About this Author
Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases.
To contact Derek email him directly: derekb.lowe@gmail.com
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October 25, 2006
Posted by Derek
There's an interesting analytical chemistry paper in the preprint section of PNAS (open access if you want to read it) that may reopen an old controversy. It's from a large multinational team (Mexico, Spain, France, NASA-Ames) investigating the GC-mass spec instrumentation that was flown to Mars on the Viking landers in 1976. That's a key instrument in the life-on-Mars debate, so an attack on it is significant. First, though, some background - it's a tangled story.
The Viking landers each had three biology experiments to look for possible signs of Martian life, whose results were famously difficult to interpret. They produced both excitement and confusion at the time (scroll down in that NASA history page) and they've been fuel for arguments ever since.
There was the pyrolytic release experiment, which incubated Martian soil with 14C-labled carbon monoxide and carbon dioxide. After several days, the sample was purged, then heated to 650C and analyzed for the release of any labeled carbon compounds that might have been formed by living organisms. A control sample was heated before incubation, to kill off any such life forms. Seven out of the nine runs of this experiment seemed to produce positive results - that is, volatile labeled carbon was produced after pyrolysis.
The gas-exchange experiment used the same sort of apparatus, exposing the soil to either water vapor or nutrient solution under a mixed atmosphere of gases. The headspace was analyzed for changes in the concentrations of the various components, which could be due to biological uptake or release. This one showed a strong release of oxygen and carbon dioxide from the samples once moisture was added, but the amount decreased over time, leading to theories that this was the product of an inorganic reaction rather than a signature of life.
The labeled release experiment put Martian soil into a dilute nutrient broth, with several small organic compounds which were all labeled with 14C. After incubation, the headspace of the experimental cell was analyzed for any released labeled gases and again, a control experiment was done with pre-heated soil. This one produced exciting data, with release of labeled gas in the experimental samples well over those in the controls. One odd result, though, was that the subsequent injection(s) of nutrient solution did not produce a further spike of released gas. The final curves ended up looking neither like what you'd have expected from a classic bacterial positive, nor from a simple chemical reaction. This ambiguity has meant that the LR results have been re-analyzed and re-fought ever since the 1970s, with the experiment's designer, Gilbert Levin, leading the effort to rescue the data as a case for Martian life.
But then there were the GC-MS data, from an experiment considered to be the backstop test in case the biology experiments were difficult to interpret. Since they certainly were that, from beginning to end, this experiment became for many people the most important one on the landers. (It already had been for the people - a not insignificant group - who thought from the start that the biology tests were unlikely to provide a conclusive answer). This one heated soil samples directly and looked for volatile organics. Heating to 200C showed little or nothing in the way of carbon compounds, and very little water besides. By contrast, another sample taken up to 500 degrees released a comparative flood of water, but still showed no evidence of organic molecules.
And that, for most observers, was that. No organic molecules, no life. Explanations after the GC-MS results mainly turned to what sorts of inorganic chemistry might have given the behavior seen in the three other experiments. Martian soil was thus hypothesized to be a sterile mixture of interesting chemicals (iron peroxides? carbon suboxide polymers?) that had fooled the biology test packages, but couldn't fool the GC-MS.
There's always been an underground, though, that has held that the results were indeed the result of life. Gilbert Levin has never given up. In 1981, he pointed out that tests of a Viking-style GC-MS instrument had shown that it was insensitive to organics in a particular Antarctic soil sample, but that this same soil nonetheless gave a positive result in the LR experiment. And he really put his opinions out in the store window in 1997, with a paper that flatly concluded that the 1976 LR experiments had indeed detected Martian life.
In the last few years, others have joined the battle. Steven Benner at Florida, whose work I wrote about here, published a PNAS paper in 2000 which maintained that organic molecules on Mars would likely be retained as higher molecular weight carboxylates, which would not have been volatile enough for the Viking GC/MS instrument to detect. And now this latest group has weighed in.
