the possibility or the occurrence of change.

But that was only done so as to be able to see these changes in a practical timeframe, as opposed to having to wait years for similar amounts of duplication to occur had the gene been in a less duplication-prone area on a plasmid, or in the bacterial chromosome.

They also didn’t engineer the gene to “give” it a second limited function, they selected it under conditions that would favor those kinds of mutations should they actually occur.

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Following up on @Rumraket’s remarks:

Nasvall et al. developed and set out to test a model for the evolution of new genes that they call the “innovation-amplification-divergence (IAD)” model:

We propose the innovation-amplification-divergence (IAD) model (Fig. 1A), which allows the evolution of new genes to be completed under continuous selection that favors maintenance of the functional duplicate copies and divergence of the extra copy from the parental allele (5). The IAD model proposes that the ancestral gene has a weak secondary activity (innovation) (6, 7), and when a change in conditions makes this activity useful, selection favors increased gene dosage (amplification), resulting in two or more copies of the parent allele. The increased copy number pro- vides multiple targets for beneficial mutations and buffers any negative effects a new mutation may have on the original activity. During continuous growth under conditions that select for both the original activity and the new activity, beneficial mutations will accumulate (divergence) in the copies. Any improved copy can be further amplified, whereas less functional copies, including the parental gene, can be lost. Ultimately, this results in a gene duplication in which one gene copy encodes the parent activity and another copy provides an improved, new activity.

To test this model, they broke it down into its three components and evaluated each step separately. For this, they focused on two enzymes that catalyze chemically-related reactions, but that are in pathways for histidine or tryptophan biosynthesis, respectively.

To experimentally test the IAD model, we examined a histidine biosynthetic enzyme (HisA), and through continuous selection we created, by duplication and divergence, a new gene that catalyzes a step in tryptophan synthesis. The original HisA and TrpF enzymes both catalyze isomerization of a phosphoribosyl compound, but each acts on different substrates in the biosynthesis of the amino acids histidine and tryptophan (Fig. 1B). HisA and TrpF enzyme activities are selectable by growth in minimal media lacking histidine and tryptophan. In addition, the enzymes are structurally related and evolved from a common ancestor (8).

Thus, briefly, they first asked whether they could identify a HisA variant that could catalyze the TrpF reaction; this was simple, accomplished by screening trpF mutants that could grow on media lacking tryptophan (and, obviously, histidine). They isolated bacteria able to do this and confirmed that they had indeed isolated strains in which HisA had acquired TrpF activity (and was thus bifunctional). This is a positive experimental confirmation for the “innovation” part of their model. (Note that, other than conduct the experiment with a mutant strain, these researchers did nothing to promote or guide the outcome.)

The researchers then set out to test the second step of the model, and specifically to ask if gene amplification could improve the growth of cells that carry the bifunctional gene. I won’t describe the set-up, other than to say that they placed the bifunctional gene into a genetic context that allowed for easy generation and assay of gene amplification, and then performed selections in strains in which the bifunctional strain was the only source of HisA and TrpF activity. They identified variants that indeed grew better, and confirmed that the improved growth was due to gene amplification. This outcome is positive experimental support for the second part of their model.

To test the third step of the model, they then allowed lineages to continue to evolve under the same selection (no his or trp) for thousands of generations. They succeeded in isolating many better-growing variants. Different of these had bifunctional enzymes with further alterations; collectively, these alterations define many (most?) of the different mechanisms by which evolution might improve the enzyme:

As predicted from the IAD model, we observed the appearance of a diverged gene copy with improved activity, relaxed selection for maintenance of the unimproved copies in the amplified array, loss of the unimproved copies, and, in some cases, reduction in the total gene copy number.

Compare what Nasvall did with Ann’s description:

The story: Näsvall et al. created a gene that encoded an enzyme that was able to carry out two functions, but very poorly.

No, they did not “create” a bifunctional gene. Random mutation and natural selection was the mechanism, not design.

They placed that gene in a strain of Salmonella that lacked the genes for those functions. Then they cultured the bacteria under conditions where they needed to carry out those functions to grow. Guess what? The bacteria duplicated the genes so as to make more of the poorly functioning enzymes.

Which was the exact point of the assay – to test the hypothesis that duplication can contribute to enzyme evolution. The answer, it turns out, is yes. (It seems to me that Ann’s objection here is quite akin to claiming that enzyme assays are not valid because the biochemist first makes extracts (and purified enzymes) and then conducts tests with non-natural substrates. In other words, the objection fails.)

Over time, the genes acquired mutations (remember, we are talking about a lot of bacteria) and the ones that helped the most gave the best growth rate, and… after thousands of generations they had evolved separate enzymes for each function — meaning not that they had evolved new enzymes, but that they had divided up the pre-existing dual-functional gene into two genes.

