Chimps throwing stones

March 10, 2009 • 8:04 pm

by Greg Mayer

My local newspaper, along with many other news outlets, had a story this morning about a chimp at a zoo in Sweden who collects and stores rocks that he later uses for throwing at zoo visitors.  The major point of the article was that the chimp made plans for something he was going to do in the future.  This didn’t seem like news to me; I’d heard stories of great apes doing things that seemed to involve at least as much planning.  I asked my friend, Eric Hileman, formerly Director of Animal Welfare and Conservation Education at the Racine Zoo in Racine, Wisconsin, and now a graduate student at the University of Wisconsin-Milwaukee, if he knew of apes planning for the future.  He told me that the Zoo’s orangutans did so.  They would occasionally get hold of some item that a keeper had inadvertently left behind, or that had rolled under a door, such as a pencil or screw.  They would then conceal the item, either in their enclosure or on themselves.  Later, the item would be produced by the orang, and shown to the keeper, but not returned.  If the keeper would offer a snack, then the item would be returned to the keeper in exchange for the food.  Holding on to the item for use in bartering for food in the future, rather than attempting an immediate exchange, seems like planning to me, although these were not planned behavioral experiments that might exclude other interpretations.  He also mentioned a story he’d heard of an orang getting hold of a set of keys, and then secreting them away until the keeper had left, but this is a third or fourth hand story.

Having a temporal sense of events is something that I could not see in my considerations of the moral sense of my cat Peyton. It seems a major advance in cognition, and also in the development of a full (rather than merely rudimentary) moral sense, allowing for retribution, admiration, gratitude, and reciprocity.

Scientific integrity

March 9, 2009 • 2:15 pm

by Greg Mayer

Jerry had written earlier about a piece in the New York Times by Dennis Overbye heralding the restoration of science to its rightful place promised by President Obama in his inaugural address.  I, too, was thrilled when I heard the new president’s words while watching the speech with a throng of travellers at an airport bar in Philadelphia. Perceptively, Overbye wrote, “Science is not a monument of received Truth but something that people do to look for truth.”

Well, the search for truth by the federal government has resumed. Having reversed or modified some specific Bush administration policies, Obama has now issued a general memorandum on scientific integrity:

Science and the scientific process must inform and guide decisions of my Administration on a wide range of issues, including improvement of public health, protection of the environment, increased efficiency in the use of energy and other resources, mitigation of the threat of climate change, and protection of national security.

The public must be able to trust the science and scientific process informing public policy decisions.  Political officials should not suppress or alter scientific or technological findings and conclusions.  If scientific and technological information is developed and used by the Federal Government, it should ordinarily be made available to the public.  To the extent permitted by law, there should be transparency in the preparation, identification, and use of scientific and technological information in policymaking.  The selection of scientists and technology professionals for positions in the executive branch should be based on their scientific and technological knowledge, credentials, experience, and integrity.

Update: From Obama’s statement on stem cell research, a clear sign that he understands how research goes, and what a “miracle” is:

Medical miracles do not happen simply by accident. They result from painstaking and costly research, from years of lonely trial and error, much of which never bears fruit, and from a government willing to support that work.

Neanderthals and sex

March 9, 2009 • 12:10 am

by Greg Mayer

A couple of news items from the past month deserve a quick comment or two. First, at the American Association for the Advancement of Science annual meeting in Chicago last month, Svante Paabo of the Max Planck Institute announced the completion of a draft genome for Neanderthal man, and that it indicated that modern man and Neanderthal man did not interbreed: the Neanderthals are our evolutionary cousins, not members of our own species.  The work by Paabo on the Neanderthal genome, and on ancient DNA in general, is fabulous, but two caveats must be noted: the first draft covers only 63% of the genome; and, most of the DNA comes from one cave in Croatia. So what you can say is in the 63% of the DNA they’ve looked at there’s no sign of interbreeding at this location. But we know secondary contact of differentiated populations in ice age Europe can be very complex; e.g. hooded crows would show evidence of interbreeding with carrion crows if sampled in some places but not others, so the case isn’t closed. And a personal quibble: according to the BBC

The draft genome can give us clues to the genetic regions which make us “uniquely human”, Prof Paabo told BBC News.

