Category: in the news

Tuataras in the news

November 23, 2010 • 1:17 am

by Greg Mayer

Tuataras are in the news today, although there really isn’t that much new about them. In fact, as Natalie Angier points out in the New York Times, they are transparently Triassic in aspect, as the following picture, of a tuatara named Henry, will attest.

Henry the tuatara, from Wikimedia.

Angier provides a review of various interesting aspects of tuatara biology– they live a long time, reproduce slowly, eat giant orthopterans, are nearly extinct, etc. What’s most interesting about them is that they are the sole living members of one of the four major groups of extant reptiles, the Sphenodontida (an order in the Linnaean hierarchy of ranks, the other reptile orders being turtles, crocodiles, and snakes+lizards); and they are found only in New Zealand, where they are restricted to a few offshore islands.  (They have recently been transplanted back to the mainland of New Zealand, whence they were extirpated centuries ago by introduced rats.)

Though they look much like lizards (iguanas or agamids in particular), and were thought to be lizards when first discovered, they are in fact not lizards, as anatomical examination reveals. They have a primitive type of skull, termed fully diapsid, which means the cheek region of the skull has two complete openings surrounded by bone, and they have at most a rudimentary hemipenis (the distinctive double copulatory organ that characterizes snakes and lizards).

Tuataras are a good example of an older group surviving on an isolated land mass, something typical of old islands like New Zealand, which separated from other parts of the former southern supercontinent of Gondwana around 80 million years ago. Tuataras had been spread about the globe during the Mesozoic (Age of Reptiles), but survived only on New Zealand.

It is distressingly common to see tuataras described as “dinosaurs”, but they are no such thing. They lived during the time of the dinosaurs (and have changed relatively little since, earning them the sobriquet “living fossils”), but their closest relatives are the lizards and snakes, together with which they form the larger reptilian group known as lepidosaurs. Dinosaurs closest living relatives are birds, which, indeed, are perhaps best thought of as actual dinosaurs themselves.

US government opposes gene patenting

November 9, 2010 • 12:14 am

by Greg Mayer

In a move that got lost in the run up to the recent US elections, the Federal government has reversed its longstanding policy that genes are patentable. Released the Friday before the elections, and covered by the New York Times the following day, with a follow up article the day before the election, the Justice Department’s brief in the case argued that gene sequences unmodified by man are products of nature, and thus ineligible to be patented; and that isolating the sequence doesn’t change its status. Here’s a summary of the argument:

The district court [which invalidated two gene patents] correctly held, however, that genomic DNA that has merely been isolated from the human body, without further alteration or manipulation, is not patent-eligible. Unlike the genetically engineered microorganism in Chakrabarty [an earlier decision, allowing the patenting of genetically modified organisms], the unique chain of chemical base pairs that induces a human cell to express a BRCA protein is not a “human-made invention.” Nor is the fact that particular natural mutations in that unique chain increase a woman’s chance of contracting breast or ovarian cancer. Indeed, the relationship between a naturally occurring nucleotide sequence and the molecule it expresses in a human cell — that is, the relationship between genotype and phenotype — is simply a law of nature. The chemical structure of  native human genes is a product of nature, and it is no less a product of nature when that structure is “isolated” from its natural environment than are cotton fibers that have been separated from cotton seeds or coal that has been extracted from the earth.

The friend of the court brief was filed in an appeal of a case brought by a group of scientific and medical societies and individuals against Myriad Genetics, which had been granted patents on two genes associated with breast and ovarian cancer. In a surprise ruling last March, US District Court Judge Robert Sweet invalidated the patents (more on the ruling here and here), and the current brief was filed in response to Myriad’s appeal of the adverse ruling. The Feds argue that some aspects of Judge Sweet’s ruling erred, but that it’s main conclusion was correct: “…products of nature do not constitute patentable subject matter absent a change that results in a fundamentally new product. … [T]he purification of native DNA does not alter its essential characteristic– its nucleotide sequence– that is defined by nature…” (pp. 107 & 132 of the ruling, full text here).

The Federal position comes as good news to the scientists and medical groups involved, and to anyone who wants the law to make  sense. The notion that a gene is a human invention, rather than a product of nature, is absurd to any biologist (unless perhaps you were granted one of these bogus patents, which may be one of those cases where, as Upton Sinclair put it, it is difficult to get a man to understand something, when his salary depends upon his not understanding it). This is one instance in which the Obama administration has followed up on his promise that “Science and the scientific process must inform and guide decisions of my Administration on a wide range of issues”.