Again, not correct. Nasvall et al. noted:

The evolved genes fell into three classes: (i) specialized genes with strongly improved HisA activity and loss of TrpF activity, (ii) specialized genes with strongly improved TrpF activity and loss of HisA activity, and (iii) generalist genes whose encoded enzyme showed a moderate increase in both activities …

Note that, among the classes of enzymes are ones in which HisA has now become TrpF (for all intents and purposes). This is a transition that Gauger and Axe say cannot occur (from the abstract):

Considering that Kbl2 and BioF2 are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution.

Note that the only “tools” Nasvall et al. used were random mutation and natural selection - exactly what Gauger and Axe claim are not tenable means for generating new functions.

The bottom line - Ann, @Wayne_Rossiter, Behe, and others object to Nasvall et al. for reasons that are completely baseless.

(Sorry this is so long - the words are needed to clear up the confusion sown by Ann and others.)

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Don’t apologize. That was a fantastic summary.

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@Wayne_Rossiter messaged me that he plans to respond to @art’s post in the coming week or so. Please keep this thread free of clutter in respect of his willingness to engage. Treat him with respect. There are several questions he has been asked, a lot of text written to him. It may take him a few post to make his point. Even if we disagree, we should try and understand him first.

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I’m still pouring over the details (some of the methods in the supplementary materials are foreign to me). However, Ann did ask (apparently she’s not on here anymore?) that I pass along her rebuttal. So, this is literally cut-pasted from her message to me:

[@moderators: the email from @agauger was moved to this thread: Gauger: Answering Art Hunt on Real Time Evolution. This thread will be reserved for dialogue with @Wayne_Rossiter]

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A post was merged into an existing topic: Gauger: Answering Art Hunt on Real Time Evolution

Thanks for this @Wayne_Rossiter. However, I would recommend that we discuss your own ideas, and not ask you to be a messenger for Ann. Any sort of back and forth with Ann will get very cumbersome and (I expect) use too much of your time. Ann left this group - if she wants to discuss the matter more with us, she should re-enlist (or whatever one might call it).

With that in mind, I will wait on @Wayne_Rossiter’s own remarks before adding anything to this discussion.

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@Wayne_Rossiter, I agree with @art on this. This thread will be reserved for your thoughts, as it was originally set up to engage with you. I do not want there to be distractions here from others.

I emailed @Agauger asking what she wanted to do. I’m pleased to report she wants to be reinstated. I have just reinstated her account. She can respond to @art here: Gauger: Answering Art Hunt on Real Time Evolution.


@Wayne_Rossiter, as you see fit, you may quote from her as needed. I do caution you that @Agauger has explained the past that she is not allowed to concede any points on behalf of Behe or Axe. If you do quote from her, I hope you can explain for yourself the reasoning. Honestly, I’m very puzzled by the ID response to this paper. I am hopeful you can help me understand.

I look forward to the conversation developing from here!

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@art, I had one question about the system. I could sort this out by reading the paper again, but it will better to just ask you so we are all on the same page. During the “amplification” phase of the experiment, @Rumraket says that the gene was placed on a plasmid. Is this correct? I thought it was placed into the salmonella genome. Was it a plasmid or integrated into the genome when the bacteria duplicated it?

It was on a plasmid, Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence

We placed this bifunctional parental gene (dup13-15, D10G) under the control of a constitutive promoter that cotranscribed a yellow fluorescent protein ( yfp ) gene. We also placed the T- his operon in a transposition-inactive transposable element Tn 10d Tet close to the lac operon on the low–copy number (about two copies per chromosome) (11) F′128 plasmid (Fig. 1C). Duplications and amplifications of this region are frequent and have low fitness cost (3), allowing experimental study of the process within a reasonable time frame. An F′ plasmid with the bifunctional gene inside T- his was introduced into a S. enterica strain with deleted hisA and trpF genes, dependent on the bifunctional gene for synthesis of both histidine and tryptophan. In the absence of both amino acids, the bifunctional gene supported a generation time of ~5.1 hours in minimal medium with doubling times of ~2.8 hours in the presence of tryptophan alone, ~2.6 hours in the presence of histidine alone, and ~1.5 hours in presence of both amino acids.

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Interesting. What is the mechanism that maintains these plasmids at low copy number?

Good question, I don’t know.

It seems that this might have been a difference between @Agauger’s study and the RTE study. Did @Agauger use a high copy number plasmid? If so, this difference might explain why she saw a loss of duplications.

I think this is an inherent feature of F plasmids.

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