Bill's Big Stuff

One of the tasks of all the Martian probes is to look for signs of water and by implication, life. In fact, several years ago, the first Martian lander created quite a stir for a while, when gas evolved from the addition of water to some Martian soil. It was later thought to be inorganic reactions from chemicals that were stable only in very dry environments. There have also been efforts to find extra-terrestrial life using the Arecebo radio telescope and a large network of home computers to analyze radio data for possible patterns of intelligent communication. These efforts are serious attempts based on the best knowledge available.

This week, in the Wall Street Journal, for Friday, January 21, in the Marketplace section (B) there was an article entitled: “Search for Other Life In Galaxy May Require A Broader Outlook,” under the byline of Sharon Begley. The article is based on a journal article in Current Opinion in Chemical Biology. Having studied evolutionary chemistry and given a lot of thought to the issue of non-carbon-based life, I consider the WSJ article, and by implication the journal article, to be junk science. The remainder of this post is both a fisking of the article and a further exposition of the factors that are not being considered that are required for living organisms to exist.

START OF ARTICLE AND THE FISKING:
Maybe we’ve been just a little too provincial about this whole life-beyond-Earth thing. Spirit and Opportunity, the rovers now working overtime on Mars, scout for minerals that form in the presence of water, which is assumed to be essential for life. Telescopes scanning the heavens for “biosignatures” look for wavelengths characteristic of organic compounds (those made of carbon), the building blocks of life on Earth. And of the 135 planets detected beyond our own solar system, the ones that get astronomers’ pulses racing are those rarities that orbit close enough to a star to receive the solar energy thought to be crucial for life. We’re like foodies who search out great meatloaf—and won’t look twice at anything that doesn’t, like our own version, contain ketchup.

This type of derisive tone to describe sincere efforts based on the best extrapolation of current knowledge is uncalled for. To reduce serious science to a quest for a common food, is disrespectful of the intent and the efforts being made. The appeal is not to the intellect but to snobbery and emotion.

“The question is, is our search for life too Earth-centric,” says chemist Steven Benner of the University of Florida, Gainesville. “If some aspects of life on Earth are historical accidents, there could be other chemical solutions to the problem” of building life out of nonliving chemicals. Or, as the Huygens mission to Saturn’s moon Titan may well show, just because life on Earth is built out of carbon, encodes genetic information in DNA, and uses water as a solvent to get chemicals close enough to each other to undergo biological reactions doesn’t mean that’s the only way to do any of these.

To describe the evolution of life on Earth as the result of historical accidents is to trivialize the billions of years of chemical and biological evolution. The Earth underwent many temperature and climate changes of a very extreme range in its history, and the number of different environments available for various chemical options to occur were many. Thus I would characterize the resulting chemistry as being the most suited to life rather than an accident. If Prof. Benner considers our Earth to be a historical accident, the burden becomes his to show the Earth’s evolution and pre-planetary environment to be exceptional rather then normal. Actually it would appear he is making the statement merely to set the stage for his own speculative ideas. The second half of the paragraph, is essentially a tautology, and useless since no one has made the claim that they are the only way to control life, just that they are the only building blocks that seem reasonable based on current knowledge.

The statement has some inaccuracies in it as well. Water is not only a solvent allowing the close association at the molecular level of biological molecules, it also participates in the reactions in critical ways. The hydrogen and hydroxyl ions that spontaneously form in water participate directly in reactions and catalyze them, and help form hydrogen bonds that hold proteins in their configurations. It is also the presence of water that leads to hydrophobic bonding, or bonding due not to electrical charge but to an expulsion of water from areas of molecules forcing the amino acid side chains closer together.

Take the challenge of getting the raw materials of living things close enough to undergo life-sustaining reactions. If they are sitting there on your desk that’s not likely to happen. But dissolve them in a drop of water and you’re in business. “You need some kind of solvent to facilitate biochemical reactions,” says Prof. Benner. But does the drop have to be water?

