DI’s Klinghoffer undermines Behe, Luskin et al. on the origin of new genes

| 511 Comments

Like I just said – as DI guy David Klinghoeffer posted yesterday, the origin of hundreds of new genes in Drosophila is just microevolution. This is a direct deduction from their own ID/creationist logic, where small amounts of change “within the kind” are no problem for normal evolutionary processes. Too bad for Behe, Luskin, etc. Here’s the full quote for when they realize the problem and take the post down:

Praised be Darwin! Do Fruit Flies Bust Behe?

Jerry Coyne is leading the Darwin Tabernacle Choir in expressions of gratitude and relief for a new article in Science that supposedly knocks down the implications of Michael Behe’s current review essay in Quarterly Review of Biology. The Science article seeks to show with what amazing rapidity scads of new genes may arise and become essential to an organism (“New genes in Drosophila quickly become essential”). The evidence is from fruit flies. Two species, D. willistoni and D. melanogaster, diverged starting about 35 million years ago. By comparing genomes, Coyne summarizes exultantly, researchers Manyuan Long et al. showed how “new genetic information can arise quickly, at least on an evolutionary timescale.”

Fruit flies are a cherished subject of such investigations because of their rapid reproduction, going from birth to death in thirty days. This avoids the uncomfortable problems posed by, say, whales. With their far slower maturation and smaller populations, whales succeeded in accumulating all the tens of thousands of wildly prohibitive and interdependent engineering modifications entailed in the transition from land-based ancestor to fully equipped sea creature. Under the Darwinian mythology, they accomplished this feat through blind, undirected searching of evolutionary pathways, all in a twinkling of as little as 10 million years.

Fruit flies are supposed to show us how quickly evolution is accomplished. Perhaps it depends on what you picture when you hear the word “evolution.” For all Drosophila‘s history of hyperactively cycling lifetimes, providing near limitless fodder for natural selection to do its work, for all the new “essential” genes, the upshot of the article may be summarized as follows: 35 million years later, it’s still a fruit fly.

Posted by David Klinghoffer on December 23, 2010 1:25 PM

511 Comments

Wow. I didn’t think anyone used “it’s still a fruit fly” in such plain language as a real argument, but as a snarky parody of Creationist logic.

Klinghoffer’s “It’s still a fruit fly” remark is just another version of “Why are there still monkeys?”

Yeah (occasionally I hold my nose and go to EN&V) I was looking at that and laughed at its obstinacy: “Yeah, we know it’s still a fruit fly, but it’s one that SOMEHOW evolved an irreducibly complex subsystem.” I mean, that’s supposed to be impossible, right?

But what the heck, details, details … no stone left unthrown.

Out of curiosity I went over to Uncommon Descent to see if there was any more talk about this. Newp. The only mention of Behe’s paper in recent entries is as background for a dirt-digging, quote-mining session on Coyne. Besides that there’s a lot of talk about the government wanting to take over the internet and the folly of “global warmists.”
Way to totally ignore the crucial point about new genes becoming necessary for the organisms to function once established, contrary to the claims of Behe that “irreducibly complex” systems can’t evolve.

The Curmudgeon said:

Klinghoffer’s “It’s still a fruit fly” remark is just another version of “Why are there still monkeys?”

On the other hand, we can look at a creationist and say, “It is still a creationist.” And we would be right all the time.

He forgot the obligatory Hitler reference.

I use the term microevolution for changes in the genetic make up of a population over time without a speciation event occurring. Macroevolution is speciation events. Is this how most evolutionary biologists use the terms? I’ve never heard the terms genusization or familyization, or the like, so I suppose speciation is all there is to macroevolution.

Your definition of microevolution is correct, but to creationists it means “whatever evolution we accept because it is so blindingly obvious that we really look like morons if we deny it, plus we can then just dismiss it as trivial, as in ‘that’s just microevolution within the kind’.”

To them, “macroevolution” is what they don’t believe in.

In evolutionary biology, “macroevolution” means more than speciation. Speciation really is it’s own thing, it’s basically the border between micro and macro. Macroevolution contains lineage dynamics (speciation and extinction of many lineages), “large” morphological change (annoying – I would ditch this if I were in charge), the evolution of “higher taxa” (also annoying, I would also ditch this), etc. It’s sort of “everything except population genetics”.

Yeah, no Hitler ref…maybe he’s out of Godwins for the year?

Behe is apparently going to reply. This will be interesting. Either he has to accept that evolution can produce lots of new genes, or that the IDer was tinkering with the genomes within the genus Drosophila, hundreds of times, and Klinghoffer is wrong that it’s all just trivial change “within the kind.”

