Life is chemistry

Hear, hear! I remember when a prominent researcher in the field, Andrew Ellington (aka "Deaddog"), used to hang around t.o. and spend a lot of time denouncing this same copout.

Sometimes creationists say things like, "Evolution doesn't explain the origins of life!"

The point you make is correct, pz, and I recall a certain cadaverous canine pointing this out on talk.origins some time back. But the workings of abiogenesis are far less understood than basic fundamentals like common descent. So allowing that chemical evolution is an appropriate research program for abiogenesis, and that there's no clear bright line between chemical reproducers and "life" still allows the anti-science crowd to scream that the open problem of abiogenesis is a fatal gap in the theory of evolution. (Therefore the screaming creationist isn't related to monkeys.)

I'll have to see about those articles, though.

Sometimes creationists say things like, "Evolution doesn't explain the origins of life!" The common reply is that that's the domain of abiogenesis, not evolution, with the implied suggestion that the creationist should go away and quit bugging us.

That's a cop-out.

I disagree that it's a cop-out when the subject is the teaching of evolution in schools. Evolution should be taught as a fact because it is so well supported by evidence. Our understanding of abiogenesis is not mature enough to teach it in high school, so there is some justification for leaving out any discussion of it. There's even room for reasonable doubt over whether abiogenesis actually occurred on earth or whether earth was seeded from elsewhere. While I agree that "it's natural processes all the way back" I don't think it's a useful argument from the standpoint of school policy. In that case, we really just want to say "Look, this is routine, non-controversial, mature science and that's why we can teach it in high school."

The other reason for keeping the two separate is that they're really different phenomena. The interesting properties of evolution assume there is self-replication, and that genes can encode adaptive traits with respect to an environment of self-reproducting organisms. It's almost a no-brainer that evolution would have to occur under such circumstances. But before you have self-replication, it's not clear how something like evolution occurs. It really seems that at the earlier stage you do need to rely on a few lucky events to get the ball rolling.

In addition to PaulC's comments, it must be pointed out that there are only so many hours in a day and genuine scientists (unlike Creationists) don't pretend to be expert in every last topic.

I don't pretend to understand BigBang cosmology beyond that of an interested layman and I don't pretend to understand abiogenetic theories better than anyone else who took organic and biochemistry 35 years ago.

I've tended to disagree with those who wish to put too high a barrier between abiogenesis and evolution. Causally, abiogenesis has significant bearing on evolution, and categories are typically artificial anyhow, so the notion that abiogenesis is truly separate from evolution won't wash.

However, one highly crucial conceptual difference between the two is that evolution does not necessarily depend upon abiogenesis in order to be the acceptable model for the last few billion years of evolutionary change. That is to say, there is nothing in evolution itself that prohibits Darwin from putting in his nod toward God creating one or more life forms in the beginning. Evolution using the genetic code(s) stands on its own. This is important in the evolution/creation battles.

I end up making another caveat, however. Darwin's nod toward God was politic and made the point well that evolution via natural selection does not necessarily depend upon abiogenesis. The trouble is that science will hardly allow Goddidit anywhere, at least not in anything we have seen heretofore. Thermodynamically and causally the God hypothesis is a dog, the sort of thing from which creationists and IDists would run screaming if they could possibly apply their objections to "evolution" to their own pet "theories". Nevertheless, from a positive evidence standpoint, evolution is very well demonstrated, and abiogenesis is full of problems, which means that in practical terms evolution has a standing that abiogenesis does not.

I agree with PaulC as well. Chemical evolution existing without the sorts of conservative information replication and transfer is significantly different from evolution occurring within RNA replication and/or DNA replication. It is not even clear how similar RNA replication might be to what we see today at a time when mistakes are very common. The trouble with chemical evolution as any kind of analogy with what we typically conceive of as biological evolution is that chemical evolution comes closer to what creationists falsely claim of biological evolution--things really do happen by accident. Even though some conservation would probably exist early on, conserved information could be overwhelmed by accident for quite some time during chemical evolution.

Science doesn't allow for any sharp categorical division between chemical evolution and biological evolution. However, what we cannot forget while battling the creationists is that the evidence for biological evolution exists independently from questions of abiogenesis, and that our lack of knowledge in the area of abiogenesis does not discredit evolution.

Creationists/IDists suppose that abiogenesis is a grave problem because they think in terms of derivation, that one has to have an adequate source of power or "reality" (essentially, God) if one is to make claims that such and such can happen some time down the road. They wish to cut evolution off at the source, and they try to do this by raising questions about abiogenesis (among other spurious questions).

Science moves in the other direction, however. We do not have to have a firm source for evolution, we need firm evidence close at hand in order to accept the theory. Then we move backward. That is to say, we have used clues from present organisms and evolutionary processes to come up with hypotheses about abiogenesis. It is evolution that is the established science, and the large gaps are at the biogenesis end. This is another of the present differences between chemical and biological evolution, simply that we are moving from the known (evolution) and using this known to explore what is not yet known.

So indeed, don't make false distinctions between chemical and biological evolution, but don't forget about the real differences, some of which will presumably fade in future times.

Glen D
http://tinyurl.com/b8ykm

*chuckle* I also recall the rants of the Un-barking One. He and you are right, of course -- prebiotic chem shades into evo as we know it. So your first paragraph is bang on: if that's all there is to the conversation, then it is a cop-out (almost as bad as the "2LoT doesn't apply to open systems" retort).

The usual way I've seen this come up is that the Creationist uses uncertainty over abiogenesis to cast doubt on all of evolution. It's a smokescreen, of course, to avoid talking about, oh, hominid fossils and genetic similarities among apes/humans. And it's a logical fallacy -- one I like to call "We don't know everything, therefore we know nothing" (it's probably got a Latin name that sounds much cleverer). It's quite legitimate to point out that it is a fallacy: lack of evidence around abio in no way impugns the transitional fossils, molecular evidence, etc, etc. And I think that's what the answer "Abio is not evo" tries to do, though it could and should be phrased more informatively.