Besides the usual need to realize that knowing the genome of “X” doesn’t mean we know what it is that makes “X” so “X-ian”, Paabo implies here that Neanderthals weren’t human.  But by any biologically coherent notion of human they were (hence Homo neanderthalensis). John Hawks (hat tip: Pharyngula) has an excellent discussion of all sorts of issues relating to the Neanderthal genome.

Second, John Long (who has a wonderful book on fish evolution) and two colleagues published a paper in Nature (abstract only) reporting internal fertilization and vivipary in a placoderm, a group of ancient fish. This is a wonderful discovery, showing again that Philip Skell doesn’t know what he’s talking about (Skell, you’ll recall, had said fossils “cannot reveal the details that made these amazing living organisms function”!!!). But the paper got twisted in media reports into these fish inventing sex.  The BBC headline said “Fish fossil clue to origin of sex“, while, even more inexcusably, the British Museum (Natural History) website had “Fish knew first about sex“. Sexual reproduction originated in bacteria, probably billions of years before these fish. These fish may be the earliest vertebrates with copulation with an intromittent organ (a penis or similar structure); such organs have evolved multiple times, including four times in the amniotes (reptiles, birds, mammals).  The price of journalism is eternal vigilance.

The palimpsest theory

March 8, 2009 • 9:01 pm

by Greg Mayer

One of the things Jerry mentioned in introducing me was that I had coauthored, with my late friend and mentor John A.W. Kirsch, a paper entitled “The platypus is not a rodent”.  While there’s a certain pure amusement value in such a title (which alludes to a series of papers concerning the relationships of guinea pigs with titles such as “Is the guinea-pig a rodent?”,  “The guinea-pig is not a rodent”, and “Are guinea pigs rodents?”; btw, the guinea pig is a rodent, and the platypus is an egg-laying monotreme, nowhere close to rodents), Jerry might have mentioned the paper because of its subtitle: “DNA hybridization, amniote phylogeny and the palimpsest theory”. In WEIT, Jerry likens the bodies and genomes of organisms to palimpsests. In ancient and medieval times, parchment to write on was expensive, but writing was cheap. To save parchment, the writing would be scraped off a book (for in those days, all books were written by hand), and a new book written over the old. Such reused parchments are called palimpsests. The original writing, however, can often be seen or retrieved, and thus the history of the parchment’s uses can be inferred from the existing parchment. (Here’s an example mentioned by Jerry.)

A palimpsest possesses both recently acquired features (the new writing) and remnants of old features (the old writing).  So do organisms. They possess immediately adaptive characters, as well as characters from earlier in their history.  This has long been recognized, and the analogy with palimpsests has been explicit. In 1910 W.K Gregory of the American Museum of Natural History made a distinction between ‘caenotelic’ and ‘paleotelic’ characters; he later called these ‘habitus and heritage’ (Gregory was the major professor of my major professor, E.E. Williams, and thus I am Gregory’s academic ‘grandson’). In 1947, Gregory christened his ideas the ‘palimpsest theory’.  As John and I explained:

Habitus characters (equivalent to caenotelic features) become in time transformed into, or at least included among, those of heritage as the collected adaptive wisdom of the lineage at more general levels, by a process of sequential adaptation …. Habitus and heritage are thus ‘correlative terms’, so that ‘the remainders of the successive habitus of the remote ancestors become incorporated into the heritage of later times’ (Gregory 1947, p. 8). Heritage features are therefore of utmost importance in determining the broad affnities of a higher-category taxon, because they may be ones shared with a similarly inclusive but different group.

