Tag: evidence for evolution

The evidence for evolution

November 11, 2014 • 7:28 am

[The internet is down at the Kirksville Holiday Inn. The only other time this has happened to me was when I was in Russia. What this means is that posting may be light today. Fortunately Greg prepared a post on a recent talk he gave about evolution, which is below. JAC]

by Greg Mayer

Jerry has posted a couple of times in the last week or so on the “creationist shenanigans” at Georgia Southern University, where a professor is apparently openly proselytizing for his religion in classes on the history of science. One of the items the professor has produced is an online document titled “No evidence for evolution“. It’s actually a rather sad document– and not just because it’s a typically dishonest creationist exercise in quote-mining, which would have us believe that Jerry Coyne, George Gaylord Simpson, Jeff Levinton, Niles Eldredge, and Steve Gould, among others, can all be rallied to the cause of creationism. Nor is it because he mixes in quotes from the likes of  Michael Denton and Francis Hitching, as though they had any authority at all. Nor is it even because of his schizophrenic view of Gould and Eldredge, who on the one hand he wields in support of creationism, but on the other he attacks (through quotes) because (gasp!) they are evolutionary paleontologists. No, it’s sad because it’s all so old. Other creationists did this decades ago– and, frankly, better. The quotes are almost all old ones– from the 1980’s and earlier (the latest quote I noted was 1997– the page is dated 2002). The reason it’s so sad is that not only does this guy know nothing about biology or paleontology, he’s not even a very good creationist– he apparently hasn’t kept up with developments in his own “discipline”!

Just a day or two after Jerry posted, my colleague Chris Noto informed me that a talk I had given at Darwin Day celebrations earlier this year was now available online. Entitled “The Evidence for Evolution”, it seemed like a happy coincidence, and so I share it with you here. (Note that the Parasaurolophus and sauropod behind me seem quite interested, the latter even bending his neck above and around me so he can read my notes on the podium! There was a human audience too, although, as usual, until a late attendee arrived, no one wanted to sit in the front seats.)

The talk was given at the Dinosaur Discovery Museum in Kenosha, Wisconsin, as part of their Darwin Day events last February. It was based on the chapter I wrote for The Princeton Guide to Evolution, edited by my friend and colleague Jon Losos, which was officially published right about the time I gave the talk. The talk is about descent with modification per se, and not on the mechanisms of evolution (except insofar as the observation of current evolutionary changes allows us to see such mechanisms directly), and the main topics were the fossil record; transitional forms; comparative morphology, embryology and genetics; biogeography; and evolution in action. I would particularly draw attention to the example of observed speciation in Spartina in England (about 30:44). It’s an example of allopolyloid speciation (a new species arises by hybdidization with increase in the number of chromosome sets), which is common in plants (though not animals), and is expected to occur very rapidly, but it’s nice to have a case where humans observed the speciation event start to finish (1829-1892).

(The camera battery went dead for a bit, so there’s about 5 minutes of the biogeography section missing; the dead space was edited out with a “wave”– you’ll notice it.)

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Mayer, G.C. 2014. The evidence for evolution. pp. 28-39 in J.B. Losos, ed., The Princeton Guide to Evolution, Princeton University Press, Princeton, New Jersey.

Preserved protein from an 80-million-year old dinosaur support the dinosaurian origin of birds

May 6, 2009 • 6:16 am

In this week’s Science we find a paper by Schweitzer et al. (total of 16 authors!) that has a quite remarkable result. (See the one page summary by Robert Service here.)  The upshot is that protein-sequence data from an 80-million-year old duckbilled dinosaur supports the dinosaurian origin of birds.

This story has a bit of a tortuous background.  First of all, we’ve known for a long time that birds evolved from gracile theropod dinosaurs; the fossil and anatomical evidence is given in WEIT.  But for some folks, DNA-based data is more convincing than is the fossil record.  And molecular evidence is what Schweitzer et al. provided.

In 2007, her group published a paper purporting to show that fragments of the protein collagen (a structural protein found in blood vessels and connective tissue), taken from a 68-million-year old fossil of T. rex, showed that the protein sequence (which reflects the DNA sequence) was more similar to that of birds than to that of modern reptiles. This strongly suggests that birds evolved from a lineage of dinosaurs that had already branched off of the lineage that gave rise to modern reptiles.  This meant that birds and dinosaurs are each other’s closest relatives compared to say, turtles or iguanas. In fact, many systematists say that birds are dinosaurs, which is the conclusion you’re forced to if you’re a hidebound cladist.  I mentioned this paper in WEIT in footnote 11 on p. 237 (this was probably the last thing I put in the book). Of course this result was no surprise to paleontologists.

As recounted by Service, this result was sharply questioned by other researchers, who claimed that the protein sequence was due to contamination; many others thought it was hard to believe that any protein could survive for so many millions of years.  I was a bit depressed about this, because I had already put the result in my book and there was no opportunity to change it before publication.  Also, it was just such a cute result — the kind of new finding that gets our juices flowing as scientists.