Unfortunately, none of the Creationists to whom I've ever tried to point out this fallacy seems to have gotten it. I guess that to use the fallacy in the first place, you already have to be too stupid to ever comprehend that it is one. *sigh*

I agree that distinguishing between abiogenesis and evolutionary theory is a cop-out. It gives the anti-evolutionists rhetorical ammunition, but it's true. If there's truly a big "gap" in evolutionary theory, where they should be playing "God [or alien] of the gaps," that would have to be it. (Not Behe's tiresome flagella or blood-clotting...) It's a big enough gap to be scientifically fascinating, anyway, and one where you can't rule out an intelligent agency.

Not that I believe it was an intelligent agency that bridged the gap. Stuart Kauffman's autocatalytic cycles sound like a way better bridging of the gap.

About the Natural History article: I was puzzled by the hard contrast between the "metabolic" and "heterotrophic" theories. As I understand the former and as they present the latter, I don't see a basic conflict between them, and the basic metabolic
theory seems more scientifically plausible. (Whether it happened around deep-sea
vents or not.)

IIRC, the core of the metabolic theory just says that something-like-metabolism evolved before something-like-genes, by the kind of autocatalysis that Stuart Feldman talks about in The Origins of Order and The Life of the Universe. Rather than having a complicated master molecule that runs the show, you have a goo of simpler chemicals that tend to promote each other's creation. This goo can spread (e.g., through pores in clay or bubbles in a foam) and evolve without genes. There is no genotype/phenotype distinction, but it can still evolve by natural selection. (Goo that doesn't maintain its autocatalytic cycle "dies", goo that doesn't may spread and ramify. And goo that incorporates new chemicals or loses old ones, such that autocatalysis works better, "survives" differentially.)

Kaufmann makes this sound much easier than evolving genes straighaway, for most kinds of chemical soup. (Given a random assortment of molecules, they'll tend to have random shapes and tendencies to catalyze reactions that create or destroy each other. And somewhere in that network of positive and negative dependencies, there's likely to be a cycle of chemicals that promote each others creation and/or inhibit each others' destruction.)

Darwinian selection requires a genotype/phenotype distinction, but natural selection in general doesn't---things can evolve by copying and changing without genes. (And a goo that grows and spreads and splits amounts to a goo that copies itself.)

(This kind of thing is familiar to me from computer science, in the guise of prototype-based object-oriented languages, where there are no classes. You just copy individual objects and change them, and then copy them again. A changed copy can serve as a template for a new "class" of objects, i.e., its descendents. Prototype-based systems are simple and powerful, if sometimes ungainly; classes add clarity, but not power.)

So it seems to me that the heterotrophic theories may be right about the kind of soup that life started in, but the metabolic theories may be right about the basic shape of the evolutionary pathways: considerable evolution of metabolism before certain molecules in an autocatalytic set specialize into complex "genes." That seems to me to be the most reasonable story, irrespective of the particular substrate (soup). (But I'm not a biologist.)

I kind of agree and kind of don't. It is a copout in a sense, because it allows one to interpret the division as an acknowledgement that there must be some kind of supernatural intervention to get life in the first place. But in practical terms, I agree with PaulC. Plus, there is the fact that we can say evolution is a fact because of the evidence and observations of it in action, but at this point the only evidence about the origin of life is the fact that life exists now. This will change once someone creates something in the lab that is indistinguishable from life as it is commonly understood.

I especially like a couple of books by A.G. Cairns-Smith (titles escape me, but one is something like '7 clues to the origin of life') about the concept of 'genetic takeover', the idea that the original replicators in prebiotic systems were minerals, likely clays. The clays then catalyze organic reactions (which they do quite nicely) and ultimately are supplanted by organic molecules as the information storage mechanism.

I don't know enough biology or this subspeciality of chemistry to be convinced, but it is a direction, and an interesting one that incorporates the principles found later in biotic systems well before the system is 'alive'

In the latest issue of American Scientist there's a very good paper by Michael Russel called "First Life". Provide some very intersteing insights derived from the stochiometry of simple chemical proto-life.

PZ, I've gotta disagree with you to an extent.

Of course life is chemistry and biological evolution is dependent upon biochemical changes at the molecular level that serves as the engine driving natural selection.

Where I disagree is that the chemical mechanisms responsible for "abiogenesis" may have perhaps been driven by a different mechanism than those governing biological evolution. Consider that there could be different explanations for the assembly of the first self-replicating "life form" that allowed it to separate the outside environment from the first "ife forms" internal environment where the nuts and bolts of chemical synthesis and replication could occur.

I think where you have a valid point is that at some time in the distant past, a mechanism based upon something similar to Thomas Cech (sp) auto-catalytic RNA came into play and that that was perhaps the prototypical mechanism that won the race. I think then that you could work in your point that abiogenesis is a subset of evolutionary theory.

The thing is, abiogenesis happened. Period. The question is, how did it happen? I don't think there were any miracles, and I know for a fact that science provides a process for puzzling out what occurred. The copout is that by divorcing abiogenesis from evolution, we are implicitly acknowledging that an unscientific methodology, that of the creationists, might have some validity in this whole suite of interesting questions that legitimate researchers are pursuing. It doesn't. So let's not back away from the issue.

I'm not very sure we can reproduce this in the lab. It probably required millions of years of chemical evolution in a very large volume. On the other hand we are already failing in science classes with something as simple as natural selection in living organisms:
http://news.bbc.co.uk/1/hi/sci/tech/4648598.stm

depressing.

Life: Chemistry but with feeling.

'one of the lines in my email sig'

What else could it be?

Thanks, PZ.

I've been using the 'cop-out' ever since I got involved in this. But you're right. "No miracles required."

PZ, I fear you have waded into a different controversy on this one...

