Transition Metal Catalysts Could Be Key To Origin of Life

An anonymous reader writes "One of the big, unsolved problems in explaining how life arose on Earth is a chicken-and-egg paradox: How could the basic biochemicals — such as amino acids and nucleotides — have arisen before the biological catalysts (proteins or ribozymes) existed to carry out their formation? In a paper appearing in the current issue of The Biological Bulletin, scientists propose that a third type of catalyst could have jumpstarted metabolism and life itself, deep in hydrothermal ocean vents."

Comments

Ah Mercury

[Ukab the Great]

Sweetest of the transition metals.

Re:Ah Mercury

[Quiet_Desperation]

It's great with fish.

Re:ok but how does this explain

[roman_mir]

you wouldn't start with citric acid and some simple metal, like iron or copper, you'd have to use something more serious. I imagine AsO(OH)3 (arsenic acid) mixed in some proportion with Strontium and Tin. I think that's how you get Beck.

Re:The electro-dynamic field came first, of course

[Black Parrot]

But materialists have just as much of an agenda as the creationists, which is why we're subjected to this crap about life emerging from a chemical soup.

If by "materialists" you mean "scientists", then your claim is true.

But the two agendas are very different: scientists are trying to figure out what has happened and how stuff works, and creationists are trying to defend an ancient tradition about what has happened and how stuff works.

As for the L-Field... are you suggesting that electromagnetism has a non-material cause?

Wasn't this answered long ago?

[sconeu]

How could the basic biochemicals - such as amino acids and nucleotides - have arisen before the biological catalysts (proteins or ribozymes) existed to carry out their formation

Didn't the Miller-Urey Experiment answer how amino acids could show up?

Re:Wasn't this answered long ago?

[Artifakt]

The problem is, the experiments showed that amino acids were much easier to get than was originally thought. But when that result was announced, the general opinion was that getting from there to protein and nucleic acid synthesis was comparatively simpler, and would happen using much the same experimental setup. People confidently predicted the full synthesis of life within a year, or at most a few. Such predictions flew about, in major places such as Life magazine, the New York Times, and official U.S. Government reports. That part didn't happen. instead, the experiment revealed protein folding and other steps in getting to actual life were probably much, much harder than had been supposed.
        Now consider this in light of the 'God of the Gaps' argument so popular among Atheists. (The reason I urge this is that the Miller-Urey experiments actually led directly to a bunch of God of the Gaps remarks in those same articles, and were hailed by Atheist spokespersons such as Sir Bertrand Russell.). The way that argument is usually phrased, the 'gaps' are not just shifting around, rather they are getting smaller with modern science. What happened here was, as one gap got smaller, another grew (as one event turned out to be much more probable than thought, another event in the chain was shown to be much more improbable than was thought by the same theories.).
        Really, Atheists don't have to prove their claim, as it's a simple negative. Even though I'm taking the side of the Theists here, I'll grant that. The thing is, Atheist spokespersons and groups have seized on many scientific discoveries, including the Miller-Urey experiments, as proof of something they don't really carry the burden of proving, and those theories and discoveries have later fallen flat (witness Sir Bertrand Russell, Howard Phillips Lovecraft and others using the Steady State universe model as a proof of Atheism, with the argument being: No moment of first creation = No first creator). A lot of Carl Sagan's rhetoric and some of Richard Dawkins' is still based on these same points, and those two have had to ignore things they knew/know about modern science to cling to their (un)beliefs.
        The Miller-Urey experiments were brilliant and fundamental to much new knowledge, but they are also something that has been widely misinterpreted and need to be groked most carefully.

Re:Wasn't this answered long ago?

[martin-boundary]

Uhm, "God" does not exist. In fact, there's no widely accepted definition of the term that's free of contradictions. It's just a word that's a placeholder for broken thinking.

Re:The electro-dynamic field came first, of course

[Gerzel]

Who says that life arose from purely chemical reactions?

Electricity has always been a factor in the more modern plausible origin of life theories. Experiments to generate complex organic molecules from base components by simulating early Earth like environment have always involved some sort of electrical component, namely in the form of simulated lightning.

