Ten Amino Acids Thermodynamically Favored

Posted 10 April 2009 by Richard B. Hoppe

One of the "criticisms" (scare quotes to indicate creationist blather) of science is that it doesn't (and, some say, can't) account for the emergence of life on earth. Now a new paper coming out in Astrobiology (pre-pub version online here) shows that 10 of the 20 amino acids in life on earth are thermodynamically favored, and would likely emerge under a variety of conditions. The implications are profound, as Supernova Condensate notes. Among those implications is that life elsewhere is likely to have some characteristics in common with life on earth at the biochemical level. The abstract of the paper:

Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these ten early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal.

More discussion at Supernova Condensate, where I found the story.

54 Comments

Mike Elzinga · 10 April 2009

There are several reasons that this paper, which is available in PDF from the site mentioned, is important.

First, it clearly shows that the formation of amino acids and other precursors to life not only are consistent with thermodynamics, the energetics of formation can be calculated and measured under at least a few types of environmental conditions.

Second, the correlations between the relative abundances, the relative concentrations and the Gibbs free energy under surface water conditions is rather impressive; the relative concentration fitting exponentially over nearly three orders of magnitude. Also the lack of correlation under conditions of hydrothermal vents is interesting. This appears to narrow the search for conditions under which these precursors form; barring, of course, other still unknown conditions that may offer catalytic assistance.

Third, the positions of codons for the genetic code are far from random. Certain arrangements are more energetically favorable when these positions are laid down in early formation. This, in turn, sets up the path for subsequent buildup of more complex structures from these early structures.

Fourth, it illustrates dramatically the effects of emergent properties as these systems gradually being build up from simpler systems to more complex systems. We can actually begin to see the relationships between levels of organization and complexity.

The ID/Creationists are going to be hard pressed to come up with a “law of nature” that forbids such processes from continuing all the way up to living organisms. Simply hiding their incredulity under such pseudo-science as “genetic entropy”, “entropy barriers”, “tornadoes-in-junkyards”, and whatever else they want to use to assert that matter in nature doesn’t form complex systems, just looks ludicrous in the light of real science.

I haven’t finished the paper yet, but already it is quite intriguing and shows how thermodynamics and the energies of formation can be used to narrow the search.

Flint · 10 April 2009

From the sounds of this, life as we know it starts to sound like an increasingly inevitable result of ordinary chemical processes, under conditions that can't be all that unusual.

So I jump way ahead to arrive at Fermi's old question - where is everbody?

Mike Elzinga · 10 April 2009

Flint said: From the sounds of this, life as we know it starts to sound like an increasingly inevitable result of ordinary chemical processes, under conditions that can't be all that unusual. So I jump way ahead to arrive at Fermi's old question - where is everbody?

The answer may lay in the fact that life as we know it exists within the temperature range of liquid water. In electron volts, that is something like between 0.012 eV and 0.016 eV. Compare that with the binding energies of solids and liquids which are on the order of tenths of an eV and with chemical bonds which are on the order of 1.5 eV. For all that complicated stuff to occur, the energy ranges are extremely restricted, and the contingencies of the planet on which we find life are never going to be exactly the same everywhere. There may be other beings elsewhere, but probably unlike us, and very likely more than four light years away.

RBH · 10 April 2009

Flint said: From the sounds of this, life as we know it starts to sound like an increasingly inevitable result of ordinary chemical processes, under conditions that can't be all that unusual. So I jump way ahead to arrive at Fermi's old question - where is everbody?

In Boat of a Million Years, Poul Anderson suggested that Fermi's paradox ignores two things. First, there is (Anderson argued) a diminishing return at the margin to space exploration. Once you've explored 100 systems, the 101st adds only a little new knowledge. Once you've explored 1,000, the gain in knowledge from the 1,001st is negligible. Hence space faring species self-limit their sphere of exploration. Second, he argued that the great bulk of members of any given species won't themselves go into space. Even with technologies like hibernation or suspended animation, there will be only a tiny proportion who set sail for the stars, and they will have longevity treatments and a moral structure that more than likely involves population limits. The rest will stay on their home planet(s) and also control their reproduction rate. In other words, the Malthusian reproduction rate Fermi's paradox assumed isn't unassailable. Finally, of course, there's Leó Szilárd's answer to Fermi: "They are already among us - but they call themselves Hungarians."

