Finally, NCBI Genomes recognises Archaea*

I’ve been complaining about this for years. They fixed it. The NCBI have reorganised their genomes FTP site and finally, Archaea are not lumped in with Bacteria.

GenBank: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/archaea/
RefSeq:  ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/

Archaea are still included in the ASSEMBLY_BACTERIA directory; hopefully that’s next on the list.

[*] to be fair, they’ve always recognised Archaea – just not in a form that makes downloads convenient

Bacteria and Alzheimer’s disease: I just need to know if ten patients are enough

You can guarantee that when scientists publish a study titled:

Determining the Presence of Periodontopathic Virulence Factors in Short-Term Postmortem Alzheimer’s Disease Brain Tissue

a newspaper will publish a story titled:

Poor dental health and gum disease may cause Alzheimer’s

Without access to the paper, it’s difficult to assess the evidence. I suggest you read Jonathan Eisen’s analysis of the abstract. Essentially, it makes two claims:

• that cultured astrocytes (a type of brain cell) can adsorb and internalize lipopolysaccharide (LPS) from Porphyromonas gingivalis, a bacterium found in the mouth
• that LPS was also detected in brain tissue from 4/10 Alzheimer’s disease (AD) cases, but not in tissue from 10 matched normal brains

Regardless of the biochemistry – which does not sound especially convincing to me^[1] – how about the statistics?

Finding the truth is a waste of time, scientists say

Before bioinformatics, I worked in both biochemistry and microbiology labs, including a stint in the field of extremophile biology. So like many other people, I’ve been following the “arsenic life” story with great interest.
It seems that far more has been written about the publication, the manner of its announcement, the ensuing online debate and the personalities involved than about the principal scientific question: can arsenate substitute for phosphate in biological molecules? My opinion, for what it’s worth, is that the Science paper presented no compelling evidence for covalently-bound As in DNA and that the editors should have asked the authors either to do better experiments or tone it down.

Now, Nature News reports that the criticisms are in, the authors have responded and as part of their response, they are willing to share samples of the bacterium with other researchers for further analysis. Good on them – that’s the right thing to do. What’s bewildering and saddening are some of the responses to the offer. They include (paraphrased): “I wouldn’t waste my time because I don’t believe it”, “if there is no arsenate in the DNA, how could I publish in a high-impact journal and get a job?” and “I have the technology to do it but I have better things to do.”

Is this what biological science has become? The single-minded, career-oriented selfish pursuit of the high-impact publication to the exclusion of everything else – including the truth? I’m afraid that the answer is “yes” and I suspect this attitude is what got the authors of this Science paper into trouble in the first place.

This is what those who imagine some glorious future open-science utopia are up against. All I can say is: be thankful for Rosie Redfield and her lab.