Lazcano is part of the whole Stanley L. Miller lineage, one that has insisted on dogmatically defending Miller's early work and has steadfastly shut down discussion and debate on other scenarios (submarine hydrothermal vent, iron-sulfur world, etc etc...) In order for the study of the abiogenic, chemical origin of life to proceed in a viable way, we need a healthy, open, collaborative debate. You notice that the article you quote, while making many good points, still nonetheless is siding back on the whole 'shallow pool' origin and essentially backing Miller's experiment. It is subtly dismissing and/or outright ignoring the many viable alternatives that are currently under active research and discussion. The fact of the matter is that there is a lot of theories, a lot of interesting work out there, and the need for a lot more experimental evidence before we can pick out a true front-runner candidate. There is exciting work out there but you wouldn't know it to read the article you cite.

May I suggest to your readers to look into this field in more detail if they are interested and be skeptical of those who don't discuss opposing points of view. The chemical origin of life is still way open and there are interesting and relevant points being made by all participants, including the Miller line, but nobody has yet achieved a dominant theory in this area.

One book that does come to mind is Hazen's, see (http://www.amazon.com/gp/product/0309094321/103-2411890-3319066?v=glanc…)
I want to say that there are also some serious issues in this book in terms of being Amero-centric and still limited to the author's familiarity, but at least it provides very good insight into the politics surrounding this area of research in the US.

We conclude that the religious nature of abiogenesis would be readily apparent to an objective observer, adult or child.

abiogenesis_scientist, I don't like it when I see people discussing opposing views too much. Your research must be consistent, there is a point you want to prove and that's what you do. Scientific papers should be short and concise. It's ok to say in the introduction what are the different views on the topic and why you pursue this one, but a paper must be biased towards a certain view. You don't need to be nice and discuss everything, in fact the opposite, you should discuss in detail only the views you are trashing. It's up to people with opposing views to write their own papers. Controversy is good, it's harder for the people who are in the minority wagon (you tend to get tough referees) but a field where everyone agrees is boring.

For certain highly non-standard values for the meaning of "objective", perhaps.

My background as a geologist shows through--I consider it a matter of geochemistry.

PZ, we're pretty sure that however life began, it was probably via chemical processes and situations that don't really fit the standard models of natural selection (since they were likely both brute force and worked without any consistent heredity). So it certainly makes sense to not claim that we know that evolution explains the origin of life, because we still don't know what does explain it, and further, we know that evolution is most strongly rooted on premises that require self-reproducing heredity with variation to be there in the first place.

I completely disagree that it's a "cop-out" to separate these two theories. Evolution requires, a priori, self-replication, variation, and some form of selection. Abiogenesis does not require any of these things, pretty much by definition. Those forces may well have been involved, and almost certainly were involved, at some point before we got to anything we might recognize as an organism. But there are other possibilities as well, that don't look much like what's happening in biological evolution. One needn't accept anything miraculous along the way. I think it does a disservice to abiogenesis to gloss over it like it's just more evolution. We shouldn't need to muddy the science to fight creationism; science is strong enough on its own.

Another thing I'd add. Even if you think of abiogenesis and evolution as inseparable, it's still not a "cop out" to distinguish them; it's a talking point. I can understand wanting to talk about both abiogenesis and subsequent evolution because they're fascinating topics. However, that's how you speak to a sympathetic audience. When dealing with adversaries, you have to look at how your own words will be turned back against you.

It suggests courage to say that you're "refusing to cop out" but I would just call this a lack of message discipline. In fact, PZ and others like him would love to discuss abiogenesis with nearly anyone, because they're probably just bubbling with ideas about it. I don't see the benefit to carrying on such a discussion with hardcore creationists. Rather, it's a denial of political reality by scientists who are too lazy to hold their tongue and avoid a rhetorical trap laid out for them.

Even if you prefer to think of abiogenesis as part of a larger process including evolution, it is in fact one of the least understood steps and one that has never been observed in the sense that mutation, speciation, and natural selection have all been observed repeatedly and are FACTS.

It IS a cop out to say that abiogenesis "doesn't matter" because clearly there is a scientific question here to be answered. But as rhetorical point, I would refuse to discuss it in an adversarial situation until I could force my adversary to concede clearly that abiogenesis is not evolution and has no bearing at all on the common descent of species from the first living things, which is what we are talking about. I would also insist that abiogenesis is not part of biology proper because in fact it deals with systems that are not alive and do not interact with living things. I would demand these concessions as ground rules of any debate and call foul at any mention of the origin of life.

PZ notes that "The thing is, abiogenesis happened." Well, so did planet formation, and so did early cosmological events. And all were necessary prerequisites of life. But there's no dishonesty in insisting that these issues stay off the table in a political debate about the teaching of evolution. And there are rhetorical points to be scored by ridiculing your opinion every time they make a sloppy segue from evolution to abiogenesis.

"Ridiculing your opinion" should read "ridiculing your opponent" above. Big oops.

I was going to say more or less what Eric Wallace said. Balls to the "cop-out" argument. Evolution as we know it is about specific mechanisms, namely those that produce heritable changes in nucleic acid sequences. Maybe there was "evolution" of a sort before the genetic code came around, but that's entirely distinct from the set of events we study today. The fact is, life assumed a particular form on this planet, and the study of how that proceeds is the subject of evolution. How that particular form arose almost certainly involved a completely different set of principles, different enough that they should be called a separate field of inquiry. Certainly the edges are gray, but I'm tired of people glomming things together merely because the boundaries are hard to define.

"The copout is that by divorcing abiogenesis from evolution, we are implicitly acknowledging that an unscientific methodology, that of the creationists, might have some validity in this whole suite of interesting questions that legitimate researchers are pursuing. It doesn't. So let's not back away from the issue."

Agreed.

However, the biggest problem is that the creationist (or the ID creationist) lumps up common-descent-evolution and abiogenesis into a muddle of incredulity, typically ranting that "Darwinism" is a faulty godless attempt at explanation of the "origin of life". The strawman of "goo to you" is specifically propped up to represent "Darwinist Faith". It is, unfortunately, still important to correct such ignorant nonsense.

