Behe Meets the Peaceful Science Forum

[Giltil (Gilbert Thill)]

@Chris_Falter

@Giltil

Adaptive loss of function mutations are not at all confined to the lab environment.

I’m sorry; did I claim anywhere that loss-of-function mutations never, ever happen in the wild? Kindly show me where I did so and I will immediately amend my error!

After rereading what you initially wrote, and thanks to your last clarifications, I can now see that you didn’t say that LOF mutations don’t happen in the wild at all.

@Chris_Falter

Behe ignores the presence of gain-of-function mutations outside of the knockout protocols.

No. Behe acknowledge that adaptive GOF mutations can happen both in the lab and in the wild. But his contention is simply that adaptive LOF mutations largely overwhelm in number adaptive GOF mutations, whether in nature or in the lab. He has captured this idea with what he called the first rule of adaptive evolution, which says: Break or blunt any functional coded element whose loss would yield a net fitness gain.

@Chris_Falter

And that’s just a critique of the paper with respect to the literature in 2008. Since then, dozens of discoveries of novel genes (which are by definition gain-of-FCT) have been published.

I think that the data accumulated since 2008 strengthen, not weaken, Behe’s thesis in DD.
Now, I would be happy if you could offer some examples demonstrating the emergence of novel gene by RV + NS.

[Rumraket (Mikkel R.)]

BSC4. Antifreeze glycoproteins in northern gadids. T-urf13? To pick a few.

[Mercer (John Mercer)]

@Giltil

But his contention is simply that adaptive LOF mutations largely overwhelm in number adaptive GOF mutations, whether in nature or in the lab.

Supporting that contention would require a wide breadth of knowledge and quantitation, neither of which Behe bothers with. Recall his pratfall with immunology in the Dover trial.

@Giltil

He has captured this idea with what he called the first rule of adaptive evolution, which says: Break or blunt any functional coded element whose loss would yield a net fitness gain.

He has not supported that rule with data.

@Giltil

I think that the data accumulated since 2008 strengthen, not weaken, Behe’s thesis in DD.

I’m pretty certain that you are not familiar with the data. If you disagree, what is the most recent paper from the primary literature that you have read–and understand well enough to discuss without any copy/pasting from the paper or from what others say about it, only copy/pasting the data (figures and tables)?

[Chris_Falter]

@Giltil

But his contention is simply that adaptive LOF mutations largely overwhelm in number adaptive GOF mutations, whether in nature or in the lab.

My point was that his quantitative analysis of the ratio of mutation types relies almost exclusively on experiments conducted in labs.

Allow me to refresh your memory:

In Behe QRB Table 1, only 8 “wild” mutations were examined, of which half are not loss-of-function. This dataset is vastly too small to support any broader conclusions.

Behe QRB Tables 2, 3, and 4 all examine the ratio of mutations in laboratory experiments.

And that’s it! That is the entirety of the data on which Behe relies to speculate that the ratio observed in the wild would (supposedly) overwhelmingly favor loss-of-function mutations rather than gain-of-function.

Anyone who has taken an entry level probability and statistics course can recognize that Behe’s conclusions are invalid.

@Giltil

Now, I would be happy if you could offer some examples demonstrating the emergence of novel gene by RV + NS.

Extensive examples have been discussed in this very forum. I notice that you have not participated in any of those threads, so I post links to them below so you can read the research papers that are linked in the threads. You will find that your diligence in reading the threads and the papers cited will be rewarded by the revelation of a fascinating body of research that you have never seen before. Enjoy!

Chris

New review of de novo gene birth

PLoS Genetics has a nice, new review of what is known about the evolution of de novo genes, which seems to be a topical of perennial interest here. De novo gene birth De novo gene birth is the process by which new genes evolve from DNA sequences that were ancestrally non-genic. De novo genes represent a subset of novel genes, and may be protein-coding or instead act as RNA genes [1]. The processes that govern de novo gene birth ( Fig 1A ) are not well understood, though several models exist that describe possible mechanisms by which de novo gene birth may occur. Although de novo gene birth may have occurred at any point in an organism’s evolutionary history, ancient de novo gene birth events are difficult to detect. Most studies of de novo genes to date have thus focused on young genes, typically taxonomically-restricted genes (TRGs) that are present in a single species or lineage, including so-called orphan genes, defined as genes that lack any identifiable homolog. I…

Mechanisms of the origination of new protein-coding genes

Rapid evolution of protein diversity by de novo origination in Oryza. Zhang L, Ren Y, Yang T, Li G, Chen J, Gschwend AR, Yu Y, Hou G, Zi J, Zhou R, Wen B, Zhang J, Chougule K, Wang M, Copetti D, Peng Z, Zhang C, Zhang Y, Ouyang Y, Wing RA, Liu S, Long M. Nat Ecol Evol. 2019 Apr;3(4):679-690. doi: 10.1038/s41559-019-0822-5. Epub 2019 Mar 11. [Title] A recent study provides important insight, and mechanistic confirmation, into the origins of new protein coding genes. This study capitalized on the availability of complete genomes of many related rice species. The abstract (below) gives an excellent summary of the study and the results. New protein-coding genes that arise de novo from non-coding DNA sequences contribute to protein diversity. However, de novo gene origination is challenging to study as it requires high-quality reference genomes for closely related species, evidence for ancestral non-coding sequences, and transcription and translation of the new genes. High-quality …

De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences

Another intriguing de novo gene evolution paper was recently published in Nature Communications: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences Some excerpts: Mutations that cause changes to the sequence or expression of established genes are typically constrained by preexisting selected effects—the specific physiological processes mediated by the gene products that are maintained by natural selection20. In contrast, emerging proto-genes are expected to mostly lack such constraints because they do not have selected effects. This would leave them more readily accessible to evolutionary changes that have the potential to increase fitness (adaptive changes)3,4. We reasoned that this initial potential for adaptive changes would give way as proto-genes mature and the adaptive changes engender novel selected effects, in turn increasing constraints and reducing the possibility of future change. This reasoning is akin to Sartre’s “existence precedes ess…