Jim Thomerson said:

I use the term microevolution for changes in the genetic make up of a population over time without a speciation event occurring. Macroevolution is speciation events. Is this how most evolutionary biologists use the terms? I’ve never heard the terms genusization or familyization, or the like, so I suppose speciation is all there is to macroevolution.

I agree with Nick’s description of macroevolution up to a point. A lot of very interesting work on taxonomic diversification in the Phanerozoic Eon (approximately the last 543-plus million years) has been done relying on lineage data at higher taxonomic levels (e. g. families and orders) of which the most notable have been done by the late Jack Sepkoski and his colleagues and former students at the University of Chicago and elsewhere. Similar work has been done too with regards to tetrapod evolution and the evolution of various types of vascular plants. So while higher taxonomic levels are indeed “artificial constructs” up to a point, robust statisticaly analyses of their diversities over time have led to some fascinating insights relevant to the tempo and mode of evolution from a macroevolutionary perspective.

typo, so here’s the corrected copy:

John Kwok said:

Jim Thomerson said:

I use the term microevolution for changes in the genetic make up of a population over time without a speciation event occurring. Macroevolution is speciation events. Is this how most evolutionary biologists use the terms? I’ve never heard the terms genusization or familyization, or the like, so I suppose speciation is all there is to macroevolution.

I agree with Nick’s description of macroevolution up to a point. A lot of very interesting work on taxonomic diversification in the Phanerozoic Eon (approximately the last 543-plus million years) has been done relying on lineage data at higher taxonomic levels (e. g. families and orders) of which the most notable have been done by the late Jack Sepkoski and his colleagues and former students at the University of Chicago and elsewhere. Similar work has been done too with regards to tetrapod evolution and the evolution of various types of vascular plants. So while higher taxonomic levels are indeed “artificial constructs” up to a point, robust statistical analyses of their diversities over time have led to some fascinating insights relevant to the tempo and mode of evolution from a macroevolutionary perspective.

I didn’t mention extinction, because it occurs at all levels from individual organism to the biosphere, but it is indeed important in the history of life. I think the macroevolution phenomena mentioned above are explainable by a series of speciation events and extinctions.

If higher taxa are monphyletic, then they are just as real as species. Are arguments about their boundaries different in kind from arguments about species boundaries? My work has been from the species to family level, so I don’t really have much to say about higher categories. But I haven’t noticed any major difference in my thinking within that limited part of the hierarchy.

Jim Thomerson said:

I think the macroevolution phenomena mentioned above are explainable by a series of speciation events and extinctions.

Exactly. If there are macroevolutionary phenomena that aren’t reducible to within-population evolution (and I think there are), they involve differential speciation and extinction, by analogy with differential reproduction and death within populations.

If higher taxa are monphyletic, then they are just as real as species. Are arguments about their boundaries different in kind from arguments about species boundaries?

Yes, almost entirely so. It’s all about the monophyly, while species don’t have to be monophyletic. Higher taxa are inferred from trees (themselves inferred from data), while species can’t be inferred from trees.

But I haven’t noticed any major difference in my thinking within that limited part of the hierarchy.

If you’re inferring species status based on building a tree, how are you doing it? Monophyly is neither necessary nor sufficient for designating species. If you aren’t designating species from trees (as you should not), the differences in thinking would seem profound.

Yes, a species is not necessarily monophyletic. I recall reading that about 25% of higher plant species are of hybrid origin. Many of the all female fish and lizard species are known to be of hybrid origin. However, I have seen no reason to think the species I have dealt with are anything but monophyletic. My work has been more taxonomic than systematic. My participation in tree making came later, after species were identified, so the trees were properly built from species rather than the vice versa.

Non-monophyly of species doesn’t have to come from hybridization. One species may be nested within another, the most famous example of which is that polar bears lie within brown bears.

Anyway, isn’t determination of species completely different from making trees? How can you say they involve identical thinking?

I think it is comparative biology all the way. In determining species, one considers possible relationships among the putative species and other populations/species. Who is similar, and how are they similar and different. Tree construction is perhaps a more formal consideration of relationships. Wasn’t the discovery of the polar bear nested within the brown bear the result of constructing a tree?

I must suspect, unfortunately, that you are confused not only about how species are determined but about how relationships among them are determined. Nesting of polar bears within brown bears has nothing to do with species status for either of them. Nor do similarities and differences have much to do with determining species status, though one might attempt to estimate recency of gene flow that way, which is potentially a clue when used in concert with other data. Sure, when describing a species you have to explain now it differs from similar species, but that’s after you have decided it’s a new species. Tree construction is indeed quite formal, or should be; no perhaps about it. But species status isn’t about relationships. And “comparative biology” is much too broad a term to make its use by both endeavors into a matter of identical thinking.

Two species, D. willistoni and D. melanogaster, diverged starting about 35 million years ago.