...those mechanisms will be taken for granted afterwards, just as Wohler's synthesis of urea is nowadays.

Now, I only learned about the monumental importance of urea synthesis within recent weeks (thru a link on this site, IIRC). Already it's clear, especially in this context, that it was a sad gap in my education. That gap was filled with the story of Francisco Redi, as I'm sure it was for most people. That's why the Law of Biogenesis is so firmly held to be true in all geologic eras. If instead kids were taught about the first time a biological product was made from non-living matter... (of course, the Miller-Urey demonstration in Cosmos left an impression, too).

mark: My background as a geologist shows through--I consider it a matter of geochemistry.

In essence, life is just the fuzz that grows on rocks, eh? Literally, in the case of the Cairns-Smith model, mentioned earlier.

There simply isn't enough evidence regarding the origins of life for the subject for science to speak on the matter, although there are of course aspects of abiogenesis fall within current experimental and paleontological grounds, and scientific speculation is always possible.

Similarly, the biological Theory of Evolution does not speak to the origins of life and has no implications beyond the field of biology.

The essential concept of evolution through natural selection, though, isn't limited to biology alone. It applies to pretty much everything, on every level of existence, and it implies that it's entirely possible that nonliving substances could have spontaneously arranged themselves in ways that made them "alive".

Biological evolutionary theory says nothing about gods or external influences. But it's long past time that we acknowledged the unspoken truth, the reality that causes so many people to desparately cling to creationism: the concept of evolution makes the concept of God unnecessary, and therefore rationality demands that it be discarded due to the Law of Parsimony. Before Darwin, it was possible to be a rational, intelligent, educated person and, without contradiction, believe in a Creator. After Darwin, it became impossible.

Like it or not, religion is now obsolete. People don't like being made obsolete, and groups composed of many people will fight harder against obsolescence than individuals will.

Two lines of argument I disagree with:

1. The idea that because we suspect different mechanisms are at work in abiogenesis, it should be set apart from evolution sensu stricto. This implies that there is a single or small set of mechanisms in evolution; there isn't. Why not say drift isn't part of evolution, then?

2. That because our knowledge of the very early history of life or chemistry is weaker, that it is fair to set that category apart. Nah. That's no fair at all. What makes it a science is that we're working on rational, natural mechanisms, not the degree of certainty.

This is another one of the posts that I print out and read over and over on the bus--great resource, great comments, great with helping me get my head around these concepts.

Have we not seen the artificial creation of amino acids in the lab? What about organic molecules detected in space, or the research being done on abiogenesis beneath the Galapagos Islands? (Appropriate, that.) I guess I'm surprised that people who launch the "Evolution doesn't explain origins of life" argument are unaware of these and so confused about chemistry. Granted, amino acids are not "life," but isn't it just a matter of time before we do observe such an emergence?

"Similarly, the biological Theory of Evolution does not speak to the origins of life and has no implications beyond the field of biology.

"The essential concept of evolution through natural selection, though, isn't limited to biology alone."

Sorry, but I think these two statements are contradictory: the Theory of Evolution *is* the concept of evolution through natural selection, and it has implications far beyond biology as the use of evolutionary algorithms in both software and design optimisation has shown. It's also the reason that nanotechnology as originally envisaged by Drexler scares the willies out of biologists who have thought about it (self-replicators *will* evolve, even if the viable mutation rate is infinitesimal).

But back to the main point: I agree that dismissing abiogenesis offhand is counterproductive, but a constructive dismissal marking the difference between the established science of evolution and the emerging (sorry) field of abiogenesis, noting the difference between origin of species and origin of life, can avoid one of the classic straw men set up by anti-evolutionists.

Hopefully in a few more years, we'll have some mature alternative potential models for abiogenesis - we've come a long way since Miller-Urey both on the chemistry and the maths of emergence.

If we want to study evolution further it naturally makes sense to do it in prebiotics and abiogenesis as well. Any fear to discuss it makes the need stronger.

PaulC, it is wrong to say that genes are needed for self-replication. As the links and comments here say, self-replication are done without it, and all of that mechanism may initally be distributed in the environment.

The replication doesn't need (indeed is probably not expected) to be very faithful in the beginning. So there is no need for "lucky events".

If one take the perspective of evolution, I don't think you will see any of those events elsewhere. Multicellulars and intelligence were evolution exploring new possibilities, perhaps they were inevitable. So why expect low probabilities here?

In fact, of the one planet that can support life as we know it, we find life. It is a really measly and skewed 'statistic' since our planetary system refused to make any more earth analogs and the observation is certainly not random. But it says, until more facts are in, that life as we know it was inevitable and not "lucky".

Caio, I believe abiogenesis_scientist are discussing the review. A review should give a fair overview.

Reading Charlie's comment (which I agree with except for singling out instead of taking on the straw man) I see that I could add something about selfreplication to my previous comment.

Charlie points out that very faithful replicators will still eventually evolve into 'nicely' faithful ones. The very unfaithful will do the same. It seems to me abiogenesis proposals tend to be one or the other, but it will fix itself in time. Again, no need for luck.

PaulC, it is wrong to say that genes are needed for self-replication.

I didn't say they were. I said "The interesting properties of evolution assume there is self-replication, and that genes can encode adaptive traits with respect to an environment of self-reproducting [sic] organisms."

I agree that a self-replicating system need not have genes. And if I were writing the sentence now, I would not say "interesting properties" because I don't presume to tell anyone what's interesting. But a typical natural selection scenario assumes a self-replicator with genes that describe adaptive traits and are subject to mutation. This is a reasonable assumption because it is true of living things. Can you eliminate some assumptions and still get natural selection? Sure. After all we got to living things without them. But for most evolutionary models, these are important assumptions in describing what happens. Whether or not genes are strictly necessary for evolution, they clearly influence the manner in which it occurs.