Jesusophile · 10 April 2009

"Ten Amino Acids Thermodynamically Favored".

That means that "Ten Amino Acids are also NOT Thermodynamically Favored".

THEREFORE, GOD.

Mike Elzinga · 10 April 2009

Jesusophile said: "Ten Amino Acids Thermodynamically Favored". That means that "Ten Amino Acids are also NOT Thermodynamically Favored". THEREFORE, GOD.

P, therefore NOT P? Yeah, that makes a lot of sense. Apparently a brain on sectarian religion.

Joshua Zelinsky · 10 April 2009

Mike, I believe that the point was 20-10=10. But regardless, I'm pretty sure Jesusophile was a parody remark.

In any event, the biochemical similarity remarked might not be so high. Even with half of them identical, left/right molecular handedness could still make our biochem very incompatible with there's. This doesn't mean we can eat the small fury creatures from Alpha Centauri.

jackstraw · 10 April 2009

I think the most favored amino acid should be renamed godamine. But that's just me.

Mike Elzinga · 10 April 2009

Joshua Zelinsky said: Mike, I believe that the point was 20-10=10. But regardless, I'm pretty sure Jesusophile was a parody remark.

Matter vs. antimatter or left vs. right chirality may vary likely be a matter of contingency followed by natural selection, or these things may be connected at a deeper level. We don’t really know yet. But there are no laws of physics being violated. At one time I was part of a group that studied the connection. This was one of a number of experiments that were referred to at the time as “Vatican experiments” (because it had something to do with the origins and handedness of life and physicists were doing the experiments).

This doesn’t mean we can eat the small fury creatures from Alpha Centauri.

:-) And if they turned out to be “other-handed”, we’d be “screwed”.

mrg · 10 April 2009

RBH said: Finally, of course, there's Leó Szilárd's answer to Fermi: "They are already among us - but they call themselves Hungarians."

I believed it was Teller who said: "Somebody's been letting out secrets!" -- and von Karman who replied to the effect: "No, that's just John von Neumann."

Dave Luckett · 10 April 2009

Take pity upon the ignorance of a non-biochemist: am I to understand from the post that ten of the twenty amino acids found in living cells are now known to have spontaneously occurred in nature, (at least potentially) given conditions known to exist on Earth even now? After all, hydrothermal vents and meteor strikes still occur, although it would be quite reasonable to posit that they were more common on the early Earth.

Ravilyn Sanders · 10 April 2009

Among those implications is that life elsewhere is likely to have some characteristics in common with life on earth at the biochemical level

So the aliens can eat us?

Gary Hurd · 10 April 2009

The thermodynamic discussion is helpful, but I did see much beyond that. Trifonov (2004) does a better job exploring the implications of a restricted AA palette.

Trifonov, Edward N.
2004 "The Triplet Code From First Principles" Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 22, Issue Number 1, (2004)

stevaroni · 10 April 2009

This doesn’t mean we can eat the small fury creatures from Alpha Centauri.

They probably taste like alien chicken anyhow.

Ernst Hot · 10 April 2009

RE: The coffin of creationism.

Sir, we are having trouble finding spots for any more nails. Advice urgently needed.

Sincerely, ....

RBH · 10 April 2009

Gary Hurd said: The thermodynamic discussion is helpful, but I did see much beyond that. Trifonov (2004) does a better job exploring the implications of a restricted AA palette. Trifonov, Edward N. 2004 "The Triplet Code From First Principles" Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 22, Issue Number 1, (2004)

PDF of that paper.

Ernst Hot · 10 April 2009

Btw, didn't Arthur C. Clarke write a short story about some guy who was chirally (is that a word? :) inverted and starved to death?

Joshua Zelinsky · 10 April 2009

Dave Luckett said: Take pity upon the ignorance of a non-biochemist: am I to understand from the post that ten of the twenty amino acids found in living cells are now known to have spontaneously occurred in nature, (at least potentially) given conditions known to exist on Earth even now?

I'm not a biochemist. That said, as I understand this, all of them were already known to occur in nature. The result implies that 10 of these are very likely to be created in substantial quantities a large variety of circumstances, not just whatever the circumstances of early Earth.

Joshua Zelinsky · 10 April 2009

Ernst, yes but the fellow doesn't starve to death. They figure out the problem first. The fellow does die at the end but from a different issue.