Russell Blackford has noticed the new anti-patent brief, and also had a nice overview of some of the issues at the time of Sweet’s ruling. NPR also noticed the new brief a few days later.

Harvard investigates Hauser

August 13, 2010 • 7:04 am

As Nicholas Wade reports in Wednesday’s New York Times, Marc Hauser,  whose work on morality we’ve discussed before, is under investigation by Harvard.  Apparently some of his work on tamarins either can’t be replicated or is not supported by videotapes and other data produced by Hauser’s lab.

These are serious charges.  Hauser’s work has been important in understanding the phylogenetics of primate behavior and cognition.  One of his papers has already been retracted, and a few others seem on the verge.  On the other hand, we shouldn’t rush to judgment before Harvard’s investigation is complete.  Remember that there are many reasons besides deliberate fraud for data to be unreliable.  There is also the matter of who is responsible, since a senior investigator, while formally responsible for the work in his lab, might not have been there to oversee every observation or data point collected by his students.  At this point we have no idea what happened.

Three personal observations:

1.  Harvard is rightly keeping its investigation under wraps until it’s complete. (Hauser is on leave for a year.)  But it is incumbent on the university to make the results public at the end.  Hauser’s own career and reputation must of course be handled with care.  But we’re talking here about a whole swath of literature on primate behavior, and scientists ultimately need to know how far to trust that swath.  There is no excuse for keeping the final report under wraps.

2.  The Schadenfreude that I’ve heard about, some of it in Wade’s report, is absolutely inexcusable.  It is shameful for scientists to cast aspersions on Hauser’s work until Harvard’s report is complete.  Even if, like Herbert Terrace, you think his conclusions have been insufficiently supported by data, you should be aware that bringing that up now feeds into accusations of fraud.  If Hauser is exonerated, such loose talk could nevertheless affect his reputation for life.  The proper response to questions about the veracity of Hauser’s work is  simply “No comment.”

3.  Finally, the superannuated Nicholas Wade, whose work has not impressed me much, should be given some other beat at the Times, or even set out to pasture.  Look how he takes Terrace’s opinion about what happened and turns it into a general indictment of primate research (my emphasis).  Yes, one has to be careful, but Wade’s repetition of this comment as reportage is simply unfair.

Dr. Hauser is a fluent and persuasive writer, and his undoing seems to have been his experiments, many of which depended on videotaping cotton-topped tamarin monkeys and noting their responses. It is easy for human observers to see the response they want and so to be fooled by the monkeys.

Dr. Terrace said there had been problems for some time with Dr. Hauser’s work.

“First there was arbitrary interpretation of the videotapes to suit the hypothesis,” he said. “The other was whether the data was real. There have been a number of papers using videotape, and all of them have to be reviewed to see if the data holds up.”

Dr. Terrace noted that it was easy for a researcher to see what he wanted in a videotaped animal’s reactions, and that independent observers must check every finding.

Did Lucy eat meat?

August 11, 2010 • 1:14 pm

According to the New York Times,  a paper to be published in tomorrow’s Nature reports indications of meat-eating in the hominin Australopithecus afarensis.   The paper, by S. P. McPherron et al., shows cut marks on animal bones that date back at least 3.4 million years and were found in a formation in Ethiopia where fossils of A. afarensis also occur.  The authors claim that these cut marks could have been made only by hominins wielding stone tools:

Fig. 2 from the Nature paper, showing an ungulate rib with putative cut marks.  Scale on SEM photos is 100 microns.

This finding, if true, pushes back the earliest hominin use of stone tools by a staggering 800,000 years.  It’s sure to be controversial, especially since no stone tools have been found at the site.  Indeed, scientists quoted in the Times story are casting strong doubt on the conclusions.  Stay tuned.

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S. P. McPherron et al. 2010. Evidence for stone-tool-assisted consumption of animal tissues before 3.39 million years ago at Dikika, Ethiopia.  Nature 466:857-860. doi:10.1038/nature09248

Video of whale pwning yacht

July 23, 2010 • 9:12 am

There’s now a video of this incident.  I can’t embed it here, but I can give you the YouTube link, which shows a southern right whale (Eubalaena australis) breaching off South Africa and crashing into a boat.  It’s from CBS News; you’ll have to endure a short commercial but it’s worth it.

A CBS interview with the couple on the boat is here.

h/t: AJ