Probably not. As Prof. Benner and his colleagues write in the journal Current Opinion in Chemical Biology, ammonia “is a possible solvent for life.” Even sulfuric acid supports chemical reactions, in particular reactions that form the bonds between carbon atoms. Sulfuric acid is a main ingredient of the clouds above Venus.

The consideration of ammonia as a solvent for life takes into account its bipolar nature, and certain similarities to water, a pair of electrons as an unbonded node and the ability to form hydrogen bonds. However the temperature regime of ammonia is much below that of water, and the entire chemistry of the analogues of nucleic acids, proteins, and cell walls would have to change. Where currently there is hydrolysis of bonds, there would be ammonolysis with the substitution of the nitrogen of ammonia for the oxygen of water in the reaction. This then leads to the question of what happens to proteins when oxygen is replaced by nitrogen? The properties change completely.

Once you break out of the water-or-bust mantra, all sorts of environments look friendly to life—perhaps even Titan. When the hubcap-shaped Huygens probe parachuted onto Titan a week ago, astronomers kept an eye out for oceans filled not with water but with methane or ethane.

First of all, no one is using a water-or-bust mantra. Science bets on the most likely things, with an eye to possible exceptions. To imply that there is some sort of straight-jacket on thought about alien life forms is to misrepresent the situation. It may be to the naïve that think as long as there is liquid there could be life, but so far the real data indicates that only water environments seem to be effective. There is more on this below.

Both are simple hydrocarbons, or molecules of hydrogen and carbon. And in the Titanesque cold, both are liquid. Organic chemicals are just as happy to undergo biochemical reactions in methane and ethane as they are in water, notes Prof. Benner. In fact they might form some bonds even more readily in methane and ethane than they do in water, and be less likely to fall apart.

I would like to know what biochemical reactions can occur in ethane and methane. None of the hydrolytic reactions will work properly or else have to have water introduced from some other molecule. The problem with forming bonds more readily and more stably is that life depends on a balance between stability and instability. Cells must be able to tear down structures and replace them in order to grow. If components are too stable cells will die from inability to renew. If they are too labile they will not be able to exist for long enough to properly reproduce.

“A hypothetical form of life living in a Titan hydrocarbon ocean would not need to worry as much” about its bonds being ripped apart, Prof. Benner noted in his recent paper. “In many senses, hydrocarbon solvents are better than water. …As an environment, Titan certainly meets all of the stringent criteria” for life. Astronomers weren’t expecting to see little green men holding up a welcome sign when Huygens landed on the squishy surface under a tangerine sky, but those hydrocarbon seas bear watching.

I have already commented on bond stability as not necessarily being desirable, but the statement about meeting all the “stringent criteria” for life is a stretch. What criteria? This is a very deep philosophical question, because in order to have criteria, one has to have definition of life. I will comment below on some of the operational issues concerning life.

In a life-friendly environment, all you need are the right ingredients. Again, we may have been too parochial in what we mean by life’s ingredients. Life on Earth is built of DNA and the 20 amino acids that make up proteins. But clever chemists have made many more amino acids than nature ever did. Prof. Benner says they could be the building blocks of “hypothetical proteins in hypothetical alien life forms.” Some of the 20 amino acids have been found in meteorites, showing that Earth isn’t the only place that has them. But if we widened the search for amino acids beyond the standard 20 there would be even more basis for suspecting that we are not alone.

Let’s start with the amino acid issue. Of the twenty amino acids (actually I believe there are over that number naturally occurring, but 20 are what are normally found in proteins.) quite a number of the simpler ones are found in meteorites as stated. Thus to look for our normal 20 would be likely to detect novel proteins since some of the amino acids appear to be common throughout the solar system if not the galaxy. I see no reason to expand beyond the common 20 unless one hypothesizes that alien proteins would not contain ANY of the common 20, even the ones found in extra-terrestrial sources.