They've also analyzed various Antarctic and temperate desert samples, and found that all of them contain organic matter that cannot be detected by thermal GC-MS analysis. And the ones that contain iron, including the NASA reference simulated Mars soil (a weathered basalt sample from near Mauna Kea), tend to oxidize their organics quickly under heating. The conclusion is that while much of the water and carbon dioxide produced in the Viking experiment from heating the Martian soil was surely inorganic, some of it could have been from the oxidation of organic material. The paper concludes that the Viking GC-MS results are. . .inconclusive, and should not be taken as evidence either way for the presence of organic molecules or life. The question, they feel, is still completely open.
The good news is that future missions are relying on other technologies. In addition to good ol' thermal volatilization/GC-MS, there are also plans for solvent extractions, laser desorption mass spec, short-path sublimation, and other nifty ideas. If these various US and European missions get off the ground (and on the Martian ground), we're going to have some very interesting data to look at. And argue about.
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+ TrackBacks (0) | Category: Analytical Chemistry | Life As We (Don't) Know It
May 23, 2005
Posted by Derek
I haven't commented on the controversy about including "Intelligent Design" in school curricula, but I don't want that to be interpreted as any kind of approval. On the contrary - until it offers some testable predictions, which would seem an unlikely thing to hope for, I don't see how ID even rises to the level of a preliminary theory, much less one that can compete with the level of evidence backing up evolution. Many of ID's advocates, to a greater or lesser degree, strike me as intellectually dishonest.
Intelligent Design proponents are fond of arguing about "irreducible complexity", the idea that some structures are too complicated to have been generated through stepwise evolution. They argue this on the anatomical level, which I don't buy, but I'm not going to debate that one in this forum. (Allow me to refer the curious to my fellow Corantean Carl Zimmer, who's had plenty of run-ins with these folks, and his fine introduction to evolution. Those interested in the latest news on the ID/evolution battles should check out The Panda's Thumb. For sheer mockery, often irresistible in these cases, try this.)
But when they start making arguments at the chemical level, the what-are-the-odds stuff about proteins and DNA, well, that's when I come out of my lair. A paper in the latest issue of the journal ChemBioChem got me thinking about this today. (If you have access to Wiley journals, it's here as a PDF.) It's an update of the analytical work still being done on the Murchison meteorite (a href="http://www.publish.csiro.au/?act=view_file&file_id=AS03060.pdf">PDF), which fell in Australia in 1969. The more than 100 kg of recovered Murchison material have been attacked over the years with just about every instrument of the constantly shifting state of the art in analytical chemistry.
Why all the interest? Well, a short answer is that the pieces of this meteorite reek. Even now, they smell like low-grade gasoline, and they had a powerful odor indeed when they were freshly collected. The Murchison fall is a wonderful example of a rare class of meteorites called carbonaceous chondrites. Many people don't realize how much organic gunk is floating around out in space, but there are surely millions of tons of this stuff wandering around our solar system alone.
What's in the Murchison pieces? The list continues to lengthen. We're up to at least 500 different soluble compounds, but much more of the material is dark polymeric asphalty stuff that's hard to analyze. Most famously, the meteorite contains many amino acids. Save glycine, those come in left- and right-handed isomers, and a major find is that the Murchison material is slightly biased toward the left-handed ones, which happen to be the ones that life on Earth is built around. This is an important point: the chemicals that life as we know it is composed of are not at all odd or unlikely. They're all over our solar system, they're in interstellar clouds, and there's every reason to think that they're smeared and splatted all over the universe.
And more of the stuff is being made all the time. In 2002, several research groups took icy mixtures of water, methanol, ammonia, HCN, carbon dioxide and carbon monoxide (just the sort of mixtures that you see in cometary ices and the above-mentioned interstellar clouds.) They irradiated them with ultraviolet light - as would come from the Sun or untold billions of other stars - at cold outer-space temperatures, and obtained over a dozen of the most common amino acids - here are some more details.