Henry J · 10 April 2009

So I jump way ahead to arrive at Fermi’s old question - where is everbody?

Kind of hard to answer that until we've actually been someplace that's else. Henry

Mike Elzinga · 10 April 2009

Joshua Zelinsky said:
Dave Luckett said: Take pity upon the ignorance of a non-biochemist: am I to understand from the post that ten of the twenty amino acids found in living cells are now known to have spontaneously occurred in nature, (at least potentially) given conditions known to exist on Earth even now?
I'm not a biochemist. That said, as I understand this, all of them were already known to occur in nature. The result implies that 10 of these are very likely to be created in substantial quantities a large variety of circumstances, not just whatever the circumstances of early Earth.

And the thinking is that those that are not energetically favorable are not found frequently in meteorites or in the early stages of the formation of self-replicating structures made from these earliest 10. Those came later. Once the early structures formed, they became the “template” or catalysts for the formation of the less energetically favorable ones. Some of the other papers mentioned lay out likely pathways that this could occur. In other words, it is a bootstrapping process with natural selection, with thermal energy, and with “guidance” supplied by various hydrophobic and hydrophilic properties of these structures in the presence of water. Also there are some arrangements that allow more combinations than others, and these produce a broader range of complex structures on which selection can take place.

KP · 11 April 2009

Ernst Hot said: RE: The coffin of creationism. Sir, we are having trouble finding spots for any more nails. Advice urgently needed. Sincerely, ....

HAAAAAAAAAAAHAHAHAHAHAHA! (Sorry. The psychotic laughter comes from living in a heavily fundamentalist part of the country.)

Dave Luckett · 11 April 2009

One of the few things my chemistry teachers were able to fix in my resistant skull was that chemical reactions that can occur will occur, and the products of them will be therefore be present in some concentration.

mrg · 11 April 2009

Henry J said: Kind of hard to answer that until we've actually been someplace that's else.

Well, the SETI people have acknowledged that it seems to be awfully quiet out there. As one of them said, so far they have determined that the sky is not crowded with transmissions from other planets: http://www.vectorsite.net/taseti.html

Steve Taylor · 11 April 2009

mrg said:
Henry J said: Kind of hard to answer that until we've actually been someplace that's else.
Well, the SETI people have acknowledged that it seems to be awfully quiet out there. As one of them said, so far they have determined that the sky is not crowded with transmissions from other planets:

Unless the creatures out there have an active policy of announcing their presence, is there any reason to believe we could detect them anyway ? I suspect humanity's RF footprint is becoming smaller and smaller as we switch to fibre communications. How many years have we been detectable ? Probably less than 100. That's not a long time in the history of the universe. Steve

JohnK · 11 April 2009

Those craving a further Ed Trifonov fix can see his computational biology based: Early Molecular Evolution, Israel Journal of Ecology and Evolution, v.52, no.3-4, pp. 375-387, 2006 Genome Diversity Center, Institute of Evolution, University of Haifa, 31905 Haifa, Israel http://www.sciencefromisrael.com/app/home/contribution.asp?referrer=parent&backto=issue,12,23;journal,7,9;homemainpublications,3,5;

Four fundamentally novel, recent developments form a basis for a theory of early molecular evolution. The theory outlines the molecular events from the onset of the triplet code to the formation of the earliest sequence/structure/function modules of proteins. These developments are: (1) Reconstruction of the evolutionary chart of codons;
. . . [see Gary Hurd's ref above: JohnK]
(2) Discovery of omnipresent protein sequence motifs, apparently conserved since the last common ancestor; (3) Discovery of closed loops—standard structural modules of modern proteins; (4) Construction of protein sequence space of module size fragments, with far-reaching evolutionary implications. The theory generates numerous predictions, confirmed by massive nucleotide and protein sequence analyses, such as existence of two distinct classes of amino acids, and their periodical distribution along the sequences. The emerging picture of the earliest molecular evolutionary events is outlined: consecutive engagement of codons, formation of the earliest short peptides, and growth of the polypeptide chains to the size of loop closure, 25-30 residues.

Predictions and confirmations. His first genes and their peptides were only 18 bases / 6 aminoacids, respectively. Then the 30-residue closed loop peptides, followed by multiloop structures of 120-150 aa residues, coded from ~360-450 base pairs of RNA -- optimal for a ring closure. These ~360-450 bp genome units encode today's protein folds/domains/motifs.

