“Why should you pay $20 million to a 32-year-old trader? He uses the office space, the I.T., the business card with a first-class name on it. If I take the business card away from that guy he would probably sell hot dogs.”

Epic failures in science communication, versions 12,385,395 through 12,385,397:

“DNA in Meteorites Suggests Life Came from Space”

“Found: A Batch of DNA Molecules That Seem To Have Originated in Space”

“DNA, possibly of extraterrestrial origin, found on meteorites”

…

The problems, of course, is that the meteorites in question were not reported to contain DNA at all. Instead they contained the nucleobases adenine and guanine, which are components of DNA in the same way that axles are a component of a car. Additionally, there were lots of other molecules, that look somewhat similar to the nucleobases found in DNA, and yet are found nowhere in DNA, like 6,8-diaminopurine.

On the other hand, NASA seems to be getting better at press releases, at least compared to the arsenic fiasco. Also, cyanophage S-2L is my new favorite virus.

I couldn’t find the relevant paper in PNAS yet, but here is an unrelated paper on the cool subject of the chemical diversity of meteorites.

Molecule of note: enterodiol

Lignin is a good invention. It protects against harmful UV radiation, and provides rigidity and structure to plant tissue. Those first, noble plants that rose up out of the muck and gave life on land a go needed lignin, and so, somewhere between 400 and 500 million years ago, they evolved it. Plants came to dominate the land. Lignin, a key to their terrestrial success, came from phenylalanine, that familiar component of proteins. Take Phe, decarboxylate it, maybe hydroxylate it, maybe methylate it, and then polymerize it, and you have lignin.

Animals also evolved that lived on land and ate the plants that had come to live there. Lignin became a fundamental component of the tissue that formed the plants they ate — it was a fundamental part of their diet. Despite that, animals never figured out a good biochemical strategy to digest lignin.

It wasn’t for lack of trying. Today’s molecule, enterodiol, is derived from lignans, which (more or less) are precursors to lignin. We eat these lignans, and they go to our gut, where our microbial symbionts then take over.

They can metabolize these lignans to compounds like enterodiol. All it takes is an ancient biochemical innovation (lignin), the co-evolution of animal life forms in the context of this evolution, and the ability of symbiotic microorganisms that evolved in the gut of the animals’ digestive systems to complete the transformations.

Phenylpropanoids. Enterodiol. Easy.

Defending Chemical & Engineering News

Over at In the Pipeline, the commenters waged a fierce attack on the American Chemical Society’s trade magazine for chemistry, Chemical & Engineering News. They were responding to In the Pipeline blogger Derek Lowe, who’d been invited to join the editorial board of Chemical & Engineering news, and who was asking for feedback on what his readers felt about the magazine.

Commenters had a lot of negative things to say about C&E News, and about the ACS more generally. I was shocked to see that so many commenters held such strong anti-immigration views. Their argument seemed to be that C&EN’s articles on the employment outlook for chemists were too rosy. They felt that H1B visa-holders were taking jobs from qualified American chemists. Some of them also felt that the ACS in general was intentionally trying to attract cheap foreign labor and drive down the wages of American chemists.

These views seem a bit far fetched to me, as I’ve noted. I was glad to see Derek Lowe address these arguments in a later post.

I have to say here, as I did in the comments to some of the posts at In the Pipeline, that I’m a fan of C&EN. I love skimming the digests of recent research. And I did start off my grad school admissions essay by saying that it was through reading C&EN that I realized that a career in the biotechnology was what I wanted. C&EN comes every week. It has research highlights, business-oriented articles, and often in-depth discussions of regulatory and policy issues facing the chemical industry. Plus did I mention their “Facts and Figures Of The Chemical Industry” articles? The other trade magazines I’ve read at one time or another — mainly ASM News, Chemical Engineering Progress, but also Genome Technology and Physics Today, don’t attempt nearly as much breadth.

In my view this breadth makes for interesting reading. It’s probably also a reflection of the breadth of interests among members of the ACS, which is after all the world’s largest scientific society. I am glad to know that my ACS dues go in part towards producing C&EN. The magazine isn’t perfect — for one, I’d like to see a bit more writing contributed by active chemical researchers — but I think it is remarkably good, both in absolute terms and in comparison to other technical trade magazines.

Good job, C&EN. You’re a good magazine.

Molecule of note: 3-formyltyrosine

I wish I had a nickel every time I hear that the “metabolome” — the collection of all of the small molecules which exist as intermediaries in the biochemical machinery of living cells — consists of only a few hundred metabolites.  “The number of known metabolites present in many organisms (e.g., yeast) is 10- to 100-fold fewer than the number of genes or proteins,” said one paper, which later went on to say that the yeast metabolome was around 600 metabolites.  Another says that the erstwhile laboratory favorite, the bacterium Escherichia coli, has “694 metabolites present in the in silico metabolome.”

