Field of Science

the first complete eukaryotic genome?

In science news this month, a paper in BMC Biology is reporting (Nozaki et al) the sequence of "the first nuclear-genome sequence for any eukaryote that is 100% complete." This might come as a surprise to many scientists, even genomics experts.
The new genome is the red alga Cyanidioschyzon merolae, and it is just 16,546,747 nucleotides long, including all 20 chromosomes from telomere to telomere. The genome had been published previously, but it had 46 internal gaps (totaling 46,469 nt) and the telomeres were missing. They also discovered that about 20 kilobases were mis-assembled previously, a common problem that I've written about elsewhere (see my editorial with Jim Yorke, "Beware of Misassembled Genomes", available on my home page.)

But wait a minute, you might ask (as I did). What about the yeast genome (S. cerevisiae), originally published in 1996 as the first eukaryotic genome? I thought that was finished some time ago. It's true that there have been many published corrections since 1996, but I know the telomeres are present on most (all?) of the chromosomes. And how about the nematode C. elegans - it was published in 1998 while still incomplete, but about four years later it was announced as complete (see the link). These papers are cited by the new paper, but oddly, it doesn't explain what is missing from these earlier "complete" genomes. And I think we finally finished the malaria parasite, Plasmodium falciparum, although the original paper (which I was a part of) appeared in 2000, before all the gaps were closed.

Of course, most genomicists know that the human genome is still far from complete - all the telomeres and centromeres are missing, and there are several hundred other gaps - but I am a bit skeptical of the claim here that the red alga C. merolae is the first complete eukaryote. Can anyone out there tell me why I'm wrong?

Politics trumping the U.S. Surgeon General on stem cells, Plan B, and more

The Washington Post reports today (July 11) that Richard Carmona, the former surgeon general of the U.S. from 2002-6, is now saying that he was "muzzled" on numerous sensitive public health issues. He is quoted saying that the Bush administration's political appointees "ignored, marginalized, or simply buried" any medical or scientific information that didn't fit their ideology.
This is simply amazing coming from a Bush appointee. We all know that Bush and his staff carefully vet their appointees to make sure they hold politically "correct" (i.e., very conservative) views that mesh with Bush's own. It turns out that Carmona, a surgeon and former professor at the University of Arizona, is just too well educated to fit the bill, and he is now speaking out - now that he no longer works for the administration. (It's too bad he didn't speak when he was the surgeon general - Bush might have fired him, but it would have gained more attention.)
Among other issues, Carmona it clear that he supports research on human embryonic stem cells - a vital issue in medical research, which is being held back because of Bush's policy prohibiting federal funding for this research. Carmona says this issue and others was determined by theology, and by "preconceived beliefs that were scientifically incorrect." The Wash Post reports that Carmona was told simply to shut up about stem cell research when the debate was being engaged nationally.
He was also muzzled on other issues, including the "Plan B" pill that induces a miscarriage and birth control. On the latter issue, he was told not to speak out on the "abstinence only" education policy that the administration insists on, even though the scientific research makes clear that abstinence-only education doesn't stop teenagers from having sex (as if it ever would).
It's too bad that we have an administration in the U.S. that ignores science and lets theology and ideology rule over such critical issues affecting human health. But I'm pleased to see another prominent former official - one with scientific expertise - speaking out in opposition.

Disappointing science funding

Many of us in the scientific research community are hoping that with the Democrats in charge of the U.S. Congress, we might see some of the recent budget cuts to science being restored. Alas, that doesn't look likely. The new Senate proposal for the NIH offers only a 2.8% increase, which is less than inflation and therefore represents a slight cut in real dollars. At least it is better than the Bush administration's proposal, which calls for a $279 million cut in the NIH budget. The House's proposal calls for an increase, but less than the Senate, and the likely result will be somewhere in between. NSF is doing much better - after years of basically flat budgets, it seems that Congress is going to give it a 10% boost, which is a real increase. The Bush administration supports the increase to NSF - surprisingly (to me).
More fundamentally, though, I am continually dismayed by the anti-intellectual, and often anti-science, attitude of many politicians, especially those on the right. They attack science whenever it seems to conflict with their political or religious agendas, most notably on global warming and stem cell research. As a result we have a U.S. population that is stunningly ignorant of basic scientific principles, with a majority still believing in such ridiculous things as the creationist myth that all living things were magically created a few thousand years ago.
I hope this changes, but I don't see it happening soon. I'm pleased that some in Congress and even in the Bush administration want to increase certain areas of science funding (NSF, at least). I hope the public will once again see science as offering cures for disease and the means to a better life, as I think they did in the past. Or is that just my rosy view of society in an era before I was born?