Though your real gripe is against that the randomness, in your view, could not have given the result of life because the chances are so small. However in order for the chances to be small they have to exist in the first place as small is greater than 0.

You are considering only the improbability of a single event under a single circumstance but not considering how many times that circumstance might occur in the universe, which is vast, old and to any reasonable point of scientific certanty contains a large number of such circumstances. You are focusing only on the single success without taking into account or having any idea of all the other times it almost but didn't happen.

Fe/Ni-S World Hypothesis?

[interactive_civilian]

Isn't this old news? (pun not entirely intended)... A couple of the more prominent abiogenesis hypotheses have been based on this for most of the decade of not more. Here's a paper from 2003 that, while it has its flaws (some of which have been rectified, some of which have been completely rethought over the last 7 years) offers a fairly complete and very compelling hypothesis for how life may have originated at warm, alkaline thermal vents like those found at the Lost City thermal vent fields:

Martin, W. & Russell, M.J., 2003. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 358(1429), 59-83; discussion 83-5. Available at: http://rstb.royalsocietypublishing.org/content/358/1429/59.abstract.

And here's a similar but competing hypothesis (still based on Fe/Ni-S, but with a different idea on the origins of membranes and cells):

Wächtershäuser, G., 2006. From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 361(1474), 1787-806; discussion 1806-8. Available at: http://rstb.royalsocietypublishing.org/content/361/1474/1787.abstract

The latter author has been writing papers about this hypothesis since 1992 (though I haven't read his first paper on the subject).

Point being, this doesn't seem to be a new thing, especially as summarized in the summary here and in the linked article. The original paper on which the article is based offers a bit more fundamental chemical details regarding the transition metals involved, and suggests good directions for experimental confirmation or refutation, but the overall idea remains pretty much the same, it seems. Still, it will be interesting to see what, if any, research and experiments result from this.

Re:The Missing Ingredients!

[Black Parrot]

The stuff has been cooking for the last thirty years, and no life has crawled out yet . . .

Hardly a surprise, since the real thing took as much as a billion years in a planet-sized beaker.

FWIW, I'm not sure the U-M experiments properly reflect our current understanding of the chemistry of the early earth, either.

Re:The electro-dynamic field came first, of course

[MightyMartian]

Most everything has an an electromagnetic field of some kind. But if you're insinuating that everythng is animated by the Force, well, then, you're a gullible moron.

Ooh look, I read a book by a guy, and he thinks scientists are a bunch of morons, so I'll go on Slashdot and talk about the evil materialists.

Guess what, guy, science is methodological naturalism. If you have a testable theory, then provide it, otherwise take your book and shove it up your ass.

Re:The electro-dynamic field came first, of course

[Black Parrot]

And what's this nonsense about biochemists and physicists having an "agenda" like creationists.

I said "materialists". For example, James Randi (the magician) is a materialist with an religious agenda.

So Randi doesn't believe in energy???

You're sending a very confused message.

Sometimes even the best scientists fall in love with their guiding philosophy.

Pray tell, what is scientists' guiding philosophy?

For me, evidence trumps tradition. Is that a philosophy?

Ribonucleotides & RNA

[drooling-dog]

Well, I know everybody's just joking around here, but...

One of the more exciting papers I've read in this area appeared in Nature a little while back (14 May 2009). It shows not only that activated ribonucleotides could have been formed directly from simple molecules that were plausibly present on the early earth, but that the necessary reactions are of high yield, are catalyzed by inorganic phosphates, and take place under mild conditions. Because the ribonucleotides are formed as the phosphates ("activated"), they're suitable for polymerization to RNA under similarly mild conditions.

To me, this seals the deal for RNA the same way that Miller-Urey did for amino acids, and maybe even more so (because the reactions take place under ambient conditions, no lightning bolts needed). It's widely thought that early forms of life were based on RNA rather than DNA, so there you go. Now we just need to figure out how to make a ribosome.

See Powner et.al., "Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions," Nature 459, 239-242 (2009).

Sorry for the geekiness here, but of you know a little organic chemistry you'll find this really cool...