Frank J · 11 April 2009

Dave Luckett said: One of the few things my chemistry teachers were able to fix in my resistant skull was that chemical reactions that can occur will occur, and the products of them will be therefore be present in some concentration.

Add to that catalysis and one can get significant concentrations real fast. A recent edition of "Chemical and Engineering News" had an article on the origin of amino acid chirality in living systems. While it addressed the progress in research, it brought home even more why anti-evolution activists' sound bites are so persuasive to most nonscientists, including those not hopelessly fundamentalist. Scientists speak openly about what questions remain answered and thus need more work. Sadly the scam artists (in every pseudoscience, not just creationism) spin that as "those scientists still have no answers, yet demand more money to putter away in labs." Meanwhile, few nonscientists realize how anti-evolution activists refuse to test their own alternative ideas, which themselves are becoming hopelessly vague. Whenever I read of some finding that suggests that the origin of life may be more probable than previously thought, the following irony comes to mind. Evolution is comfortable with the origin of life as a once-in-a-universe event. Or even a once-in-many-universes event, since we can't rule out the existence of other universes. Meanwhile, those creationists who imply (or state outright, if any sill do that) that many independent origins of "kinds" occurred on earth, do require the origin of life to be a relatively probable event. They can't have it both ways; if they want to spin the improbability of abiogenesis as evidence of "intervention" then they must concede (as Behe at least did) that, with or without a Creator/designer, the simplest explanation is still that life originated only once. And if they want to pretend that ID or creationism is scientific, they need to get off their armchairs taking potshots at scientists (& baiting-and-switching evolution with abiogenesis, etc.) and start stating and testing their own hypotheses of how - and when - life originated, and how - and when - past and present species originated.

mrg · 11 April 2009

Steve Taylor said: Unless the creatures out there have an active policy of announcing their presence, is there any reason to believe we could detect them anyway ? I suspect humanity's RF footprint is becoming smaller and smaller as we switch to fibre communications. How many years have we been detectable ? Probably less than 100. That's not a long time in the history of the universe.

That's discussed in the referenced URL. SETI is based on a set of assumptions and the people who are working on it have a very clear understanding of the limitations of those assumptions.

Gary Hurd · 11 April 2009

JohnK said: Those craving a further Ed Trifonov fix can see his computational biology based: Early Molecular Evolution, Israel Journal of Ecology and Evolution, v.52, no.3-4, pp. 375-387, 2006 Genome Diversity Center, Institute of Evolution, University of Haifa, 31905 Haifa, Israel

Do you have a link to the PDF?

Mike Elzinga · 11 April 2009

Dave Luckett said: One of the few things my chemistry teachers were able to fix in my resistant skull was that chemical reactions that can occur will occur, and the products of them will be therefore be present in some concentration.

And it isn’t just chemistry. Chemistry deals primarily with the reactions among atoms and molecules that involve the exchanges and sharing of the valence electrons of the atoms. But nature is much richer than that; even “neutral” atoms and molecules interact by redistributing their charges as they near each other. That gives rise to things like Vander Waals forces which produce potential wells that lead to further interactions and arrangements at a higher level of complexity. Once solids and liquids are formed (out of "neutral" atoms or molecules), there is a whole host of emergent properties that begin to determine what happens next. And so on up the ladder of complexity. The physicists have extended your chemistry teachers’ aphorism to “whatever is not forbidden in nature happens somewhere with some probability.” The ID/Creationists have a built-in revulsion to these kinds of phenomena; therefore they keep preaching that “mindless” interactions among featureless particles cannot produce anything without supernatural intervention; which is true, by the way. But that doesn’t describe the real universe in which we live. The ID/Creationist “universe” really is sterile. They live in a universe in which these physical phenomena are taking place right before their eyes, yet they refuse to look.