That must be a typo. I’m sure they meant to say “less than 6000 years ago.”

wamba said:

Two species, D. willistoni and D. melanogaster, diverged starting about 35 million years ago.

That must be a typo. I’m sure they meant to say “less than 6000 years ago.”

DI folk generally do not challenge mainstream science chronology. The more politically correct ones may add a “scientists say” qualifier to throw a bone to the YECs in their audience. But most YECs tune out or forgive the concessions, as long as it comes from one who reassures their unreasonable doubts of evolution.

I don’t recall using the term species in referring to brown and polar bears. I will leave that to the mammal taxonomists. So far none of the 20+ species I have described have been synonomized, although only the last four benefited from information from DNA. Several have been transfered to other genera. One of my earliest new species is now in its fourth genus. This is a result of increased understanding of relationships within the group. Of course I look at similarities and differences before deciding I have a new species. How else would I know?

It was not I who referred to brown bears and polar bears as species. I’ve described some 20 + new species, and none have been synonomized so far. I had the benefit of DNA information on only the last four. Of course one examine similarities and differences to identify a species, or recognize it as new. How could one make an identification decision otherwise?

Sorry for the double comment. I thought the first one was lost. 20th century person me.

I must suspect, unfortunately, that you are confused not only about how species are determined but about how relationships among them are determined. Nesting of polar bears within brown bears has nothing to do with species status for either of them. Nor do similarities and differences have much to do with determining species status, though one might attempt to estimate recency of gene flow that way, which is potentially a clue when used in concert with other data. Sure, when describing a species you have to explain now it differs from similar species, but that’s after you have decided it’s a new species. Tree construction is indeed quite formal, or should be; no perhaps about it. But species status isn’t about relationships.

The real question is, if you don’t have reciprocal monophyly, can species delimitations be made in an objective way? Or is it just an exercise in drawing lines on what is in reality a continuum?

Nick (Matzke) said:

Behe is apparently going to reply. This will be interesting. Either he has to accept that evolution can produce lots of new genes, or that the IDer was tinkering with the genomes within the genus Drosophila, hundreds of times, and Klinghoffer is wrong that it’s all just trivial change “within the kind.”

It really doesn’t matter because all invertebrates are just “worms” and thus of one Kind. They were worms before and are still worms, so the differences between them are not “macroevolution”.

Technically speaking, vertebrates are basically also just highly developed worms once you get right down to it.

Nick (Matzke) said: The real question is, if you don’t have reciprocal monophyly, can species delimitations be made in an objective way? Or is it just an exercise in drawing lines on what is in reality a continuum?

The answer to your real question is “yes”, particularly if you are using the “biological” species concept. Monophyly, reciprocal or otherwise, is not a criterion. It’s propensity to interbreed that counts, nothing else, and propensity to interbreed is plesiomorphic. If there’s a genetic isolating mechanism that keeps two populations from combining into one, they’re two species. Even if all interbreeding stops immediately, it would be very unlikely for either species to be monophyletic immediately; that would require every locus to coalesce in an instant. It can take millions of years for complete reciprocal monophyly to arise. But all it takes for speciation is fixation of different alleles at a few loci that influence interbreeding, and the rest of the genome is dragged along.

Now of course speciation is a continuum, but that’s another issue. You can have absolute reproductive isolation without even a hint of reciprocal monophyly.

But apparently there are cases of critters which have been geographically isolated for tens of millions of years, and exhibit consistent morphological differences, and yet when brought together exhibit a propensity to interbreed, and have fertile offspring. Because of the geographic separation, there was never any selection for genetic isolating mechanisms. So, what do we do with them?

As said, allopatric populations cannot have selection for reproductive isolation as such. If there is reproductive isolation, it is a happenstance. The biological species concept is not a universal theory. It has its virtues and sometimes generates testable hypotheses. Where it is least helpful is when comparing similar allopatric populations. Basic practice is if they look different enough, call them separate species for the moment. Making hybrids in the lab may or may not tell you anything. In terms of the BSC, the question is what happens when allopatric populations come together in nature. If they happily hybridize, the question is, so what? Are the hybrids of low fitness and there is little or no introgression and thus selection for isolating mechanisms? Sometimes we get hybrid swamping where hybrids backcross with one of the populations, lower its fitness, and drive it to extinction. Maybe we get one big happy species. There are lots of possibilities, and knowing that hybrids are fertile is useful but not definitive. There are a lot of examples of expanding ranges, etc, and hybridization events in freshwater fishes. There are examples of just about any outcome one can think of.

The first sentence was serious. The second was comedic reductio ad absurdum .

Vaughn

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This page contains a single entry by Nick Matzke published on December 24, 2010 12:33 PM.

If Science and Religion Conflict, is it Unconstitutional to Teach Science? was the previous entry in this blog.

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