This certainly points to a selective function at work that involves deliberate direction by the organism itself. The usual explanation of such mutations as being part of a random process just doesn’t cut it here.

Roy, assuming you are just being critical of the writing here. The notion of an organism directing its own evolution intentionally is not what this article or the research is implying. We only see the end result of successful adaptations derived from genetic variation, and as such they may seem “intentional”. Describing adaptation through natural selection as something the animal “does” is just a metaphor, although writing this way is unfortunately common in popular press accounts of science (as in the first sentence of this article). The last sentence of the article clarifies this correctly – that random genetic variation is a mechanism for successful natural selection only in the context of an animal’s changing environment.

Jim, when Yokoyama says “Evolutionary biology is filled with arguments that are misleading, at best,” I take that as a reference to what many are coming to see as the current and yet mistaken resistance to any evidence of directed mutations occurring under any circumstances. Direction as a mechanism within the organism doesn’t have to be any more “intentional” than random genetic variation to achieve the same effect or purpose would be labeled intentional.
So no, I’m not critical of the writing, although I suppose I could be critical of the usual ambiguity found in such articles where science writers often don’t see the full import of what they are supposed to be writing about.
I did look into the National Academy of Science issue where these findings were originally published, and I suggest you do the same, even if you may not agree with some of the inference to be drawn.

Roy, my point is that your characterization of the observations made by this research, what is essentially the successful (i.e. useful) end result of adaptive selection in this case, as “deliberate direction by the organism itself”, leading to your conclusion that “the usual explanation of such mutations as being part of a random process just doesn’t cut it here” appears either to draw too literally from the article’s unfortunate writing style, or simply embodies a misunderstanding of evolutionary theory. When the writer says that the “scabbardfish shifted from UV to violet vision by deleting the molecule at site 86” she, nor the scientist, means that the fish, in a moment of enlightenment, actually deleted its own amino acid molecule from its genome in order to improve its vision. This is a science writer’s metaphor, a way of telling the story – “as if”. Similar to describing the evolutionary “behavior” of genes as “selfish” – they are not actually selfish, and organisms do not “intentionally” direct their own evolution. There is enough misunderstanding of science and of evolutionary theory by the public without science writers contributing to the problem with misleading statements. Roy, you are trying in your metaphysical mindset to see something that is not there and not intended by this article or by the research. Naturally occurring, random genetic variation within individuals in a population of organisms, in the context of environmental forcing, leads to natural selection, adaptation and change in the population as a whole, occasionally leading to distinct new species where there is enough isolation of the breeding group. Environmental forcing is the key. Does anyone else out there read this website yet? Are there no other critiques?

Well, I simply do not agree that organisms can play no part in the selection of beneficial mutations. The odds that this organism luckily had the advantage of a random mutation that specifically, and what appears to be deliberately, deleted this particular molecule that allowed it to see what was to its distinct, necessary, and immediate advantage to see are so slim that, if this was a coincidence, it’s among the rarest seen to date. And in fact it was just this kind of functional mechanism that the scientists were expecting or at least attempting to find some evidence of. You use the term “intentionally” as if the organism acted in some conscious fashion to do this, having figured out by some abstract process that this move would work, and then inventing the mechanical means to do so on the spot..
But if this, as some scientists believe, is part of the long evolved process of directed mutation, such as we observe in e.coli, for example, it’s more likely an automatic process dictated by the particular and present circumstances, as this process may (and if so, must) have been dictated by the evolutionary history of life billions of times before.
“Environmental forcing” as you put it is the “force” of necessity that drives the evolution of these functions within the organism, rather than in some magical way reminding the organism, over many billions of such occasions, to get ready again to be advantageously mutated.
Evolutionary theory is a work in progress, with auxiliary theories having been developed since its birth, some now fully incorporated in the main body, some falling away, and some still waiting to get a firmer hold and place in the main structure. Directed mutation is gaining ground on the old school who have turned from explorers to true believers. Get used to the idea of such changes, even if you can’t accept that this portends to be one of the most significant to date.

“The odds that this organism luckily had the advantage of a random mutation that specifically, and what appears to be deliberately, deleted this particular molecule that allowed it to see what was to its distinct, necessary, and immediate advantage to see are so slim that, if this was a coincidence, it’s among the rarest seen to date.”

Are you kidding? This is not at all difficult to explain.

1) Fish feeds at shallow depth, encounters stiff competition.
2) Fish moves deeper where less competition exists but does poorly because vision is bad.
3) One fish randomly has mutation allowing it to see the violet spectrum.
4) This fish does very well because it can see.
5) It reproduces frequently because it is successful.
6) Its descendants do well, move deeper.
7) They start reproducing with each other more or less exclusively because they encounter only each other at depths its UV-sighted relatives can’t reach.
8) Soon the population has collected a number of advantageous mutations for living deep; they differ enough to be considered a distinct species.

Roy, I hate to be the one to break the news to you but there is no need for your complex, automatic (as yet undocumented and unexplained) mechanism generating mutations in response to selective pressure. Finding such a system would fly in the face of contemporary understanding but, given the lack of evidence of or need for such a system, I doubt one will be found.

dnarom, I hate to break the news back to you, but this was about the DELETION of a molecule that was far from random and not at all explainable by your rote presentation of contemporary catechismic principles of natural selection. No need you say to search for a mechanism generating mutations in response to selective pressures? Tell that to the people who authored this study. Tell that to those numerous others who have already discovered forms of such a mechanism in other species. Tell that to evolutionary biologists like Margulis or Jablonka. Burn all those papers and books – we won’t be needing them.