John Kwok · 11 April 2009

Mike, Of course these assumptions would assume automatically that life would be based primarily on carbon-based amino acids. Just to play devil's advocate, I wonder whether it might be possible to create life based on silicon:

Mike Elzinga said:
Flint said: From the sounds of this, life as we know it starts to sound like an increasingly inevitable result of ordinary chemical processes, under conditions that can't be all that unusual. So I jump way ahead to arrive at Fermi's old question - where is everbody?
The answer may lay in the fact that life as we know it exists within the temperature range of liquid water. In electron volts, that is something like between 0.012 eV and 0.016 eV. Compare that with the binding energies of solids and liquids which are on the order of tenths of an eV and with chemical bonds which are on the order of 1.5 eV. For all that complicated stuff to occur, the energy ranges are extremely restricted, and the contingencies of the planet on which we find life are never going to be exactly the same everywhere. There may be other beings elsewhere, but probably unlike us, and very likely more than four light years away.

Appreciatively yours, John P. S. I don't think Proxima and Alpha Centauri have been around long enough - assuming that they could support Earth-like planets - to allow for enoough time to have at least one planet which could support a biosphere as diverse as ours (Or have a planet that would have an orbit that is sufficiently stable and at a suitable distance from these suns to support life.).

Mike Elzinga · 11 April 2009

John Kwok said: Mike, Of course these assumptions would assume automatically that life would be based primarily on carbon-based amino acids. Just to play devil's advocate, I wonder whether it might be possible to create life based on silicon:

John, Elements in the fourth column of the periodic table do indeed have interesting combinations of possibilities. Under the “right conditions”, there might be a chemistry that could produce self-replicating structures. The bigger issue here, however, is what emergent properties occur and what do these allow in the way of further development higher up the chain of complexity? Recall that life as we know it exists within a very narrow energy window (on the order of a few thousandths of an electron volt). With the carbon based compounds we know about, a lot happens within that narrow window in which water is a liquid and supplies many of the catalytic properties needed for further reactions. What other chemistry and analogous physical environment, energy ranges, and emergent properties might produce elsewhere in the universe is unknown at the moment. Supercomputers can’t even calculate what happens with what we already know about let alone “compute” what could happen in other environments, with other chemistry and other emergent properties.

P. S. I don't think Proxima and Alpha Centauri have been around long enough - assuming that they could support Earth-like planets - to allow for enough time to have at least one planet which could support a biosphere as diverse as ours (Or have a planet that would have an orbit that is sufficiently stable and at a suitable distance from these suns to support life.).

I think you are referring to my mention in a previous comment of “at least four light years.” That wasn’t intended to imply that life exists there. That’s just the nearest star. Anything supporting life as we know it would have to be much farther out than that (unless we still find simple life on moons within our own solar system).

John Kwok · 11 April 2009

Mike, I concur. As RBH has noted, the issue of emergence poses a serious problem to those creationists who still contend inanely that, somehow, evolution violates the Second Law of Thermodynamics:

Mike Elzinga said:
John Kwok said: Mike, Of course these assumptions would assume automatically that life would be based primarily on carbon-based amino acids. Just to play devil's advocate, I wonder whether it might be possible to create life based on silicon:
John, Elements in the fourth column of the periodic table do indeed have interesting combinations of possibilities. Under the “right conditions”, there might be a chemistry that could produce self-replicating structures. The bigger issue here, however, is what emergent properties occur and what do these allow in the way of further development higher up the chain of complexity? Recall that life as we know it exists within a very narrow energy window (on the order of a few thousandths of an electron volt). With the carbon based compounds we know about, a lot happens within that narrow window in which water is a liquid and supplies many of the catalytic properties needed for further reactions. What other chemistry and analogous physical environment, energy ranges, and emergent properties might produce elsewhere in the universe is unknown at the moment. Supercomputers can’t even calculate what happens with what we already know about let alone “compute” what could happen in other environments, with other chemistry and other emergent properties.
P. S. I don't think Proxima and Alpha Centauri have been around long enough - assuming that they could support Earth-like planets - to allow for enough time to have at least one planet which could support a biosphere as diverse as ours (Or have a planet that would have an orbit that is sufficiently stable and at a suitable distance from these suns to support life.).
I think you are referring to my mention in a previous comment of “at least four light years.” That wasn’t intended to imply that life exists there. That’s just the nearest star. Anything supporting life as we know it would have to be much farther out than that (unless we still find simple life on moons within our own solar system).

Thanks, John

Mike Elzinga · 11 April 2009

John Kwok said: Mike, As RBH has noted, the issue of emergence poses a serious problem to those creationists who still contend inanely that, somehow, evolution violates the Second Law of Thermodynamics:

The issue of the Second Law is extremely annoying. These IDiots have been corrected repeatedly for over four decades, yet they still keep pushing the same misconceptions and misinformation. I can only conclude that the leaders of ID/Creationism know very well they are pushing a falsehood just to keep the rubes in their grass-roots base arguing for them.

