“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.

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.

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.

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.”

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

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.

“The bottom line is that you can’t meet your nutritional needs in six cookies and one meal a day. It’s not possible,” said Keri Gans, a registered dietitian in New York City.

Water Footprints of agricultural products and production volume in the U.S.

1. Inconsistent time frame of analysis. The water footprint for beef, as calculated, stems mainly from the water inputs into feed production over the entire lifespan of the animal, from birth to slaughter. Waterfootprint.org assumes cattle take three years to reach maturity, which sounds reasonable enough. Certainly it takes water to grow feed for the cattle in all three years of its life. But the failure to base the water footprint of a product on some consistent unit of time leads to some strange consquences. Take a calf named Betsy. Some of the same water molecules that grows the grass that feeds Betsy in the year after her birth get evapotranspirated back into the atmosphere; others get diverted to streams and rivers and flow to the ocean, from where the evaporate again. Eventually they fall again as rain. The turnover time for this process is much less than a year. For example, water draining to the Mississippi River basin reaches the Gulf of Mexico in less than one month. The mean residence time of moisture in soil before evaporation might be ~90 days. (These numbers are coming from Figures 5.5 and 9.1 of this book.) Thus, those water molecules that we counted as part of the year I water footprint for production of our hypothetical calf might be the same molecules that are counted again in year 2!

COUNTERPOINT AND RESPONSE: Prof. A. Y. Hoekstra, perhaps the chief proponent of water footprint analysis, points to FAQ Question 4 at the waterfootprint.org site:

…But in a certain period one cannot use more water than is available. A river can be emptied and in the long term one cannot take more water from lakes and groundwater reservoirs than the rate with which they are recharged. The water footprint measures the amount of water available in a certain period that is consumed (i.e. evaporated) or polluted. In this way, it provides a measure of the amount of available water appropriated by humans. The remainder is left for nature.

To me, this “answer” acknowledges the problem but provides no indication that water footprint analysis solves it.  Water footprint analysis does not reveal the “amount of available water” that humans could appropriate “in a certain period”, it reveals the amount of water that humans do appropriate in a certain period.  And it appears that in many cases, the period used for water footprint analysis is longer than the time it takes the water cycle to recharge itself.

2. Failure to consider substitution effects. At waterfootprint.org, note the following text:

… to produce one kilogram of boneless beef, we use about 6.5 kg of grain, 36 kg of roughages, and 155 litres of water (only for drinking and servicing). Producing the volume of feed requires about 15300 litres of water in average.

In the US, the grain is probably mostly corn. Even if it were the ostensibly more water-intensive wheat, the water footprint per kg of beef from grain would be only 8450 L (from 6.5 kg grain per kg of beef × 1300 L of water per kg of wheat). That’s only about half of the feed water. The remainder, 7100 L, must come from the roughage. At waterfootprint.org, roughage is described as “pasture, dry hay, silage and other roughages”. Fair enough. But what happens if the beef industry decides it doesn’t need to produce Betsy, and as a result, Betsy is never born? Do we save 7100 L of water for every kg that Betsy would have weighed in year 3 of her life? Possibly, but only if none of the pasture, dry hay, and silage that would have gone to feed Betsy is produced in her absence. If Betsy’s portion of hay is grown anyway, it will still evapotranspirate water that could have been directed to other uses, even if the hay is left on the field instead of harvested. In short, it seems far easier to change the water footprint attributed to a product than it does to change the perturbations to the water cycle caused by the production of that product.

COUNTERPOINT AND RESPONSE: Prof. Hoekstra says: “If not appropriated for human consumption (e,g, hay as input of cows that provide meat), then the water is available to sustain natural vegetation (or in the case of river water: sustain aquatic life)”.  True enough…but why design a method of water use accounting that stacks the deck in favor of “natural” vegetation so highly?  From a water use perspective, what is the difference between a prairie grazed by a “natural” bison population which people do not eat, and a pasture grazed by cattle, which people do eat, other than in the former case people have less food?

3. Double-counting. Even if Betsy does get produced, and even if we ignore the incommensurate time scales of Betsy’s life and the terrestrial water cycle, there’s yet another problem in adding up the water footprints of various agricultural commodities, as I did above. In the US, about 55% of the US corn crop is used as feed for meat production. That means that 55% of the water we’ve attributed to corn production gets counted again when we tabulate up numbers for beef, chicken, or other meats.

COUNTERPOINT AND RESPONSE: Prof. Hoekstra agrees with me that water footprints cannot be added in the way I attempted.  Opinions may differ, I suppose, on whether this property is a feature or a bug. But in my view, since mixing a gallon of water with a gallon of water results in two gallons of water it would be nice if water footprints had the same property.

I was very curious to hear a proponent of water footrprint analysis point out flaws in my reasoning or defend waterfootprint.org’s use of these numbers. To that end, I contacted Professor A. Y. Hoekstra, whom I believe to be the primary exponent of water footprint analysis, and shared with him my three concerns.  Graciously, he has responded, and I have included his rebuttals (and my response to them) inline with my arguments above.

I mean, if I made more money, would I actually be able to relate to that list? Blegh.