I would add that even a completely abstract model of self-replication like a von Neumann universal constructor does include a self-description analogous to genes. On the other hand, there is Langston's loop, which is a more limited kind of self-replicating CA, and perhaps a useful analogy when thinking about the appearance of early self-replicating entities. You could also call that process a type of evolution, but it's actually not what biologists usually mean by evolution or what they usually study.

Above should read "Langton's loop." My thought is a little garbled. The loop itself does not demonstrate evolution as it is deterministic, although there actually are mutating CAs that demonstrate adaptation of such loops. I find this interesting (and understand it a lot better than I understand biology). But I do think that the theory of evolution is a much richer field and much of this richness derives from the notion of gene. Take that away and there are interesting things to study, but I don't see any reason to be forced to call it evolution, particularly when you wind up helping creationists to spread their FUD.

Torbjorn, I didn't get the impression abiogenesis_scientist was talking about review papers. If he was, then he was right ofcourse, I thought he was saying that scientists should avoid dissent. As an "outsider" (non-USA) I confess I was suprised that some people were arguing based on how creationists might react to this subject. It's something alien to me. A field were there are so many possibilities will generate a lot of controversy inside the scientific community, there is no way to avoid it. If some religious fanatics will use this to go against science it's a problem, but it can't be a major concern of the scientists. The thing which depresses me is that even in countries where creationism is not an issue schools are not making a good job of explaining science to their students.

Abiogenesis is something that will rely on some limited way in experiments but mostly on numerical models which will mimick the natural selection of the pre-biotic entities. Whatever is your approach to the field it will always involve the concept of evolution (the entities will change with time) and natural selection (entities will be removed from the pool or not according to a set of criteria).

All, This may be a bit OT, but it would be great to see a discussion here of the implications of prions (particularly in yeast) to the beginnings of evolution and abiogenesis. I have been reading a number of articles by Susan Lindquist et al. from the Univ. of Chicago and there's some amazing stuff here that I wasn't aware we even knew. Long story short, prions, while not truly self replicating, do represent a type of non-RNA/DNA, molecular basis of heredity. They even cause inheritable phenotypic diversity in yeast, that has been shown to be subject to natural selection and Darwinian evolution. Before prions were known, some of these strains of yeast were thought to break Mendel's laws. It was only until researchers realized that there were the additional hereditary contributions of the prions to phenotypic traits that this issue was resolved. Maybe someone else can comment on this, or I would also love to see PZ take this up as a new entry?

you already have to be too stupid to ever comprehend that it is one

No, there are some people who are dishonest enough to use it anyway, eg one such over on the BBC boards just this past week or two. While they are not apparently particularly competent at anything much other than being a troll, I doubt that they are unaware they are being dishonest. Their trollishness is too widespread and their dishonest, false objections are too specific and deliberate looking. They have just enough intelligence to be knowingly evil.

Of course life is chemistry!

I'm a chemist and I'm alive. Ergo.

Get yourself right down there in the middle of the Kreb cycle and ask yourself what's happening. Well, chemistry is happening.

And, why is it happening? Well, it's just doing it's thing and there ain't nobody at that level asking 'why.'

I don't know anywhere else to post this. Sorry if it's unrelated but... I am tired of programs and movies that portray a mad scientist! Besides A.Q. Kahn (sold Pakistan's nuclear technology, an Islamisist) I don't know of any. This is a sad stereotype and all scientists should be insulted at the vast overuse of the Frankenstein stereotype.

I feel that it is part of the reason that science in general is being undermined by groups like the DI. The Sci-fi channel produces programs where it is a standard that some creature is created by a scientist, with unlimited funding, with strange or deviant reasons; or a creature results from DNA infected by pollution or irradiation. I know it's all in fun, but the stupid, after years of indoctrination, believe this crap! And the history channel, Keeps producing pseudoscientific content - Nostrodamus, need I say more. They never talk to someone who could debunk this superstitious nonsense on one of their programs, or air a program that would.

All the Intelligent design protagonists need to do is state a stereotype and 90% (not a scientific estimate) will believe it. I see it day after day, time after time. Today on Stargate Atlantis (Sci-Fi channel) an actor asserted to a weak and ineffectual scientist character that "scientists always get it wrong" without any push back.

So I am pissed! Just thought I would vent!

Guys like the Korean; we catch without anyone else's oversight. We need to push back!

PaulC,
"And if I were writing the sentence now, I would not say "interesting properties" because I don't presume to tell anyone what's interesting."

Fair enough. I made a mistake, and you pinpointed why.

We seem to agree on much (and I think your algorithmic examples are really interesting) except that I don't think all of abiogenesis could be singled out as a qualitatively different phenomena. It probably had replication of sorts, possibly early but almost certainly later.

Caio,
I didn't get that impression from hime, but I think some other here did as you described. I can agree with all of your first paragraph, I feel much the same.

(On your second paragraph I would say that biological models such as in the links PZ provided seems to give more info than simulations at this time. And nitpick that I think you meant to say that evolution contains at least random change (ie your "evolution") and directed selection.)

I usually find myself nodding my head in agreement with much of what I read on your blog, but this time I have to respectfully disagree.

I don't deny that abiogenesis was/is an entirely natural process involving natural mechanisms, and that there are parallels between biological evolution and what you call chemical evolution. But I would argue that more directly uniting the two together is perhaps stretching biological evolution beyond its capabilities.

The very basis for the process of evolution is genetic changes in reproducing populations due to differential reproduction. Yes, other minor forces come into play, but the primary initiative to genetic change is differences in reproductive success. So how, precisely, could evolutionary forces have a significant affect without reproduction? Until biological units were able to actively reproduce themselves, and until some were better at reproducing than others, how could biological evolution have occured?

The fields of study are related, granted. But I can not see that it is a cop-out to acknowledge that biological evolutionary processes are necessarily limited to those organisms that are, well, biological. It also seems to me that by trying to stretch these processes beyond biological to the chemical, we are setting evolutionary theory up for more attacks from creationists who might just recognize (yes, this is likely a stretch) that the mechansims of evolutionary theory were not designed (pardon the pun) to explain change in non-biological, non-reproducing organisms.