John Kwok · 11 April 2009

Mike,

Yes indeed, I was referring to your nearest star comment in a recent post. If I'm not mistaken, the closest stars are those in the Centauri system, approximately 4 light years away.

Regards,

John

John Kwok · 11 April 2009

No disagreement here either. I find the whole "issue" with the Second Law of Thermodynamics to be extremely annoying (especially when I know that many had demolished that inane assertion by the late 1970s if not before, and I had seen Ken Miller do this so effectively in his very first creationist debate, which was held at Brown against ICR Vice President Henry Morris):

Mike Elzinga said:
John Kwok said: Mike, As RBH has noted, the issue of emergence poses a serious problem to those creationists who still contend inanely that, somehow, evolution violates the Second Law of Thermodynamics:
The issue of the Second Law is extremely annoying. These IDiots have been corrected repeatedly for over four decades, yet they still keep pushing the same misconceptions and misinformation. I can only conclude that the leaders of ID/Creationism know very well they are pushing a falsehood just to keep the rubes in their grass-roots base arguing for them.

I think creationists are counting on the scientific ignorance of their followers - which is among the many reasons why I refer sarcastically to the DI IDiot Borg Collective and the AiG Dalek Collective - since if any of them had some understanding of science, then they'd realize just how stupid and fallacious the "issue" really is. Regards, John

Mike Elzinga · 11 April 2009

John Kwok said: ...- which is among the many reasons why I refer sarcastically to the DI IDiot Borg Collective and the AiG Dalek Collective - ...

:-) Spot on!

stevaroni · 11 April 2009

Just to play devil’s advocate, I wonder whether it might be possible to create life based on silicon

Some time ago, over a couple of beers, I had an interesting conversation with a colleague who's a chemical engineer. He felt that, given the average temperature of small celestial bodies with liquid seas looked to be much colder than earth, any life there was likely based around nitrogen compounds. Apparently, once you drop 100 degrees or so from where us carbon based monkeys like it, nitrogenous chemistry has many of the same properties of organic chemistry.

stevaroni · 11 April 2009

As RBH has noted, the issue of emergence poses a serious problem to those creationists who still contend inanely that, somehow, evolution violates the Second Law of Thermodynamics

Um, if evolution violates 2loT, wouldn't that darling of ID explanation "microevolution" also violate 2loT? Um, but we can actually demonstrate "micro" evolution exists, and ID already admits it exists... Owie! my head hurts again.

mrg · 11 April 2009

stevaroni said: Um, but we can actually demonstrate "micro" evolution exists, and ID already admits it exists...

There is NO SUCH THING as a FREE LUNCH! But free snacks are OK! Actually, I think some folks like R@y M@rt1nez even deny microevolution -- but it's hard to say for certain, their thinking being slightly lacking in specifics, and requests for such being more than slightly unrewarding. MrG http://www.vectorsite.net

Mike Elzinga · 11 April 2009

stevaroni said: Apparently, once you drop 100 degrees or so from where us carbon based monkeys like it, nitrogenous chemistry has many of the same properties of organic chemistry.

There are literally endless, unexplored possibilities. Silicon compounds in seas of liquid H₂S, selenium oxide seas, and so on. Then there are the ranges where super-fluidity and superconductivity occur. We often forget that pressure is also as important as temperature in making available energy states that determine what physical and chemical reactions can occur. Also, systems need the occasional higher energy jolts from UV, X-rays, gamma rays, etc. in order to pump systems into meta-stable states from which they can decay into states that normally couldn’t be reached from the ground states that exist in a given environment. We, in our carbon-based world in the presence of liquid water, are quite parochial.

wamba · 11 April 2009

I misread the title at first as "Ten Amino Acids Thermodynamically Flavored".

I still think that would have been a much more interesting paper.