Re:Ribonucleotides & RNA

[interactive_civilian]

You really shouldn't need to apologize for "geekiness" on Slashdot. If we can't reference and/or link to actual scientific research without apology, then something must be very wrong with this site. ;)

That said, the paper you mentioned looks really interesting. AND, a Google Scholar search offers a link to a freely downloadable PDF for those of you, like myself, that don't have access to Nature.

I'm looking forward to reading this. :)

Re:Ribonucleotides & RNA

[Ungrounded Lightning]

It's widely thought that early forms of life were based on RNA rather than DNA, so there you go.

In particular, TFA (at least as characterized by the slashdot article) seems to be hunting for a "missing link" programmable catalyst bridging a perceived gap between DNA/RNA and proteins for chemical synthesis, and proposing transition element complexes to fill this gap. But RNA works just fine as self-folding charge/shape/leverage-based molecular machinery, as well as self-copying genetic information "tapes". So it can be the whole ball of wax for the initial startup. There IS no gap to be filled.

Of course it's less effective than protein for molecular machinery, and less stable than DNA as a data repository, etc. But those can be evolved-on upgrades later.

Now we just need to figure out how to make a ribosome.

Ribosomes are a case in point: They're the bulk of a very complex chemical factory for building proteins. But when you tear them apart you'll find that MOST of the pieces are RNA enzymes. And other parts of the machinery are RNA as well - notably the T-RNA that gets bound to the various amino acids, carries them into the ribosome, and lines them up in the sequence specified by the M-RNA "tape" being transcribed.

Seems to me the logical sequence is for the whole protein synthesis mechanism to initially be built out of RNA, then (once directed protein synthesis is up and running), some pieces of it - such as chunks of the ribosome and aminoacyl tRNA synthetases - would eventually be replaced by proteins that would do the job better.

Re:The electro-dynamic field came first, of course

[Artifakt]

You need to learn what materialism is. The way you are trying to use the word is nothing like the way any educated person uses it. Talk about sending a confused message. Alternately, you are trying to create a strawman argument. If not, learn to high school physics, learn to freshman college philosophy, or at least read something as modern as Locke or Berkeley. Then spend ten years on Quantum Mechanics and Information Physics, and you might be able to add something constructive to this discussion.

And the answer to your rhetorical question at the end is actually a clear "Yes!". You should also read Sir Karl Popper and Thomas Kuhn so you learn why it's a yes and not anything else. Here's a hint, don't waste people's time treating a real question as a mere rhetorical tool. There have been hundreds of thousands of man hours devoted to creating a philosophy of science and dozens of brilliant books written on the subject. Most working scientists took at least one philosophy of science course to get their degree. If you want to insult all of them that took that course seriously and didn't just treat it as a nonsense prerequisite to the subject, go ahead, but claiming that there is no such thing puts the burden of proof squarely in your court.

To any Atheists reading this far, Black Parrot is claiming to be defending your position against religious ones. Unfortunately, following his argument logically means that to justify Atheism, you have to give up all physics post Isaac Newton and all modern philosophy of science. Do you really want to say "I am an Atheist, so Einstein isn't science. I reject all modern science post Newtonian strict materialism to cling to my unreligious non-beliefs." Because, I thought, you know, just as a vague impression up till now, that maybe some of you Atheists actually have a logical argument or two to explain why you support it instead. If Black Parrot is speaking for you, you don't. I could deliberately pick the most stupid sounding religion ever (maybe something with a creation myth involving spaceships like gold colored DC-10s, and a big volcano), secure it wasn't nearly as absurd as the Atheist position as it's being stated above.

Re:The electro-dynamic field came first, of course

[smidget2k4]

Ah the classic, "you don't know what this, so you're dumb, but I'm not going to tell you what it is!" rhetorical move. Very nice. According to this, materialism is just that there is no magic "soul" or "spirit" and everything is simply composed of matter and energy. This seems to be in line with general scientific thought: science doesn't need to account for something that isn't observably there.

Philosophy of science classes just teach the ideas behind the scientific method, how it came to be, and how the early scientists worked. I don't see what relevance that class has to anything you're talking about, this is not a philosophy that scientists are pushing on people, it is the history of scientific pursuit and tools to be used for future work. There is no agenda, scientists aren't trying to push the ideology on you. The evidence says that is what happened, so they report it. Because you feel persecuted by it because it doesn't jive with your beliefs doesn't make it wrong. It doesn't make it right either, it is simply the best idea we have given the evidence presented thus far. That is all science is.

