Some Links #9: Sowing the Seed of doubt

This isn’t the first time Seed has sacrificed editorial independence. A worrying article about scienceblogs’ parent company, Seed, and how they restricted the publication of a column on the basis of it being critical of Dow Chemical — someone they were seeking an advertising contract with. As Gaia Vince points out in an email she received from Seed:

We’re not running the bhopal piece, and we’re passing on the Maldive shark ban (a bit late now… Too bad it got caught up in prod week… ). As for Bhopal, it’s a cautionary call on our part as we’re in the midst of advertising negotiations with Dow (who have been inspired by Seed’s photography in their own brand campaigns). RE: the payment, as you’re on a scheduled direct-payment, the bhopal fee covers the Kerry/Carbon trading news piece fee that was outstanding. Let me know if that’s clear.

It’s a great article that’s not only revealing about Seed, but the underlying motivations of the journalism industry in general. I never thought I’d find myself linking to Chomsky’s politics, yet, given the nature of this article, maybe it’s time I dug out my copy of Manufacturing Consent.

Scientific Certainty Argumentation Methods (SCAMs): Science and the politics of doubt. H/T: Ben Goldacre. A good paper looking at what happens when science and politics mix, and how the two have different expectations of what science is. Here’s the abstract:

At least since the time of Popper, scientists have understood that science provides falsification, but not “proof.” In the world of environmental and technological controversies, however, many observers continue to call precisely for “proof,” often under the guise of “scientific certainty.” Closer examination of real-world disputes suggests that such calls may reflect not just a fundamental misunderstanding of the nature of science, but a clever and surprisingly effective political-economic tactic—”Scientific Certainty” Argumentation Methods, or SCAMs. Given that most scientific findings are inherently probabilistic and ambiguous, if agencies can be prevented from imposing any regulations until they are unambiguously “justified,” most regulations can be defeated or postponed, often for decades, allowing profitable but potentially risky activities to continue unabated. An exploratory examination of previously documented controversies suggests that SCAMs are more widespread than has been recognized in the past, and that they deserve greater attention in the future.

The secret history of X and Z. An excellent article from Ed Yong on Chromosome evolution in humans and birds. Key paragraph:

Why the similarities? It’s possible that both X and Z evolved from autosomes with features that made them more likely to become sex chromosomes. Perhaps, for example, their genes were already sparsely distributed. But Bellott ruled out this idea. He compared X to its closest counterpart in chicken, and Z to its equivalents in humans – none of these relatives had any structural features that made them stand out among other autosomes. There’s nothing that singles them out as ideal candidates for the role of sex chromosome.

You are not authorized to see these pictures of the oil spill, citizen… Do not look. Washington’s Blog has some fairly harrowing photos of the recent gulf oil spill and the damage it’s doing to wildlife. Here’s one example:

What conclusions can we draw from Neanderthal DNA pt.2

ResearchBlogging.org4. Nuclear DNA: Forays into 3 billion base pairs

4.1 Before Vi-80

The Vindija-80 (Vi-80) specimen is an important find for geneticists: it yielded a minimally contaminated sample and provided those first steps into Neanderthal genomics.

Previously, attempts at retrieving ancient nuclear DNA sequences proved to be a notoriously difficult process, plagued with problems of degradation, contamination and chemical damage (Hofreiter et al., 2001). Researchers also need to contend with quantities of nuclear genome available: for every nuclear genome there are approximately several hundred mtDNAs (Green et al., 2008). The severity of these problems, especially contamination, is magnified through Neanderthal genetic similarity with humans (Green et al., 2006). This is troubling because nuclear DNA presents far less variability than mtDNA (Russell, 2002). As a result, huge stretches of nuclear sequences are required to find a significant number of polymorphisms (ibid). Such implications meant that discovering endogenous DNA sequences requires sifting through a large corpus of “[…] more than 70 Neanderthal bone and tooth samples from different sites in Europe and western Asia” (Green et al., 2006, pg. 331).

Continue reading “What conclusions can we draw from Neanderthal DNA pt.2”