John Kwok · 11 April 2009

How dare you mock the one, true Messiah of the DI IDiot Borg Collective; William A. Dembski. He'll send the Department of Homeland Security after you all (which, regrettably, is what he did to University of Texas ecologist Eric Pianka three years ago. But it was Bush time then, and it's Obama time now.... so I don't think Homeland Security will listen to his rants and raves now.):

mrg said:
stevaroni said: Um, but we can actually demonstrate "micro" evolution exists, and ID already admits it exists...
There is NO SUCH THING as a FREE LUNCH! But free snacks are OK! Actually, I think some folks like R@y M@rt1nez even deny microevolution -- but it's hard to say for certain, their thinking being slightly lacking in specifics, and requests for such being more than slightly unrewarding. MrG http://www.vectorsite.net

There is a FREE LUNCH if you join with Dembski and embrace his Messiah, Jesus Christ (But in Dembski's case, the real Messiah he is serving is Lucifer, the Lord of Light.). John

Torbjörn Larsson, OM · 12 April 2009

Torbjörn Larsson, OM replied to comment from John Kwok, since the thread is closed for reasons unknown to man:

John Kwok said: I was kidding of course

I thought so, that's why I replied with a joking (and of course mocking) comic. Btw, if Eric Finn is reading this (there seems to be no mail address): this thread looks like we could continue our discussion from that closed Conolophus thread on abiogenesis and be close enough on topic. What say you? [I've never started to use the AtBC forums, since IIRC there is a waiting period before one can comment which somehow trips my ADD threshold (which is hilarious because I have to the best of my knowledge no ADD :-o), but if you prefer that we could try that instead.] I'll see if I post something anyway, but as I'm bushed out after my trip I will take the opportunity of the interruption in blogging service ;-) to take a rain check, at least for today.

Frank J · 13 April 2009

As RBH has noted, the issue of emergence poses a serious problem to those creationists who still contend inanely that, somehow, evolution violates the Second Law of Thermodynamics:
— John Kwok

Alas, you and I and Judge Jones can spot the "breathtaking inanity." But we must also admit that the subtle bait-and-switch between evolution and abiogenesis is quite clever, and has managed to fool most people who don't have the time or interest to look past the feel-good sound bites.

Stanton · 13 April 2009

Frank J said:
As RBH has noted, the issue of emergence poses a serious problem to those creationists who still contend inanely that, somehow, evolution violates the Second Law of Thermodynamics:
— John Kwok
Alas, you and I and Judge Jones can spot the "breathtaking inanity." But we must also admit that the subtle bait-and-switch between evolution and abiogenesis is quite clever, and has managed to fool most people who don't have the time or interest to look past the feel-good sound bites.

And I wonder how these same busy and or uninterested people will feel when they realize that Creationists are neither interested nor capable of producing the same, or even remotely invaluable products that Evolutionary Biology produces, such as agricultural crops, and antibiotics and pets.

John Kwok · 13 April 2009

Frank J, Well obviously we're not the only ones who can spot such "breathtaking inanity". The trouble is that most people aren't scientifically literate, which means they can easily be swayed by inane comments from the likes of "Doctor Lewis" (who, like your typical creo PT poster has gone AWOL), Kurt Wise, Ken Ham, Paul Nelson, Casey Luskin etc. etc.:

Frank J said:
As RBH has noted, the issue of emergence poses a serious problem to those creationists who still contend inanely that, somehow, evolution violates the Second Law of Thermodynamics:
— John Kwok
Alas, you and I and Judge Jones can spot the "breathtaking inanity." But we must also admit that the subtle bait-and-switch between evolution and abiogenesis is quite clever, and has managed to fool most people who don't have the time or interest to look past the feel-good sound bites.

Cheers, John P. S. @ Torbjörn, I am glad you realize I was kidding. I recognized instantly that you were injecting some well-deserved Swedish humor.

Eric Finn · 13 April 2009

Torbjörn Larsson, OM said: Btw, if Eric Finn is reading this (there seems to be no mail address): this thread looks like we could continue our discussion from that closed Conolophus thread on abiogenesis and be close enough on topic. What say you? [I've never started to use the AtBC forums, since IIRC there is a waiting period before one can comment which somehow trips my ADD threshold (which is hilarious because I have to the best of my knowledge no ADD :-o), but if you prefer that we could try that instead.] I'll see if I post something anyway, but as I'm bushed out after my trip I will take the opportunity of the interruption in blogging service ;-) to take a rain check, at least for today.

This thread looks like a good place. In fact, the article on amino acids in the introduction of this thread might add to that discussion. Of course, there is some territory to be covered before we can reach life and the phylogeny of bacteria, eukaryotes and archaea. I had a closer look at the links you provided earlier, and found them quite intriguing.