Well,  Schweitzer and her team persisted, and her new result supports the old one.  This time the group extracted protein fragments from the femur of a duck-billed dinosaur, Brachylophosaurus canadensis, collected in Montana. Great care was taken to prevent contamination.  They found that some of the elements in the demineralized bone bound to  antibodies made against bird collagen, indicating that collagen fragments similar in sequence to those of birds were present in the bone.  The same was found with antibodies for hemoglobin and two other structural proteins.

Some biochemical wizardry on bone extracts identified eight fragments of collagen, and their sequences (also determined in a separate lab to preclude contamination) were determined.  Sure enough, they were similar to the T. rex fragments that were questioned earlier, and were more similar to collagen sequences of modern birds than to those of modern reptiles. (See the phylogeny below.)  Note that there’s a small disparity between the fossil and biochemical evidence:  T. rex, as a theropod (the group that gave rise to modern birds), should be more closely related to modern birds than is B. canadensis.  This discrepancy might be an artifact of not having a complete protein sequence.

Let’s be clear: the phylogeny that we get doesn’t really tell us anything we didn’t know before.  Birds are highly-evolved dinosaurs, and that was already confirmed by the fossil record.  Still, it’s nice to have this molecular confirmation, and perhaps the most surprising result is the ability to determine the sequences of protein fragments that have survived for millions of years.  If this can be done with other fossils, we’ve suddenly gained the ability to solve many long-standing puzzles about ancestry and evolutionary relatedness.

phylogeny

Phylogeny showing closer relationship between dinosaurs and birds (Gallus = chicken, Struthio = ostrich) than between either of these groups and modern reptiles (alligators and Anolis lizards).  Ergo, birds are dinosaurs.


hadriosaur

Brachylophosaurus canadensis, the duck-billed dinosaur whose proteins were sequenced.  Illustration by Julius T. Csotony from Science article.

Schweitzer, M. H. et al.  2009. Biomolecular Characterization and protein sequences of the campanian hadrosaur B. canadensis. Science 324:626-631.

What counts as evidence for evolution?

April 4, 2009 • 7:07 am

A couple of reviewers of WEIT (and some of my friends and colleagues) have pointed out the book’s dearth of molecular evidence for evolution.  For example, why didn’t I stress that organisms thought to be related based on morphological similarities also show similar relationships in their DNA sequences?  That is, DNA phylogenies generally match morphologically-based phylogenies — doesn’t that count as evidence for evolution?  To my mind, not very strongly, and for two reasons.  First, at least for protein-coding genes, morphology and DNA are not independent: the genes are blueprints for the organism’s appearance, so the coincidence of trees is not independent evidence for evolution.

My strategy here was to use as evidence for evolution only those data that rule out the most widely-accepted alternative scenario, i.e., some form of creationism.  Similarities of molecular and morphological trees don’t necessarily rule out the action of a celestial designer.  He/She/It could have used similar genes to make similar organisms.

Well,  you ask, what about those parts of the DNA that are “neutral”?  (E.g., the third positions of codons, in which a mutation doesn’t necessarily change the structure of the protein made by that gene.)  Well, yes, those could count provided that they really are neutral.  As molecular evolutionists examine genomes more thoroughly, they often find that “neutral positions” aren’t really neutral, but could play some role in the fitness of the organism.  In such cases, their phylogenetic match to appearance-based phylogenies again fails to rule out creationism.

The one type of molecular evidence that does absolutely rule out creationism, I think, involves pseudogenes: those genes that were once active in ancestors but have become inactivated. I describe several cases in chapter 3 of WEIT; they include olfactory receptor genes in humans, many of which have become inactivated in the human lineage as we gradually lost reliance on our sense of smell and became more vision-oriented.  DNA changes in pseudogenes can hardly be subject to natural selection, so pseudogenes change in a purely time-dependent manner as those dead genes accumulate mutations over time.  Thus, the match between phylogenetic trees based on pseudogene DNA sequences (reflecting only the passage of time) with phylogenetic trees based on organisms’ appearance are expected under an evolutionary scenario but not a creationist one.  Creationists largely deny common ancestry (and don’t accept that organisms change with the passage of time). They wouldn’t, then, predict a phylogenetic match between features that simply mark the passage of time and features that independently reflect ancestry (e.g., the placenta of placental mammals that is not found in marsupials).  This is why I concentrated on pseudogenes in my book.  I’ve never seen a creationist explanation for why DNA trees based on pseudogenes match traditional trees based on morphology.

Similarly, people often cite Hox (“homeobox”) genes as evidence for evolution (these are the genes that demarcate different segments of animal bodies). It turns out that in organisms which are very dissimilar, such as humans and my beloved fruit flies, Hox genes nevertheless play similar roles in building bodies.  Why don’t I count this as evidence for evolution? Because it doesn’t rule out the alternative of a celestial designer.   Such a designer could have used the same genes in different species as His/Her/Its way of building bodies.  There’s no reason why a designer couldn’t hit on certain fundamental ways of making bodies, and then use them over and over again.

This, then, was my strategy throughout the entire book: to use only that evidence that could not easily be explained by creationism or other alternatives to evolutionary theory.  This, of course, is precisely the strategy that Darwin used in The Origin, since he had to convince readers that his theory was superior to the reigning creationist paradigm of the day.  I guess you can say that, given prevailing opinions in the US and some other countries, I adopted the same evidence-based strategy.