The key words are “known” and “in silico”.  Of course if you limit yourself to what you know about, or limit yourself to “in silico” databases of metabolites that other people know about, you won’t find anything new.  But that doesn’t mean that we know what all of the metabolites are!

Leah C. Blasiak and Jon Clardy provide an excellent counterexample to the idea that we have a handle on the chemical diversity of microbes in a recent paper in the Journal of the American Chemical Society, which details their discovery of 3-formyltyrosine and related metabolites in a marine bacterium.  Drs. Blasiak and Clardy went searching through genomic databases for genes that seemed to encode proteins similar to a newly discovered class of rather funky enzymes, the “ATP-grasp-type ligases”. They found an interesting set of genes from Pseudoalteromonas tunicata, a seabound bacterium which is often found on the surface of seaweed, floating debris, and intervetebrates. They moved those genes to E. coli cells, and then looked in cellular extracts for blips in their mass spectra that did not show up in E. coli cells. They found a few, and after extensive chemical characterization of those blips, they were ready to announce to the world that 3-formyltyrosine was a biologically produced metabolite.

It wasn’t in anyone’s database and hasn’t yet appeared in an in silico metabolome yet, to my knowledge, despite it having been in the Pseudoalteromonas tunicata metabolome for hundreds (at least) of years. How many more metabolites like 3-formyltyrosine are there waiting to be discovered? My money says, “more than a lot of people think.”

Mystifying rules for restaurants

I don’t mind it when wait staff at restaurants tell me their name (#7) or when wait staff come to take my plate away when I have finished eating but a companion is still going (#17). Neither did I realize that offering a compliment to someone is an insult to everyone else present (#42).

Maybe I am just an oafish plebe with no class…and I’m clueless about restaurant “trends” to boot.

Preposterous extrapolations: climate change and marathon runners

Burning fossil fuels has increased atmospheric levels of carbon dioxide. Yet an inevitable corollary of this fact remains widely unappreciated. Combustion theorists have long noted that fire, whether it occurs in a coal power plant, an internal combustion engine, a gas turbine, both fuel and oxygen. Both are consumed by the fire.

So stoichiometry tells us that oxygen levels in the atmosphere must be going down. Have they? Yes, they have: Andrew Manning and Ralph Keeling of the Scripps Institute of Oceanography have measured the decrease in atmospheric oxygen arising (mostly) from combusion of fossil fuels. From 1990 to 2000, oxygen in the air decreased by about 0.0031% 0.015%.

I find that fact to be amazing in and of itself. “But how will having less oxygen in the air change your life,” you might say. “Where’s the news I can use?” If you’re a runner, well, here we go…the atmosphere is thinner at altitude, and as a result, runners go slower. Conveniently for preposterous extrapolaters, some intrepid physiologists have developed a semi-theoretical (does that sound better or worse than semi-empirical?) estimate for the effect that altitude has on running. At sea level oxygen partial pressure is about 160 mmHg, but air up at an elevation of 520 meters has an oxygen partial pressure of 150 mmHg or so. And the physiologists’ semi-theory says that marathon world record equivalent times at 520 m are about 128 seconds slower.

Combining the atmospheric and phsyiological data, we see that world-record equivalent marathon times in the year 2000 might be 0.067 0.32 seconds slower than in 1990, due to the depletion of atmospheric oxygen by fossil fuel combustion. And, since the decline in running performance at altitude is somewhat offset by decreased wind resistance in the thinner air, decreasing oxygen at a constant pressure might be twice as worse as just thinning out the air.

For men between 18 and 34, the qualifying time for the Boston Marathon is 31:10:59. That’s about 51% slower than world record pace, meaning that slower runners huff, puff, and struggle for oxygen for a longer time. So I think it’s reasonable to assume that fossil-fuel-driven depletion of oxygen from the atmosphere lowers finishing times by a corresponding lower amount.

The end result? If you’re a runner, and you miss qualifying for the Boston Marathon by 0.2 1 second or less, you can use climate change as an excuse.

(The exercise of calculating the most probable number of people who have missed qualifying for Boston due to climate change is left to the reader.)

UPDATE: I was off by five-fold! The change in atmospheric oxygen from 1990 to 2000 was not 0.0031%; it is closer to 0.015% (as should have been clear to had I read the caption to Table 2 in this paper more carefully.) That means that world-record equivalent marathon times may have gone up by between 0.3 and 0.6 seconds due to oxygen depletion in the atmosphere. Times for male would-be Boston qualifiers have gone up from 3:10:59 by a full second. Thanks to Ralph Keeling for the correction, and also be sure to check out his new web site on atmospheric oxygen research.