Thus the habitus characters are the new writing, the heritage the old. The palimpsest analogy had been published earlier by the great South African paleontologist Robert Broom (best known for his later work on australopithecines, the predecessors of our own genus, Homo) who in 1924 wrote about turtles that

Unfortunately members of the order are all extremely specialized and in some respects degenerate, so that the picking out of the ancestral [=heritage or paleotelic] characters amid the more recent specializations [=habitus or caenotelic] is somewhat like the reading of a difficult palimpsest.

Broom and Gregory were well-acquainted with one another, and Broom visited the American Museum in 1913-1914, so the use of the term palimpsest by the two of them is probably not independent.

Not all historical processes leave clear traces of their paths: if a ball rolls downhill to a resting place, we cannot infer from where on the surrounding heights it began; and one molecule of water is just like another (of the same isotopes), no matter whence it came.  We are fortunate that descent with modification is a history-conserving process: bodies and genomes of organisms are documents of evolutionary history. As the many examples in WEIT show, even when a fossil record is lacking, we can learn much about an organism’s evolution.

Caturday cricetid

March 7, 2009 • 12:42 pm

by Greg Mayer

To give a little equal time to other trophic levels, this Saturday we have a meadow vole, a member of the rodent family Cricetidae.

Voley
Voley

Nicknamed ‘Voley’, this Microtus pennsylvanicus was rescued from a mechanical access shaft into which it had fallen and become trapped. What many people think of as ‘field mice’, and what many house cats bring home, are actually voles: they can be distinguished by their short tails, and smaller eyes and ears compared to other mice. Evolutionarily, meadow voles are known for being geographically variable, with many described subspecies, including a number restricted to small islands off the coast.  Since most of these islands are land-bridge islands, isolated from the mainland only since the post-glacial rise in sea level, the differentiation of the voles inhabiting them is quite recent. The most distinctive of these small island derivatives of the meadow vole is a distinct species, the beach vole, Microtus breweri, found only on Muskeget, a very small island to the west of Nantucket Island, Massachusetts. (My friend and colleague James ‘Skip’ Lazell calls it “defiantly” distinct from the meadow voles on nearby islands.) They have been isolated on Muskeget only 2000-3000 years, and are thus an example of rapid divergence. Jerry deals with  the nature of species and species formation in chap. 7 of WEIT, and in much more detail in his 2004 monograph with H. Allen Orr, Speciation.

Deep time

March 6, 2009 • 2:19 pm

by Greg Mayer

Seed Magazine has a nice video showing The Evolution of Life in 60 Seconds.  It gives you a good feel for “deep time“: the immense span of ages that is the history of the Earth.  It is especially notable how brief the entire Phanerozoic (from the Greek for “visible life”), the last 550 million years or so of largish animals with hard parts, is.

Coat color in wolves

March 6, 2009 • 11:08 am

by Greg Mayer

An alert reader has directed my attention to an interesting paper on coat color in wolves (abstract only without subscription) in today’s issue of Science by Tovi Anderson of Stanford and 14 colleagues from the US, Canada, Italy, and Sweden. Coat color in wolves is a polygenic trait affected by age, but Anderson and her colleagues show that black color in young wolves is associated with a 3 base-pair deletion in a gene called CBD103, and that there is a habitat correlation with the frequency of this color: black wolves live in the forests, gray (or white) wolves on the tundra.  This would be very interesting on its own, but Anderson et al. go further.  By careful phylogenetic analyses, they show that the gene for black color has entered North American wolves, and coyotes and Italian wolves as well, by hybridization with domestic dogs; and that the gene has been subject to recent positive natural selection (shown by low variability in the part of the chromosome immediately surrounding the gene, indicating what is known as a “selective sweep”).  Thus, a correlation between habitat and coat color that is suggestive of adaptation, is shown to be based on heritable variation undergoing natural selection.

