{"id":9175,"date":"2010-12-02T15:34:17","date_gmt":"2010-12-02T15:34:17","guid":{"rendered":"http:\/\/scienceblogs.com\/gregladen\/2010\/12\/02\/nasas-new-organism-the-meaning\/"},"modified":"2010-12-02T15:34:17","modified_gmt":"2010-12-02T15:34:17","slug":"nasas-new-organism-the-meaning","status":"publish","type":"post","link":"https:\/\/gregladen.com\/blog\/2010\/12\/02\/nasas-new-organism-the-meaning\/","title":{"rendered":"NASA’s new organism, the meaning of life, and Darwin’s Second Theory"},"content":{"rendered":"

\"ResearchBlogging.org\"<\/a><\/span>In his highly readable book, One Long Argument<\/a>\"\", Ernst Mayr breaks down the body of thought often referred to as “Darwin’s Theory” into five separate and distinct theories, the second of which being “common descent.” Darwin’s second evolutionary theory (second by Mayr’s count, not Darwin’s) is really a hypothesis that could be worded this way:<\/p>\n

All life on earth descended from a single, original, primordial form that arose eons ago.<\/em><\/p>\n

The evidence in favor of this hypothesis is strong, but the test of the hypothesis … the means of disproving it, which is, after all, the point of stating it to begin with … is difficult to define, but like pornography to a judge, one would know it when one sees it.
\n<\/p>\n

The question at hand is, does the current finding reported moments ago by NASA relate to this concept at all? The answer, as you’ll see, is yes. And no.<\/p>\n

The evidence for a single origin is this: There are a lot of potential variations in how life works, but only a very small and rather quirky subset of those variations exists in every known organism on this planet, strongly suggesting a single origin which left, as a sort of timeless imprint, that selectivity and quirkiness. Hundreds of amino acids are known to exist, but only 20 are used as the basic building blocks of life. The genetic code (the codons that specify those building blocks) is odd and quirky, but exists with very little variation across all lifeforms. Certain complex molecules, most notably the ribosomes that are key in forming complex molecules such as proteins on the basis of the genetic code, are large, clunky, and made up of sequences that could easily be very different than they are and still work, but nonetheless follow a very limited pattern, strongly suggesting that all existing forms have but one ancestor. DNA itself is pretty much the same everywhere, suggesting, again, a single origin.<\/p>\n

If life arose on Earth more than once, there would likely be more than one quirky, finger-print like pattern of coding, building blocks, and complex molecules. And there isn’t. Right?<\/p>\n

Well, if you’ve read my blog long enough, you probably know that I would not have explained all of this if there was not some way to turn around and explain how it’s all wrong.<\/p>\n

First, we have the latest news from NASA. It turns out that there is a form of life that is different, in a very fundamental way, from all other life forms on the planet. It is a bacteria-like form that appears to be able to use arsenic instead of phosphorous in forming its DNA, and probably in other functions as well, known by the term “strain GFAJ-1 of the Halomonadaceae” (hereafter referred to as “the bacterium”). Given the model I’ve just described, this is a potential falsification of the Darwinian hypothesis that life originated once.<\/p>\n

Now, before we go all “Darwin-was-wrong!!!11!!” on this, let me be very clear: This hypothesis … that all life has a single origin … is singularly unimportant to overall Darwinian or Evolutionary theory. If, indeed, life originated different times and different places so that today there were different environments (or continents, or whatever) with diversified forms of each separate origin, that may have been noticed by Darwin (or later biologists) and the multi-origin would simply be a fact. If each set of life types had diversified into different species and otherwise been very Darwiny in history and behavior, with Natural Selection working in all the distinct lineages, etc., the other four of Darwin’s theories (as told by Mayr) would be very strongly supported, because Darwinian processes would be seen to play out in multiple instances. Similarly, if we find that life started up at different times and different places elsewhere in the universe (on other planets) then this would address similar questions. Who knows? There may even be non-Darwinian life forms that arose in a certain pattern and never changed thereafter. Darwinian evolution requires that imperfect copies are made each generation. A life form that copies itself perfectly, or one in which imperfection always leads to termination of a lineage, would never posses the variation that Natural Selection works on. You can see why the discovery of extra-terrestrial lifeforms would be very interesting to biologists!<\/p>\n