Finally, chemistry, a subject I feel comfortable with! I agree with Doc Bill, that all life is chemistry. As an organic chemist, it is always a little puzzling when people refer to "natural" chemicals as opposed to "unnatural" ones.

I believe it is perfectly acceptable to refer to abiogenesis and evolution as completely separate fields. They deal with different but related questions. If there is a scientific field that should really scare the fundies it should be abiogenesis and not evolution.

When I was in grad school, I was lucky to go to a lecture from a chemist who studied abiogenesis. It was very interesting. Scientists have actually synthesized many, many types of molecules that are "self-replicating" or "self-assembling." That is not that difficult. I think the difficult question has to do with chirality. All of the molecules in the body have the same chiral configuration. Why is this? Maybe I'm behind in the literature, but I don't think there is a good explanation for this. Organic chemists spend a lot of time trying to control chirality of molecules, however, they need chirality to create chirality of one configuration. The question becomes how did the first chiral molecule form? Scientists have not been able to create this yet.

The more I think about it, the main reason I like the abiogenesis/evolution distinction is purely rhetorical. I agree with PZ that abiogenesis is something that really happened and we're making progress towards understanding it. I also agree that both are part of a larger topic that is coherent from a scientific perspective. We really do want to know how the earth, which started out lifeless, got to be how it is today.

My view is that that's a big enough topic to split up, so we're justified in making the distinction if we choose to. There's nothing dishonest about it. I would argue that if we had a name for the study of the bigger topic, any conversation would about it would soon get to: so, do you study the part before life existed, or after it existed? It's a natural separation.

Now, note: creationists have a huge arsenal of apologia, much of which functions ONLY by conflating evolution and abiogenesis. An unfortunate part of the job of life scientists is to counteract creationist rhetoric. So if you can frame any debate by first making sure everyone understands that there are two topics, and you're talking about one, and politely (in your best Eddie Haskell voice) make it clear when your creationist opponent ventures into that other topic, then you've put your opponents on the defensive. Now they're the ones who have to think on their feet, and we know how that usually turns out.

Sure, it's a cop out if you suggest that the problem of abiogenesis leaves any reasonable doubt that there is a naturalistic explanation. But I don't advocate this. I only advocate insisting that the discussion stay focused on the topic and not venture into abiogenesis, planet formation, cosmology, or anything else that isn't evolution.

PZ wrote:

The common reply is that that's the domain of abiogenesis, not evolution, with the implied suggestion that the creationist should go away and quit bugging us.

Yes, that is the idea. If you can get a creationist troll to admit their game is up and go away with so little effort, you have energy left for the more persistent ones.

It seems to me that this approach is honest and effective. In a perfect world, it would be fun to go into digressions, but this debate does not allow it. I think that keeping a firewall between abiogenesis and evolution is the killer rhetorical tactic of our side.

Maybe you think our case is so strong that we don't need it. I agree, but why make things tough? We're not trying to make things sporting. We're trying to fight a well-funded movement that is bent on harming science education. This doesn't give us the right to be dishonest, but it does give us the duty to fight with whatever weapons scientific integrity allows us, and the distinction between evolution and abiogenesis is one of them. It works; use it.

The Theory of Evolution is the concept of evolution through natural selection *applied to biology*. It's been quite thoroughly proven that life has evolved, and selection is strongly supported by the available evidence. Ergo, it's a Theory with a capital 'T' in biology.

The concept itself cannot be 'proven'. It is not a hypothesis, or a conjecture. It's a tautology.

While we're at it, we need to clarify our terms. Just as 'theory' means something different in science than it does in everyday English, 'natural' means something different, too.

Blue jeans are obviously unnatural in the everyday sense, but not in the scientific sense. 'Nature' is defined to be open-ended: if we verify observations that don't fit within our concept of what's natural, we change our concept.

There is a very good reason why science does not accept supernatural explanations. It's not an arbitrary rule (like writing journal articles without using the letter 'e'). We need to make people understand what that reason is.

1. The idea that because we suspect different mechanisms are at work in abiogenesis, it should be set apart from evolution sensu stricto. This implies that there is a single or small set of mechanisms in evolution; there isn't. Why not say drift isn't part of evolution, then?

There is no small set of mechanisms in evolution; however, there is a small set of requirements for evolution. Those conditions (replication, variation, selection) are the end goal of abiogenesis; once we can explain how those conditions were met, then we will have successfully stitched together the story of life starting with inorganic matter.

Let me ask this of PZ: if you want to put abiogenesis and evolution under the same framework, why stop there? Those inorganic molecules got here through natural mechanisms, they were formed in stars via natural mechanisms...why, we can absorb all of cosmology into evolution!

What the Prof. said.

Because you can't trust those religionists to leave the ineffable as simply the ineffable; they have to go and fill it up with godwottery and then yell that scientific enquiry is forbidden.
So, however it hurts your brain to understand that there is an inorganic springboard for the riot of life, it is the only logical way to look at the ineffable.

A few thoughts motivated by my insomnia...

Bravo on the "cop out" comment. As an evolutionary biologist working largely much closer to the tips of the tree of life - but interested in the root and that which lies "below" the root - I think we should all try to avoid the arbitrary "that is abiogenesis, not evolution" BS. Studying abiogenesis requires skills and expertise that is different from studying developmental biology...so what? Studying developmental biology equires skills and expertise that is different from phylogenetics, or ecology, or etc. (fill in any number of the subfields of biology). But development, phylogenetics, ecology, etc. are all subfields of biology.

Even if a strong scientific arguement could be made to uncouple study of the origin of life from other aspects of evolution, I suspect the "that is abiogenesis, not evolution" looks to the public like a cop-out. So it would be better to approach it head on.

That said, the political argument I would promote for the teaching of evolution (and exclusion of creationism) would minimize the origin of life discussion. I would suggest that a strong argument that many outside of biology might respond to is the following:

1. The purpose of school is to expose students to the best knowledge and information possible and (more importantly) to teach students how to evaluate information they may get in the future.