Not even DNA is sacrosanct. Scientists have created synthetic DNA by substituting different molecules for those that form standard DNA. For instance, Prof. Benner’s team has come up with 12 alternative “letters,” beyond the four that make up the DNA in all life on earth. The result is “DNA” that is quite adept at copying itself, just as real DNA is. Equally important, the synthetic DNA makes copying mistakes—mutations—that are the raw material of evolution. So alien DNA would be capable of that key aspect of life, too.

This is a complete misrepresentation of what was done. From what is stated, the purine and pyrimidine bases of normal DNA were replaced with other analogs. The backbone structure of the DNA still was there. In order for these synthetic DNA’s, which were true or real DNA’s, just not natural ones, to act the same they would have had to have the same configurational changes due to various bond migrations. Thus all the mechanisms of natural DNA would operate, and there is nothing particularly profound with respect to alien life. The significance is that so many of the DNA properties appear to be due to the fundamental structure and not the specific “letters” from which it is formed. The final sentence totally negates any attempt to remove DNA as a necessity of life. As I will note below, that has implications as well.

Life may not need water, or DNA, or the 20 amino acids that make up life on Earth, but one thing is nonnegotiable: a sourc of energy. Scientists had long assumed that only planets bathed in a star’s light could support life. But there is another source of life-giving energy, namely, heat generated by radioactive elements.

So far I fail to see that the necessity for water has been refuted, and the DNA’s discussed were still DNA, just with different bases, and even if one doesn’t use the same 20 amino acids, the chemistry of proteins is still being assumed. But in keeping amino acids and DNA, one has to keep the chemistry that uses them which is water-based. There is no mention of any experiments with life materials in any solvent than water.

The heat generated from either radioactivity or from the sun, has as its value the raising of temperatures high enough for the chemical reactions of life to take place. Note that life uses chemical reactions which produce excess energy in the form of heat. They do not take heat and convert it into other energy forms. When life processes in plants trap sunlight, they trap energetic photons and use their energy to drive reactions that convert Carbon dioxide and water into plant sugars and oxygen. This is not the same as taking heat and producing a life process from it.

That means that planets wandering the galaxy far from any star might be perfectly able to cook up a little life, suggests planetary scientist David Stevenson of he California Institute of Technology, Pasadena. “Such planets might hold the vast majority of life in our galaxy, all living without a sun on the decay of radioactive nuclei,” says Prof. Benner. If he’s right, then weird life quite different from Earth’s might be just as possible as meatloaf without ketchup.

Given the heat from radioactivity makes water liquid, the above scenario is perfectly valid. In fact a version of it occurs on the ocean floors of Earth at the rift zones in the mid-Atlantic, where the upwelling rock, heated by radioactivity in the core and mantle heats the water, dissolving minerals that provide energy sources for bacteria that then form the first layer of a deep-sea food chain. As for the final sentence, the weirdness is far less than might be thought when one looks above at how little different the supposed differences were.

END OF ARTICLE AND FISKING

START OF COMMENTARY ON NON-TERRESTRIAL CHEMISTRY

Many of the clues on extra-terrestrial chemistry come from experimental work on evolutionary chemistry. The landmark experiment by Urey and Miller in 1953, was the start of a continuing field of research into the pre-biotic chemistry. They filled a sealed globe with a hypothetical atmosphere of early Earth, and then heated it and passed electrical discharges through it to simulate volcanism and lightning. After some time there was a lot of tarry residue built up. When the residue was analyzed, it contained amino acids, simple, five carbon sugars, purines and pyrimidenes, and hydrocarbons. These molecules are the simple building blocks of living organisms. Research since then has shown that these molecules can form polymeric structures similar to those seen in living organisms today, and under primitive conditions can even form cell-like objects. The same results occur given a broad range of starting conditions.