The sort of combined field and lab study done by Anderson et al., using classical genetics (they have pedigrees of the wild wolves!), ecology, and now molecular genetics, is among the kind of work that first attracted me to evolutionary biology, and is known as ecological genetics. This field of study, pioneered by the great British geneticist E.B. Ford, was once characterized by the great American geneticist Dick Lewontin as carrying on the British “genteel upper-middle-class tradition of fascination with snails and butterflies”; I’m glad the fascination has moved to some of the colonies and beyond, and been extended to wolves, coyotes, and dogs.

Skell pwned again

March 5, 2009 • 12:13 pm

by Greg Mayer

I think I’ve been able to figure out why chemist Philip Skell’s attack on Jerry in Forbes was so unresponsive to what Jerry actually wrote: he probably wrote most of it before seeing Jerry’s article!  P.Z. Myers noted a piece in the Eugene, Oregon, Register-Guard by teacher Stuart Faulk rebutting Skell’s arguments.  Addressing Skell’s claim that evolution is irrelevant to medicine, Faulk (who is Skell’s son-in-law!) does some research:

The contention that evolutionary science is not useful is easily shown false by counter-example. The necessary research is accomplished by walking the five feet to my coffee table and picking up the March edition of Scientific American magazine, in which the article “New Tactics Against Tuberculosis” describes progress against the spread of drug-resistant TB….As the authors state of one promising approach, “It allows us to harness the power of natural selection in our quest to thwart (drug-resistant TB).”

He also notes that Skell’s claim that for evolution to be relevant  to medicine, then paleontology must drive its research agenda, is an “absurd idea”,  “introduced by Skell, not evolutionary scientists.” Faulk goes on to note that Skell’s real concerns are religious, not scientific, as “any Web search will show”.

That Skell’s arguments are easily rebutted is not surprising; what is surprising is that Faulk was responding to something Skell wrote in the Register-Guard that appeared February 12, the same day as Jerry’s piece in Forbes, and 11 days before Skell’s piece in Forbes.  The Register-Guard piece is only available on the web as an excerpt, but it seems to be much the same as what appeared in Forbes. You compare:

The Register-Guard, Feb. 12: “Darwin was great, but too often he’s oversold”

In 1942 Nobel Laureate Ernst Chain wrote explicitly that his discovery (with Florey and Fleming) of penicillin, and the development of bacterial resistance to that antibiotic, owed nothing to Darwin’s and Alfred Wallace’s evolutionary theories. The same can be said about a variety of other 20th century discoveries: that of the structure of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; and various new surgeries.

Forbes, Feb. 23, “The dangers of overselling evolution”

In 1942, Nobel Laureate Ernst Chain wrote that his discovery of penicillin (with Howard Florey and Alexander Fleming) and the development of bacterial resistance to that antibiotic owed nothing to Darwin’s and Alfred Russel Wallace’s evolutionary theories.

The same can be said about a variety of other 20th-century findings: the discovery of the structure of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; new surgeries; and other developments.

I can understand why Jerry found Skell’s Forbes piece off-point:

The curious thing is that Skell’s piece is not, as it pretends to be, a critique of what I said in Forbes, but merely a repetition of the argument, which he has been making for years, that evolution is of no practical use for humanity and of no use to experimental biology

The one thing I would add to these critiques of Skell is to point out his curious use of the phrase “experimental biology”, and his disdain for what he seems to consider unobservable or uncertain knowledge.  He seems to imply that chemistry and “experimental” biology, are good science, because they are observable; other sorts of biology (i.e. evolution), and (if the apparent criterion is to be applied uniformly), geology and astronomy are not, because we have not seen a live trilobite, or Gondwanaland, or a star moving along the main sequence.  Thus creationists seek not just to eliminate biology, but much of the rest of science as well. All knowledge in empirical science, including chemistry, is tentative; and the changes in the kinds of plants and animals you see as you travel up slope on a fossiliferous exposure are much more observable than any chemical bond.