One link Smith provides is to a post from last fall by Drew Conway, who created a Data Science Venn Diagram that defines, for Conway, where data science falls in the intersection of “hackers, statisticians, [and] subject matter experts.”

When I grow up, I want to be a data scientist.

Yesterday members of the Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium published a paper in Nature stating that they have found that human gut biomes fall into three major classes, or enterotypes. These enterotypes are not correlated with the national or even continental origin of the humans studied.

I find these results surprising (not that I know anything about the human microbiome, but the results run counter to my intuition about biology), and I wonder if the classification is an artifact of the analysis. We’ll know soon, since this is a booming area of research powered by high-throughput sequencing and computational analysis.

Excellent summaries of this research can be found on Ed Yong’s Not Exactly Rocket Science blog (“Divided by language, united by gut bacteria—people have three common gut types”) and in an article by Carl Zimmer in The New York Times (“Bacteria Divide People Into 3 Types, Scientists Say”). Carl Zimmer has further comments on his own blog, The Loom (“Blood type, meet bug type: My new story for the New York Times”).

Reference:

Arumugam, Raes, et al. 2011. Enterotypes of the human gut microbiome. Nature http://dx.doi.org/10.1038/nature09944.

A quick summary of the results:

• Eight hours of sleep each night for two weeks: No cognitive impairment.
• Six hours of sleep each night for two weeks: Cognitive impairment equal to 24 hours without sleep, which is equivalent mentally to being legally drunk.
• Seven hours of sleep each night: Some cognitive impairment that does not get worse after three days.
• Sleep-deprived subjects underestimate their impairment.

Get more sleep.

Dr. Lipscomb, whom I did not know, seems to have been a wonderful, fun-loving scientist. In a paragraph that made me laugh out loud, Rifkin writes:

He was not above dropping comical elements into his scientific publications. In one 1972 paper, he noted: “We admittedly made this observation with the benefit of hindsight. This science is known as retrospectroscopy.”

 

There is a growing discussion of cheat sheets at BioStar.

I have found that my web site is a great place to store a cheat sheet. For example, when I can’t remember the single letter codes for DNA or protein, I know exactly where to look them up.

In this paper, the authors explore some fairly old metagenomic data collected by the famous Global Ocean Sampling project. The authors created phylogenetic trees using the small subunit ribosomal RNA, recA, and rpoB genes, these being highly conserved genes that appear in nearly all organisms. Their goal was to identify deep branches in the phylogenetic trees that might indicate a fourth domain of life in addition to the Bacteria, Archea, and Eukaryota.

And indeed they found some deep branches in the recA and rpoB phylogenetic trees, but they found the results difficult to interpret. (It is a relief to read a paper in which the researchers do not overinterpret their data, unlike certain researchers associated with NASA.) One hypothesis put forward by the authors is that the deep branches of the phylogenetic tree represent viral genes. But the authors pose their alternative hypothesis:

It has not escaped our notice that the characteristics of these novel sequences are consistent with the possibility that they come from a new (i.e., fourth) major branch of cellular organisms on the tree of life. That is, their phylogenetic novelty could indicate phylogenetic novelty of the organisms from which they come. Clearly, confirmation or refutation of this possibility requires follow-up studies such as determining what is the source of these novel, deeply branching sequences (e.g., cellular organisms or viruses). Then, depending on the answers obtained, more targeted metagenomics or single-cell studies may help determine whether the novelty extends to all genes in the genome or is just seen for a few gene families.

It has not escaped my notice that the first sentence above deliberately echoes Watson and Crick’s famous sentence in their 1953 paper describing the structure of DNA.

It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.

I don’t know who was responsible for this deliberate echo, but it suggests that at least some of the authors believe they have found evidence for a fourth domain of life. Eisen, in the absence of additional data, favors the idea that these are viral genes.

I eagerly wait for additional data that can resolve these questions.

Reference

Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, et al. (2011) Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees. PLoS ONE 6(3): e18011. doi:10.1371/journal.pone.0018011

Check out these radiation charts, which attempt to put things into perspective.

• A Layman’s Intro to Radiation
• xkcd’s Radiation Chart

[Updated 27-Apr-2011]

Randall Munroe has updated his radiation dose chart on xkcd.com.

Especially droll is the archives. (I won’t spoil the joke here.)

But I let both subscriptions lapse. The problem is, there is more information in each issue than I have time to read. I have wide interests, and I have am omnivorous in my ability to soak up information on a wide variety of topics. Since I have been reluctant to discard issues until I have had time to read them cover to cover, I usually let them stack up until I find a Sunday to devote to a marathon reading session in which I attempt to catch up. Those Sundays have been rarer lately, and I finally conceded that I can’t keep trying to drink from the fire hose of new scientific data.

There is one problem with my plan. Although my subscriptions expired two months ago, both Nature and Science are still sending me issues, trying to tempt me back. And it might work; I almost resubscribed to both this week.