But I digress, somewhat. What we have now is a proposal that all life on Earth has the same origin because all known forms have the same somewhat to very quirky variants in how they work that act as an individual, unique fingerprint pointing to one origin. The Mono Lake find, however, is an organism with at least one aspect of that quirky how-life-works pattern that is different. Does this falsify the Darwinian hypothesis?<\/p>\n

The Mono lake life form is a bacterium. A team of scientists started with a culture of bacteria from Mono lake, an utterly inhospitable environment in California (near Nevada, east of the Bay Area) in which life seems to thrive against the odds. This was placed in a medium that contained all the necessities of bacterial life, to allow the bacteria to be alive, to thrive, to grow, and to reproduce, except phosphorus. This soup also contained a high level of arsenic.<\/p>\n

They did this because the lead scientist on the team, the Carl Sagan-like Felisa Wolfe-Simon, was considering the preposterous idea that arsenic could substitute for Phosphorus in some biological systems. There were no known cases where that actually happened, but arsenic does in fact replace phosphorus very easily, which is why it is a poison for many organisms. If you put together the elements that make up key organic molecules in a test tube and shake it, usually nothing happens unless there is a set of other molecules (enzymes) and some ATP and stuff to make it assemble as it should. But if you put arsenic instead of phosphorus in the same soup, you get at least partial reactions that look like the formation of organic structures. In other words, given an atom of arsenic and an atom of phosphorus, the arsenic had a better chance of insinuating itself into certain key positions than the phosphorus element. Also, arsenic is more reactive than phosphorus.<\/p>\n

Here’s the thing: Phosphorus is often used in molecules in places where it provides important stability, once it is in place. It forms the very backbone that keeps the DNA molecule together. If arsenic, chemically similar to phosphorus but more reactive, is accidentally substituted, the stability is compromised. Arsenic is such an effective poison for this very reason. It’s like a suicide bomber dressed like a security agent. It easily gets into an important location, then it ‘reacts’ with stuff and messes everything up.<\/p>\n

But owing to some sort of brilliant insight, Wolf-Simon thought arsenic could sometimes substitute for Phosphorus, and she reasoned that the best place to find that biological difference would be in organisms that had evolved in a place where there was a LOT of arsenic, yet life still existed despite the presence of this nominal poison.<\/p>\n

Thus the experiment. And it worked. Even in the absence of phosphorous, in an arsenic rich environment, a bacterium thrived. (This is an oversimplification, but that is the general idea.) When they looked more closely, they discovered that the arsenic had substituted for phosphorus in part of the DNA of the bacterium.<\/p>\n

Now, consider for a moment (but no longer than a moment) a life form that uses arsenic instead of phosphorous. As the backbone of the DNA, as part of the energy-system molecules of ATP, and elsewhere, arsenic is used instead of phosphorous. That would be a life form that had a quirk that was distinctly different from the usual finger-print like quirks that generally convince us that all life has a single origin. It might be an organisms that evolved from a separate origin.<\/p>\n

Is that the case here?<\/p>\n

No, I don’t think so, but there are two ways in which this finding can inform and guide research into the possibility of multiple origins of life on earth.<\/p>\n

It has not yet been demonstrated that arsenic substitutes for phosphorus in all reactions in these bacteria. The bacteria could have had some of their own phosphorus, and only most but not all was substituted. It also seems that this organism uses arsenic in a facilitative rather than obligatorily manner. In other words, this bacterium uses phosphorus in the usual way, but can substitute arsenic under certain conditions. Also, it has not been demonstrated that the other quirky bits of the inner workings of the cell are different from the norm in this organism. So, it would appear that this is a bacterium that has secondarily evolved a trait, viable substitution of arsenic for phosphorus, and not a separate lineage.<\/p>\n

There are two (really, three) ways that this finding could speak to Darwin’s second theory.<\/p>\n