So, here's another key point: the really big step is between making random chemical combinations and having carbohydrates and amino acids as inevitable products. Believe me, the molecules of life are an infinitesmal sliver of all the possible backbones of up to ten or twelve carbon, nitrogen, and oxygen atoms. But organic chemistry, with no active hand on the controls, turns out uncountable heaps of them. Compared to that, the gaps that need to be filled in on the way to living systems don't seem so large.
This, to me, is one of the major stories of the last few decades. Starting hundreds of years ago, astronomy gradually moved the Earth out of its supposed spot in the center of the universe and placed it in the huge (and hugely strange) context of the universe that we now know. Now chemistry is moving us away from the view of life as a strange and precious anomaly - granted, perhaps, by a divine being? - to something that could be everywhere and may well start of its own accord. The building blocks are ubiquitous, and if you give them half a chance they start to stack themselves up.
For better or worse, the presence of an active Designer does not suggest itself. That may not seem right to some people, for many different reasons. But if there's one thing that science has been showing us, it's the the universe doesn't much care what we think about it.
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+ TrackBacks (0) | Category: Intelligent Design | Life As We (Don't) Know It
February 23, 2005
Posted by Derek
Back in the early days of my pre-Corante blog, I wrote a piece about some other kinds of chemistry that might be used in living systems. There's now a wonderful one-stop review for all sorts of speculations on this topic, which incorporates everything I've ever thought of and plenty more. Steven Benner at the University of Florida, who my fellow Corantean Carl Zimmer has interviewed, and two co-workers (here's his research group) published "Is There a Common Chemical Model for Life in the Universe?" in Current Opinion in Chemical Biology late last year. (here's the abstract; I can't find the full text available yet on the Web.)
I can't say enough good things about this article. This is the sort of topic I've enjoyed thinking about for years, but there were still plenty of things in this review that had never occurred to me. Benner goes over the likely requirements for life as we know it, life as we'd probably recognize it, and life upon which we can barely speculate. As a chemist, he's particularly strong on discussions of the types of bonds that could best form the complex molecules that chemical-metabolism-based life needs. Energetic considerations - how much chemical bond energy is available, how soluble the materials are, how reactive they are at the various temperatures involved - are never far from his mind.
He devotes sections to ideas about living systems without chemical solvents (gas clouds, solid states) and the more familiar solvent-based chemistry. There's plenty of water out there in the universe - which is why bad movies about aliens coming to drain our oceans are so laughable - and it's natural enough that we should concentrate on water-based life. But there's plenty of ammonia out there, too, along with methane, sulfuric acid, and other potential solvents like the supercritical dihydrogen found in the lower layers of gas giant planets.
So, is all this stuff out there? Is life something that is just going to happen to susceptible chemical systems, given enough time? If so, which ones are susceptible? Benner's thoughts are, I think, best summed up by his take on Titan:
"Thus, as an environment, Titan certainly meets all of the stringent criteria outlined above for life. Titan is not at thermodynamic equilibrium. It has abundant carbon-containing molecules and heteroatoms. Titan's temperature is low enough to permit a wide range of bonding, covalent and non-covalent. Titan undoubtedly offers other resources believed to be useful for catalysts necessary for life, including metals and surfaces.
This makes inescapable the conclusion that if life is an intrinsic property of chemical reactivity, life should exist on Titan. Indeed, for life not to exist on Titan, we would have to argue that life is not an intrinsic property of the reactivity of carbon-containing molecules under conditions where they are stable. Rather, we would need to believe that either life is scarce in these conditions, or that there is something special, and better, about the environment that Earth presents (including its water)."
As for me, I can't wait to find out. I want Titan rovers, Jupiter and Saturn dirigibles, Venusian atmosphere sample return, instrument-laden miniature submarines melting down through the ice on Europa and Enceladus: the lot. How much of this will I ever get a chance to see in my lifetime? Current betting is running to "none of it, damn it", but things can change. Depends on how easily and cheaply we can get payloads up to (and out of) Earth orbit.