As early as 1970 I attended a paper at a conference that analyzed the organic materials from meteorites, and showed they were amino acids and other precursors of life compounds. The presenter was a scientist from NASA and his final conclusion was that given the early conditions of the solar system and Earth, life could not help but form. But why did it form as it did? Why do we not see any nucleic acids using other than the five bases, Adenine, Cytosine, Guanine, Thymine in DNA, and Uracil in RNA? Why do we not see more than the 20 amino acids we do? Nature had almost a billion years to experiment before life was extant on the surface of the Earth, and probably had more years after than in some environments. Without going into an analysis I cannot support at the present, I would speculate based on my background knowledge that these compounds are energetically favorable to form and remain stable over a broad range of conditions. This would imply that many of the analogues proposed are not as energetically favorable, not as stable, or require much more effort to form.

One of the characteristics of life that has always struck me, since studying biochemistry in graduate school, is that energy is produced in steps. About 35% of the energy contained in sugars and lipids can be recovered as useful energy for the cells use. If this were done all at once, the cell would incinerate. It is done under stepwise degradation. There is nothing at all strange about this. If one considers that over the billions of years that organisms evolved before becoming multi-cellular, first one bit of energy is obtained, and as survival pressure mounts over time, then the next bit is obtained by some mutation, and so forth. Over time a long chain of reactions is built up. Some organisms have the complete chain all the way to carbon dioxide and water. Others stop at earlier places in the chain. Some use sulfur instead of oxygen as an electron donor. But the common thread is that at each step of the way energy is obtained in usable pieces, and in a common currency, ATP or Adenosine Tri-Phosphate. ATP is used in every reaction that requires an energy input, being broken into either ADP, Adenosine Di-Phosphate and a phosphate ion, or AMP, Adenosine Mono-Phosphate (Also a potent cellular communications medium in a modified form) and a diphosphate ion. So when we discuss the possibility of alien life forms, we need to consider the requirement of energy supply. The energy must enter the form in a compact way and then be broken down in discrete steps. The steps must be small enough that the waste energy in the form of heat does not destroy the host. It also means that there has to be some common currency for handling the energy, a chemical bond that can easily form and be broken as necessary depending on the energy flow.

When considering possible solvents for life processes, it is necessary to keep in mind that the solvent is not just a carrier of the reactants, but is a necessary partner and participant in the reactions. Amino acids condense into proteins releasing water, and are hydrolyzed by the addition of water to the bond between the carbonyl and the amine, recreating the original carboxylic acid and amine groups. At the same time the solvent needs to be liquid throughout a useful temperature range—the colder the temperatures, the slower the kinetics of the reactions. Some reactions will not even go if the temperatures are too low. There is insufficient energy in the bond vibrations for them to reach a breakage point energetically. If the temperatures are too high, then competing reactions to destroy or alter the structures become important.

Despite attempts to claim otherwise, with various other elements that form polymers, carbon has no true analogues. The bonds it forms and the energy to form and disrupt them are unique. Silicon has sometimes been proposed as a possible life-form base, but its polymers are much more stable, and the analogous compounds don’t necessarily behave the same. Sulfur polymerizes but it is more suited to a role as an oxygen analogue.

In thinking about alien life-forms, I restrict myself to the most primitive. The wonderful diversity of species we have on Earth started from single-cell organisms. Once their chemistry was worked out, it became the base of all other biochemistry on Earth. I do not consider this as accidental, that one type just happened to succeed over other possible types of biochemistry. Nature is not particularly choosey. She lets all the organisms fight it out and the best will win to continue to reproduce and make more of themselves. Thus I consider the biochemistry we see on Earth to be likely anywhere that water existed for a period of time. We are looking for conditions that would produce primitive forms in our current explorations.

As for solvents other than water allowing the evolution of life, the entire chemistry would have to change. There would have to be different protein analogues, different DNA functional analogues, completely different energy utilization. When the solvent is different everything else must be different also. Considering that we don’t see precursors for other than water-based life in extra-terrestrial sources (No, we do not close our eyes to the possibility and not look for them.), it appears extremely unlikely to the point of impossibility that non-aqueous based life exists. The chemistry is too adverse.