One is that the above is wrong … that it will be discovered that this “bacterium” has a different ribosome, and other differences, and really is a different form of life that originated separately from the rest of life on earth, but has not been investigated closely enough yet to know these things. My reading of the paper and observation of today’s press conference at NASA makes me think not, so let’s leave that one aside. Maybe we’ll be shocked later on this issue, but I think not.<\/p>\n

So, the other two ways in which this finding relates to Darwin’s second theory are 1) This could suggest a high diversity of life forms early in life, which could mean that the origin is not a point so much as a committee of diverse experiments that finally settled on the current system of double-helix phosphorus-spined DNA, RNAs, ribosomes, and so one and 2) By demonstrating that an entire life system could use arsenic and not use phosphorus at all.<\/p>\n

The first of these may be a bit esoteric, but nonetheless interesting. What I’m suggesting here is that the origin of life involved several different biochemical experiments that would now and then spatially overlap, and when they did so, sometimes combined. There may have been arsenic based systems and phosphorus bases systems, and they may have combined at different times and places, and most life subsequently evolved from a subset of these different bowls of primordial soup. One of those primordial soup bowls happend to be just like all the others but for the bit about arsenic. The test of this hypothesis (a partial test, anyway) would be to reconstruct the phylogeny of this bacterium. Did it separate from the other bacterial lineages at a time near the origin of life, or much more recently? Wolfe-Simon and her team are at present not saying anything about the phylogeny of this bacterium, and when asked about it at the press conference indicated that they just don’t know yet.<\/p>\n

The second idea is more likely, and relates closely to the thrust of the research team’s presentation in their paper and in the press. At a large scale, arsenic substitution for phosphorus simply means that we should not be ignoring phosphorus-poor arsenic-rich environments on other planets. At en even larger scale, we should consider that other substitutions are possible (silicon for carbon is a common idea along those lines, at least in science fiction!).<\/p>\n

But with respect to life’s origins on earth, related to Darwin’s second theory, there is a more direct implication that I think would be easy to explore. Irregardless of the phylogenetic position of this particular bacterium, its existence today suggests the possibility of the existence of something like it in the past. So, the question is, biochemically, is there either a stage in the origin of life in which arsenic is the key element for certain chemical activities in stead of phosphorus, or, more interestingly, can we find populations in one part of the ancient earth (as fossils, of course) of phosphorus based bacteria and other populations, in different geological regions, of arsenic-based bacteria, living contemporaneously?<\/p>\n

Get cracking, ancient biochemists!<\/p>\n

Wolfe-Simon, Felisa, & Et.Al. (2010). A bacterium that can grow by using arsenic instead of phosphorus Science<\/span> : 10.1126\/science.1197258<\/a><\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

In his highly readable book, One Long Argument, Ernst Mayr breaks down the body of thought often referred to as “Darwin’s Theory” into five separate and distinct theories, the second of which being “common descent.” Darwin’s second evolutionary theory (second by Mayr’s count, not Darwin’s) is really a hypothesis that could be worded this way: … Continue reading NASA’s new organism, the meaning of life, and Darwin’s Second Theory<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"1","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[],"tags":[191,34,162,4595,4596,4597,1688,187],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"","jetpack_shortlink":"https:\/\/wp.me\/p5fhV1-2nZ","jetpack_likes_enabled":true,"_links":{"self":[{"href":"https:\/\/gregladen.com\/blog\/wp-json\/wp\/v2\/posts\/9175"}],"collection":[{"href":"https:\/\/gregladen.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/gregladen.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/gregladen.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/gregladen.com\/blog\/wp-json\/wp\/v2\/comments?post=9175"}],"version-history":[{"count":0,"href":"https:\/\/gregladen.com\/blog\/wp-json\/wp\/v2\/posts\/9175\/revisions"}],"wp:attachment":[{"href":"https:\/\/gregladen.com\/blog\/wp-json\/wp\/v2\/media?parent=9175"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/gregladen.com\/blog\/wp-json\/wp\/v2\/categories?post=9175"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/gregladen.com\/blog\/wp-json\/wp\/v2\/tags?post=9175"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}