Matt G · 13 April 2009

Steve Taylor said: Unless the creatures out there have an active policy of announcing their presence, is there any reason to believe we could detect them anyway ? I suspect humanity's RF footprint is becoming smaller and smaller as we switch to fibre communications. How many years have we been detectable ? Probably less than 100. That's not a long time in the history of the universe. Steve

Reminds me of a little back-of-envelope calculation I did years ago to figure out what fraction of the galaxy could have received our RF signals. I estimated the volume of the galaxy (a disk) and the volume of a sphere with radius 60 light years (since RF broadcasts of adequate strength to escape the atmosphere was first emitted 60 years earlier). The fraction was something like 0.000000000001 (and star density in our neck of the woods is pretty low...).

Matt G · 13 April 2009

That's: RF broadcasts WERE first emitted. Didn't proofread very well....

Matt G said: Reminds me of a little back-of-envelope calculation I did years ago to figure out what fraction of the galaxy could have received our RF signals. I estimated the volume of the galaxy (a disk) and the volume of a sphere with radius 60 light years (since RF broadcasts of adequate strength to escape the atmosphere was first emitted 60 years earlier). The fraction was something like 0.000000000001 (and star density in our neck of the woods is pretty low...).

stevaroni · 14 April 2009

I estimated the volume of the galaxy (a disk) and the volume of a sphere with radius 60 light years ... The fraction was something like 0.000000000001

Also, don't forget that the earth might emit a fair amount of RF energy, but there are few single sources of really large size. That means that the RF the earth emits has very little phase or frequency coherence - in other words, it's a lot of energy, but it's spread over a very wide spectrum, so the energy density is actually pretty low. In RF terms, the earth dosen't "shout" a coherent message so much as it "hisses" with a lot of energy at fairly low frequencies, which is going to dissipate into the cosmic background noise fairly quickly. And, as time goes on, the earth hisses more softly. The heyday of really big broadcast transmitters (think Wolfman Jack and his Mexican FM stations) peaked in the 70's and 80's is starting to wane as more content is delivered by wired and fibered digital services instead of open-air broadcast. Probably the "brightest" single signals the earth emits are the microwave uplinks for telecommunication satellites. They're fairly narrow-band, tightly focused, purposely projected outwards and high enough in frequency that they don't look like cosmic background. Of course, they also sweep the heavens as the earth turns, so if you were an alien listening to his radio, you'd have just enough time to say "what is that?" before the signal disappeared forever.

RBH · 14 April 2009

Here is the Wired story on the same paper. One quote

If the observed patterns of amino acid formation — simple acids require low levels of energy to coalesce, and complex acids need more energy — indeed follow thermodynamic laws, then the basic narrative of life's emergence could be universal. "Thermodynamics is fundamental," said Pudritz. "It must hold through all points of the universe. If you can show there are certain frequencies that fall in a natural way like this, there is an implied universality. It has to be tested, but it seems to make a lot of sense."

Flint · 14 April 2009

But we must also admit that the subtle bait-and-switch between evolution and abiogenesis is quite clever

Except of course, to a creationist there is no bait-and-switch. Creation was a single, unified event. During which all kinds were created as we see them today, all at once. Abiogenesis MEANS, the creationist god poofed everything. Evolution can ONLY be an alias for this same event, that being the only event there was. After which, nothing changes very much, and evolution simply does not occur. The origin of life, and the origin of species, are one and the same thing in creationist doctrine. To paraphrase Judge Jones, they cannot be decoupled.

RBH · 14 April 2009

Flint said:
But we must also admit that the subtle bait-and-switch between evolution and abiogenesis is quite clever
Except of course, to a creationist there is no bait-and-switch. Creation was a single, unified event. During which all kinds were created as we see them today, all at once. Abiogenesis MEANS, the creationist god poofed everything. Evolution can ONLY be an alias for this same event, that being the only event there was. After which, nothing changes very much, and evolution simply does not occur. The origin of life, and the origin of species, are one and the same thing in creationist doctrine. To paraphrase Judge Jones, they cannot be decoupled.

There are times when you scare me, so good is your take on the creationist mindset. I'm usually pretty good at getting into an alternative mindset, but the creationist set is sufficiently alien that it's tough for me.