2. Who should have a say in determining the best and most important pieces of information? Should it be experts in specific fields or anybody with an opinion (even if they only formed it two minutes ago)?

3. Think of an (admittedly artificial) scenario. Imagine that there is a group of people who decide they have an alternative way of treating disease (well, unfortunately quacks are always with us, so we don't have to stretch our imagination too far). How would you view that group if they:

(a) Demanded their methods be added to medical school curricula by going to individual state legislatures and/or boards of regents, without ever working to convice any actual M.D.s or D.O.s that the novel approach is at least as good as traditional approaches.

-or-

(b) Attempted to prove their case to the medical community, and only stated to push for the addition of their methods to the curriculum for med students AFTER at least a fairly large plurality of qualified professionals were convinced of the merit of their ideas.

4. Point out that creationists (er, ID proponents...) are doing (a) rather than (b). And the creationist excuse for short circuiting the processes of vetting their ideas by the professional community? They claim the community is closed-minded... Because scientists are closed minded they want high school students - who (because of their age) haven't gotten all of the information necessary to evaluate the issues or developed the confidence or reasoning skills to acually evaluate information of this type - to evaluate the ideas. I say it again, simply because it is so silly - creationists want high school students rather than professional scientists to evaluate the validity of claims about science

5. Emphasize that the debate is NOT evolution vs. creationism (since that debate - if it were to be held - would be scientific) it is really between presenting the BEST information possible at the moment, as determined by professionals vs a smorgasborg of information from which students are expected to pick out the best info. I'm sure medical books contain info that is "wrong" in the sense of not being the best possible response to a particular issue - but what do you want? Doctors educated using the best possible information, where "best" emerges from a vetting process by practicing doctors who are being successful, or doctors told to peruse a bunch of disconnected factoids presented on an equal footing?

To bring this to a high school (or younger) level - should random folks on the street determine the content of a literature classes (ok - let's can Shakespeare and Flaubert for Jacqueline Susanne, oh, and that Bill O'Reilly guy writes real good...) or people with a background in literature? Will any process result in the absolute BEST set of decisions regarding curriculum possible? Of course not, and perhaps Jacqueline Susanne has merits (I know O'Reilly doesn't, so don't even go there...) but it is probably important to expose students to Lear or Hamlet. And I suspect most people could be convinced of that.

I wonder if put that way a few people who - quite frankly - don't really understand evolution but feel the truth probably lies somewhere "in the middle" because there are scientists on both sides couldn't be brought onboard.

However, given this criterion of "is topic X the scientific equivalent of a literary giant's search for le mot juste" I'm not sure if abiogenesis makes the cut. Perhaps some exposition upon the data (beyond the simple "we're here") supporting the contention that abiogenesis is reasonable, but I would find it hard to justify too much more. The area is too up in the air to justify much treatment, and there is to much important and more basic material (those equivalents of Lear and Hamlet, like natural selection, sexual selection, common descent...not to mention phylogeny, evo-devo, even evolutionary genomics).

I think I've succeeded in curing my insomnia by transfering it to the good readers here. Peace!

The Theory of Evolution is the concept of evolution through natural selection *applied to biology*. It's been quite thoroughly proven that life has evolved, and selection is strongly supported by the available evidence. Ergo, it's a Theory with a capital 'T' in biology.

Evolution is theory *derived from biology*, but it has applications and potential implications far beyond.

The concept itself cannot be 'proven'. It is not a hypothesis, or a conjecture. It's a tautology.

It's only a tautology if stated in the form of that horrible phrase "survival of the fittest." The "tautology" is one of those misconceptions or fallacies about evolution so readily seized upon by lazy critics.

http://www.talkorigins.org/faqs/evolphil/tautology.html

In any system of heritable replication, those traits which confer greater survivability of offspring will tend to spread through the population, and imperfections in replication promote continued variability within the population. That's not a tautology. It's just so blindingly obvious (once Darwin pointed it out...) that it seems so. Modeling (both computer and mathematical) has shown how powerful a force this sort of selection is, and biology - indeed, life - is just our greatest example of the consequences of selection pressure given effectively unlimited time and complexity of environment.

How the first true replicators came to form, and from there how protocells started is a fundamental question vital to closing the gap between chemistry and biology (and possibly one that we'll never know for sure - if we have more than one plausible model we might have no way to tell which of them was closest to the path life on Earth took).
As it is, it's simply too open a question at the moment - however fundamental it is to science - to be drawn in on by anti-science baiters. Yes, I'd love to be able to genuinely discuss and debate abiogenesis with honest opponents or critics, but as we've seen over and over, there is a group out there that is anything but honest over these matters. In their case, their oft-repeated "evolution blah blah origin of life" needs to be shot down. Unless of course they're specifically being fallacious about abiogenesis research, in which case, yes, embrace it as PZ suggests and defend the truth...

Edward has posted a lot there to think about too, mind. Great post.

In my opinion, allowing the Creationists to group evolution and abiogenesis together plays into the hands of people like Kent Hovind, who insist that evolution requires that there is a completely natural explanation for all of life and the universe and helps them support the notion that it is not possible to be a Christian and someone who accepts evolution.
Of course it is an interesting and valuable area of research that would not be dismissed totally, but as with the big bang theory, evolution does not depend on how life or the universe started. Were it to be somehow proven that it was not possible for life to begin through natural chemical processes, it would not change any of the evidence for evolution, or the conclusions that come from them.

As an emergent materialist, I actually disagree with the statement that life is only chemistry. Life has chemical properties (and physical ones), but also properties of its own. Homeostasis is probably the most crucial one.

Of course. But then, I didn't say life is only chemistry.

Evolution was first recognized in a biological context, but the concept itself is a statistical one.

It's not evolution that requires that everything in the universe have a natural explanation, but science itself. Of course, all we have to do to satisfy that requirement is to not define a cause as being outside of nature, a point that goes right over the heads of creationists.