“but this was about the DELETION of a molecule…”
-Deletions are mutations. You do know that, right?

” that was far from random and not at all explainable by your rote presentation of contemporary catechismic principles of natural selection.”
-I believe you have conflated the means by which mutations arise and the purpose they serve for the organism. While the mutation is undeniably useful, no evidence exists for it to have arisen by any means other than natural selection of random mutation.

” No need you say to search for a mechanism generating mutations in response to selective pressures? Tell that to the people who authored this study.”
-Have you even read this study? You cannot have because they make no such claim.

“Tell that to those numerous others who have already discovered forms of such a mechanism in other species. Tell that to evolutionary biologists like Margulis or Jablonka. Burn all those papers and books – we won’t be needing them.”
-You certainly have a flair for the dramatic. Unfortunately, Margulis’ endosymbiotic theory has nothing to do with the claims you make. Nor does Jablonka’s work on epigenetic inheritance. I find it ironic that you cite the well-accepted, clearly demonstrated work of mainstream scientists in defense of your fringe view. Your claim, unless you want to alter it, is that there is some system in the organism devoted to determining the need for evolution, choosing specific alterations to make to the genetic code (on a systemic scale, mind you), and then enacting that change. Please provide some evidence for such a system, since all of current evolutionary theory denies it.

Margulis, Jablonka, and others are seeking to demonstrate that life has found ways to assist in its own evolution. Epigenetic inheritance involves one of those ways. Therefor it is a bit silly to assume that’s the only one. Especially as your catechism didn’t foresee that mechanism as either needed or useful either.
Margulis has written about more than endosymbiotic theory. Try reading What is Life, for example. In any case my point was that they, among many others, are searching for such mechanisms, regardless of your contention no-one needs to. Yes, I did read the study, which was open-ended as to exactly what results were expected. Rather it was clear that these results were not unexpected as far as recognizing the implications involved. Some studies look for what they will recognize when they find it, rather than look for and recognize only what they set out to find.
And what you lay out as my “claim” is nothing but your own alteration of it. The organism doesn’t conceive of a need for evolution any more than under your theory it conceives of a need not to interfere with it, or a need to adapt at all. It certainly doesn’t conceive of a need to survive. What it “conceives” of us a need, at least under current theories, to seek pleasure and avoid pain. Consequences follow from that conception or that seeking that you may regard as necessarily intended, but that’s your problem, not mine.
This is me quoting me, with no alterations needed, especially not yours: “But if this, as some scientists believe, is part of the long evolved process of directed mutation, such as we observe in e.coli, for example, it’s more likely an automatic process dictated by the particular and present circumstances, as this process may (and if so, must) have been dictated by the evolutionary history of life billions of times before.”

“All of current evolutionary theory,” as you put it, does not deny this distinct possibility. Before asking me again to provide evidence to the contrary, which apparently must then meet your exacting standards for satisfaction, please provide some evidence that all such theories, or theorists (or whatever “all current theory” consists of) do so deny that something like this can be out there to find.
In the meantime google for theorists who are already testing for directed mutations and the like. Do let us know later that you haven’t found any.

Really, Roy, you’re the one proposing the addition of a novel, strangely anthropomorphic and quite incredible evolutionary mechanism to the “canon”. The burden of proof is entirely on you to show that any of these researchers you have listed have produced evidence that mutation itself is in any circumstance non-random.

There are numerous mechanisms by which an organism may control aspects of its own evolution, and this is a topic which has been the subject of a great deal of recent research. Certainly an organism may choose sexual partners, seek to maximize or optimize the recombination with its mate, use imprinting to control the next generation’s expression, or use behavioral patterns such as mating rituals or migration to consolidate or combine populations. One way in which mutations are “controlled” is through accumulation and release of cryptic mutation using HSPs, and this may be what you have confused with “directed mutation”. But alas(for you), the mutations themselves are not directed in this case, rather the organism has adopted a mechanism for hiding and revealing many randomly accumulated mechanisms.

Again, I advise googling directed mutations. Also there’s autopoiesis (which Margulis has discussed, among others), there’s the rejuvenated interest in the Baldwin effect, etc., etc. And where’s the anthropomorphism, or are you one of those who still contend that cells can’t learn, and therefor can’t evolve in any way that has some connection with that learning?
But since you apparently do concede that there are researchers interested and working in this subject (that you nevertheless have characterized as novel and incredible), you now move the goalpost and ask for proof that the hypotheses will not fail to deliver. Like no-one should attempt a proof that hasn’t already seen it in his dreams, perhaps? Did you ever hear of the term plausible? Ask me if these concepts are plausible, and again I refer you to those others who believe the are.

As an aside, I note the typical use of euphemisms as a form of denying the otherwise undeniable. Like calling something “controlled” as an alternative to conceding there’s any form of direction involved.
Maybe we should all go google “controlled mutation” and see where that leads us. LOL

Thanks for posting, I very much enjoyed your newest post. I think you should post more often, you obviously have talent for blogging!