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+ TrackBacks (0) | Category: General Scientific News | Life As We (Don't) Know It
August 13, 2002
Posted by Derek
As for phosphorylation, I've had some folks write to talk about the importance of phosphate cleavages for cellular energy production, and about the conformational effects of phosphorylation. All that's well taken - but I guess what I was getting at yesterday is that (for example) sulfation would seem to be a perfectly reasonable way to modify proteins. Why didn't life end up using it?
Perhaps the phosphate energy part is the key. That's such a basic mechanism that enzymes to handle phosphate groups must be archaic indeed. It could be that evolution just found a use for them, since they were there anyway, and that competing methods of post-transcriptional modification (like sulfation) never got off the ground. Of course, there's always glycosylation - wonder when that kicked in, evolutionarily?
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+ TrackBacks (0) | Category: General Scientific News | Life As We (Don't) Know It
March 19, 2002
Posted by Derek
No longer can I say that the topic of allergenic extraterrestrial life hasn't been taken on in science fiction. Patrick Neilsen Hayden of Electrolite, who is certainly in a professional position to know, passes on the word that the 1999 novel BIOS (by Robert Charles Wilson, reviewed) includes this very idea.
On a related topic, a number of old sf stories made use of the chirality of amino acids and the resulting proteins, with a plot point usually being the possiblity of starvation when trapped in an environment full of the wrong-handed food source. Given that such enantiomeric compounds can have very different properties in the body, I'd think that such an environment would not only be non-nutritious, but extremely toxic.
But are there any such places (stipulating an abudance of life-as-we-know-it in the universe to make it more possible)? That gets right into the question of how we ended up with only L-amino acids (and only D-sugars, which get less attention, undeservedly.)
There are plenty of theories. One thing that most everyone agrees on is that what we see now is a founder's effect - life got started with the series that we know, and stuck with it ever since, across billions of years. (Reminds me of Microsoft.) But was it a pure 50/50 chance at the beginning, or was the deck stacked? For that to happen, you have to have a chiral environment somewhere for it to develop.
Explanations such as seeding by meteorites containing chiral amino acids (or planetary formation from a cloud containing a chiral mix of compounds) just push the question back a bit. Where did those excesses come from? I should note that a paper on the amino acid ratios in the Murchison meteorite was just presented at the same meeting that Jay Manifold has been reporting from over at "A Voyage to Arcturus." Maybe he can give us a report.
For some years, the explanation that was hauled out invoked the weak nuclear force, which is the first place you can find symmetry breaking down in the laws of physics. Trouble is, that's such a small effect on the thermodynamics (if there's an effect at all!) that it's really like sticking with the 50/50 chance.
Another interesting idea was that circularly polarized radiation, potentially from neutron stars, preferentially breaks down one enantiomer of simple molecules over another. This still doesn't give you much of an edge, but it's a lot more compelling explanation that the weak nuclear force.
Last year a theory was proposed that formation of simple biomolecules on rock surfaces (a hot topic in origin-of-life research) might have something to do with it. Calcite seems to absorb different enantiomers on different faces of its crystals, which could have led to local excesses - too local, some say - of one enantiomer. If one of these microenvironments was the first to start things on the road to life, though, that would be all you need. It's still another form of 50/50 chance, depending on what crystal face you pick, but at least (as with polarized radiation) you have a semi-plausible mechanism for generating an excess of one chiral form.
These ideas and others are discussed on this site, but note: that page also brings up an experiment from a few years ago that suggested that magnetic fields could induce chiral chemistry. This result has since been throroughly discredited. No one could ever reproduce it, and it turned out that one of the original graduate students faked the results. Not a smart career move, considering how much interest (and scepticism) the first report got.
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+ TrackBacks (0) | Category: Life As We (Don't) Know It
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