Your last paragraph is nonsensical. Why do we have to give up quantum mechanics? There is nothing magical about it. It may not even be how things work, it just makes very good predictions. What argument are we following to its logical conclusion? You are simply making statements without fully explaining them. What do atheists have to reject about quantum mechanics?

Re:The electro-dynamic field came first, of course

[Chrononium]

The philosophy of science, like any philosophy, impacts how a person understands the subject. You can go really wrong if you try to supplant the philosophy with another (e.g. Creationism), but it is important to understand why science has worked so well. It isn't that science necessarily rejects anything metaphysical (such as causality, at least up to quantum physics), but simply minimizes the metaphysical requirements of any theory, since science is supposed to be experimentally verifiable. This is a good way to work, since no reasonable arguments can arise without some way to resolve them ultimately. It is important, however, to distinguish between the evidence and the interpretation of that evidence (theory!). The evidence never, ever, ever explains itself, since that requires some metaphysical interpolation (e.g., invoking objective reality, objective truth, integrity of the senses, perhaps causality, etc.).

I agree with most of your comments, except that philosophy does not equal history and science is more than a black box model. Indeed, a great temptation in science, especially the venerable physics, is to consider it simply as mathematical modeling. I have found throughout my doctorate the most useful theories are the ones which attempt to give a non-mathematical description of how the universe works in some particular way. In my field, numerical simulations are entirely possible for some complex situations, but one cannot be considered an expert if one simply presses a button to execute a mathematical model. In my opinion (as an engineer), the real test of a scientific theory is whether it can be used for a realistic engineering application. The typical engineering application requires one to assume a vast amount about the problem at hand and therefore becomes a tedious, uninspired exercise if only mathematical models are used to engineer the device. Whether we are ultimately describing epicycles or true orbits can make a really big difference in the difficulty and expense of the engineered device (imagine designing a satellite to keep up with the motions of the planets if they really moved in epicycles!). The closer we are to completely explaining a physical event means that we have a closer mental model of reality, which is the real pursuit of science.

That said, I am unfamiliar with any necessary interpretations which quantum mechanics places on the student that forces a particular metaphysical result on the question of the existence of God. References?

Re:The electro-dynamic field came first, of course

[Black Gold Alchemist]

It has nothing to do with philosophy. Vitalism is a tested and disproven theory. Materialism is a tested theory that has not been disproven. If you would like to undisprove vitalism, you must limit it. Vitalists first said that organic chemicals could be synthesized outside of living creatures. Then we synthesised those compounds from rocks, oils and air. Then we synthesised those oils from gases. So vitalists are wrong about the chemistry of life. End of story. You can say that life has a soul, but that will be disproven when a computer becomes sapient.

I can show you that matter causes electric fields. All I need is salt water, copper, and iron. The result is that an electric field will be created from the matter in iron-air battery. The opposite effect would mean that if I produced 0.7 volts, I would have an iron-air battery. Life has an electric field because the material process of evolution choice electric signals as a communication mechanism, because they are fast and readily cause chemical effects. That's also why sapient biological robots (us) used machinery to assemble arrays of semiconductor materials to assemble non-sapient computers. The disproof of this hypothesis will occur when a sapient (or at least self staining) robot is built. If we wanted we could then build a sapient mechanical computer (Babbage style), thus disproving the necessity of electric fields to sapience.

To show that your hypothesis has merit, you must take a set of electric fields, from solar panels or other inorganic sources, and a lot wires, and have organic life pop out. Also, double check to prevent contamination by bacteria. The little critters are everywhere and will clog up the experiment. Now, chemical experiments have not yet have life pop out of them yet. There have been some self-replicating RNA enzymes that came out of nowhere but a pile of individual RNA monomers. Meanwhile, increasing amounts of research (like TFA) is showing where this RNA mixture could have come from. I'm guessing everything, from transition metals, to radio active decay, to rare earth metals and other forms of unobtainium where involved.