Another example of devolution!
Here is Mike Behe’s comment on this:
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There is nothing like “devolution”. In a narrow sense the deletion of genes from chromosomes or extrachromosomal DNA is called gene loss, not devolution. Gene loss can be beneficial, neutral, or deleterious.
Evolution by gene loss is called reductive evolution and is common with parasitic or symbiotic organisms. Why Behe chooses to use a bogus, misleading term (“devolution”) and not a more appropriate terminology is a mystery. Behe is an embarrassment.
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Considering how « reductive evolution » is defined by Wikipedia (see below), it seems that this terminology isn’t appropriate for describing the Plasmodium falciparum escape variants referred to in the Nature Microbiology paper and that «devolution» is in fact a better one.
Important to note how he defines it in the article:
But when the environment changes and the proteins become a net drawback, the quickest evolutionary solution is to get rid of them. That’s an interesting fact of biology and can be medically important. However, it’s important to note that it’s just one more example of devolution — the beneficial loss of genetic information.
He specifically calls this beneficial.
The same fundamental problem with Behe’s argument continues. It’s not that beneficial “loss of X” doesn’t occur, nor does one need to deny that it is a more likely or “easier” mode of fitness-gain under many circumstance. One can grant all of that, and yet Behe’s thesis that this somehow undermines the evolutionary history of life just doesn’t follow.
It is well-recognized that much of evolution is reductive in one sense or another. Adaptive genome streamlining is a real thing, this is not in dispute.
You could, for example, have periods of overwhelmingly mostly losses of function co-occurring with minor restricted gains in a few functions.
There could be a situation where a population of organisms over the course of a million generations loses 50% of it’s non-essential genes because these genes had become burdensome rather than beneficial in some new environmental circumstance, yet concomitantly with this loss a molecular function grew from requiring 3 to requiring 10 proteins to perform it’s function, with 6 of the 7 proteins being added to the machine coming from diverging duplicates of already existing proteins, and one novel gene gained. Thus you could have a period of evolution be consistent with Behe’s so-called “first rule of adaptive evolution” simultaneously with some cellular machine or organelle growing in complexity.
We can look to the evolution of endosymbionts like mitochondria from their free-living alpha-proteobacterial ancestors as an example. When they became obligate endosymbionts in their archaeal hosts, they lost most of their genes they required to live outside the host, yet their outer membrane became much more complex and took on a more specialized role, and they lost a lot of ribosomal RNA while their ribosomal proteins became substantially larger and more complex(mitochondrial ribosomes seem to have exchanged ribosomal RNA for ribosomal protein, oddly enough). Overall, they suffered a net loss of complexity when the environment favored this, yet a small part of their existing systems became more complex.
What Behe never seems to deal with or even try to understand are the conditions that favor gains over losses. Generalists over specialists. Environmental complexity and switching ecological opportunity rather than competitive growth in a constant environment.
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What the debate is over is whether the environment favoring advantage can overcome a sequence that is more likely to degrade than advance.
The empirical results he is seeing are predictable given the large sequence space and a smaller functional space.
The other issue is the potential lack of correlation between function and fitness. If they are poorly correlated then most of evolution is simple adaptions. In the Lenski experiment we saw continuous improvement in fitness but did we see recognizable new function at the sequence level?
What is “new function at the sequence level”? Define it.
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An example would be a new gene coding for a new enzyme from a NC region.
That’s not a definition. I specifically ask for a definition rather than an example because I want to be able to use your definition to analyze different examples so as to understand what it is that makes you say that an enzyme evolving from a non-coding region constitutes one such example.
What is the essence of a “new function at the sequence level”?
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You have got to be kidding me. When organisms lose genes to better adapt to their environment that is called reductive evolution and that is exactly what happened to the Plasmodium falciparum parasites as described in the study: the parasite population in the surveyed areas deleted their pfhrp2 and/or pfhrp3 genes to enable them escape detection by diagnostic tests which target the protein products of both genes, allowing them to flourish.
The above describes adaptive reductive evolution, but there can also be neutral reductive evolution. Behe’s baseless terminology (“devolution”) has no place in the discussion of evolution by gene loss or inactivation.
When gene or gene family loss increases fitness, we say adaptive reductive evolution has happened not “devolution”. There is nothing like devolution in mainstream evolutionary science because evolution is directionless.
A broad definition would be changes from SNP’s in a DNA sequence that generates a new function. This could be from a gene duplication, a NC sequence. or a modification of an existing gene.
Thanks Bill. I think that’s a substantial improvement and comes close to a good definition. Now I just need to know where you draw the line for “new” function.
I regret if this may seem overly pedantic, but if we are to analyze multiple different examples (say we want to “score” various genetic changes from a collection of published experiments) we need to have a sense of what distinguishes something like a “modification of an existing function” from something we truly consider “new/novel”.
In that respect I think it would also be useful to get clear when we should use the term “loss”. Taking the example of enzymes, suppose an enzyme reduces the rate at which it catalyzes a specific reaction, should this be considered a loss of function, or merely a modification of an existing function?
In my mind it is not a loss of function as long as it has the ability to catalyze a specific reaction.
Okay, but that still leaves me wondering what should count as new function. What is the essential nature that separates, for example, an increase in an existing function, from a new function?
In the case of enzymes it would be the ability catalyze a reaction of a new molecule.
Generally it would perform a new output vs the quality or speed of the same output.
Right but now we’re just back to this being an example using enzymes, rather than a general principle we can apply to understand what “new function” means when we look at a lot of different molecular entities, be it regulatory and DNA-binding proteins, membrane transporters or channels, structural/scaffolding proteins, and so on.
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You need to be able to define a unique new function for what ever output you are observing. The simplest might be catalyzing a molecular reaction. The most complex might be abstract thought.
One takes a single protein the other may take thousands.
I take it “output” is supposed to be a synonym for phenotype?
Output is what you are directly observing. A flagellar rotating or a single molecule becoming 2 separate molecules. From observing of the output you then determine the function. Mobility in one case and catalyzing a chemical reaction in another.
I have to say I get the experience that as I try to ask for more clarification, I end up with less of an understanding of what principles you use to classify functions as gained vs lost or modified. It is still not obvious to me at what level of resolution I am supposed to be looking at the “outputs”.
When speaking of enzymes you have suggested looking directly at the molecules produced in the catalyzed reaction as the “output”. When speaking of the flagellum it’s “mobility”(that would be organismal behavior). It’s not clear to me which of these two I should then carry over to look at some other arbitrarily picked molecular or cellular entity.
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