The good thing about the abiogenesis=evolution argument is that clearly if that is the case, abiogenesis has certainly occurred. In fact I think that is not only an argument against creationists and IDCists, when it is appropriately modified to take note of the actual distinctions between the two areas of study it is indeed an appropriate argument to indicate that abiogenesis must have occurred. We don't have a causal break between the two, some place for the Deity or Designer to act, and so the proper conclusion from the evidence for evolution is that when we follow it back far enough we come to abiogenesis.

I think it's great when creationists/IDists conflate them (whether more so than is appropriate, or not), because the evidence for evolution is so overwhelming that, if evolution is said to entail abiogenesis, we then have as much reason to believe that abiogenesis happened as that the flagellum evolved.

That said, we do insist on evidence for our claims, so we still must be more cautious in our claims about abiogenesis than about evolution, since the former is rather more lacking in evidence. Even though all evidence and reasons that we have at present lead us to believe that abiogenesis took place, scientific skepticism is the reason that we have to treat the two differently, if not differently in kind. Scientifically, and in terms of evidence, it is not sufficient simply to conflate the known evolution with the much less known abiogenesis. It's just that in an argument with someone willing to conflate the two without the proper demands for evidence I am willing to do so for sake of argument, and to proceed to point out that such strict equation of evolution and abiogenesis leads to only one legitimate conclusion, which is that abiogenesis occurred.

Glen D
http://tinyurl.com/b8ykm

An issue is the definition of life in the context of its origins. Commonly, it involves reactions which are self sustaining (process useful energy), self replicating, and subject to Darwinian evolution. This kind of definition does not go beyond the abiogenesis barrier like the common argument of the evolutionaries.

That being said, I think it is extremely important to be clear that the definition of life extends back to distributed, bulk reactions that most would not recognize as living. And this form of life also evolved.

I think Edward succeeded in putting his insomnia to productive use. But is abiogenesis at this time solid enough to put specifically in schools? Maybe there is no problem there, yet.

I still wonder about the stress put on selfreplication, which the linked articles doesn't seem to cover; it's only one critera among others. Naturally there are scenarios that will gradually close on selfreplication.

One, probably totally off scenario: (Hey, I'm not doing this stuff for a living. :-) For example, if one has a large supply or production of simple chemicals and reactive sites, natural selection would make some more robust products more common. Sooner or later some partly selfreplication appears, as they must, and survives better when the environment and its production/supply varies, because those systems are even more robust. And on it goes... With evolutionary processes all the way.

If I can come up with a totally unsupported and probably inconsistent armchair hypothesis, I'm sure nature can do better. :-)

"An issue is the definition of life in the context of its origins. Commonly, it involves reactions which are self sustaining (process useful energy), self replicating, and subject to Darwinian evolution."

Interesting definition, but I'm not sure it's correct and that it's really feasible to define or even that it's a problem. As some said it will be a quantitative and not a qualitative transformation from abiotic to biotic systems. I don't think you will ever be able to point at some stage and say "this is exactly where life starts". A parallel is perhaps the difficulties in doing that on foetuses.

The process picture of chemical to biological evolution
should be enough. Perhaps 'life' is a concept beside the point just as 'soul' are? At least it seems to be as hard to define as 'consciousness', which doesn't prevent us from doing studies on how it acts.

Hmm. I think the problem here is a cart + steam engine issue. As in, people knew a whole hell of a lot about carts, and some other people could build neat toys with steam, one of which could spin really fast, but no one understood steam system well enough to attach one to a cart. Abiogenesis will, I believe, inevitably get attached to the cart of Evolution, but for now all we have is a funny spinning globe than makes people go, "Wow!", when they see it. Its too soon, given the limited understanding of it and the more serious problem that we have already seen from the opposition, whose response is, "So, it spins. So what?" Especially since I am not sure it has even gotten that far yet.

Creationists don't just lump together abiogenesis with evolution. They frequently use "evolution" as a shorthand for the entire naturalistic picture of the history of the universe provided by modern science: Big Bang cosmology and the formation of the solar system and geology and the history of life; since none of this is chalked up to miracles, it's all evolution, and if we don't have a solid naturalistic explanation for where the Big Bang came from, that's a great big hole in evolution. God wins the debate, creationism is true, QED.

One way of defeating this sort of all-or-nothing thinking is to partition things off into separate disciplines, the way scientists actually do in their day-to-day work. Of course Big Bang cosmology isn't part of biological evolutionary theory, so if we don't know where the Big Bang came from (any more than if we don't know where life came from) that's absolutely no problem for evolution. Simple, and strictly accurate.

On the other hand, even that is in a larger strategic sense a cop-out. All this stuff really is connected in a grand naturalistic view of the world, and within every discipline there are pieces we know a lot about and pieces we don't. Creationists really are attacking this basic way of looking at the world: the idea that scientific analysis involves looking for naturalistic explanations based on broadly applicable and testable principles, rather than assuming early on that something is probably supernatural in origin.

We should be trying to get across the idea that no matter what you call a scientific discipline--whether the thing you're studying is cosmology or evolution or abiogenesis or something else--science isn't this brittle, that it isn't a thirteen-billion-year-long mathematical deduction that will all fall down if you find one hole in it somewhere. Glen Davidson said it: we work back from the evidence, not forward from some set of a priori postulates about how the universe began. And Lt. Kizhe said it: "we don't know everything, therefore we know nothing" is a fallacy. The whole point of science is that you can learn things this way without knowing everything.

So while abiogenesis and evolution aren't exactly the same thing, on the other hand, it really shouldn't matter to our rhetorical arguments whether we think of them as part of the same thing. The point is that the existence of one unknown in a scientific body of work doesn't bring it tumbling down.

It's not just creationists either; this is something that pseudoscientists and anti-scientists never seem to understand. They always think of the sciences they attack as brittle logical edifices that will disintegrate if cracked at the crucial weak point, so they attack the founding figures ("Darwin recanted") or the logic of the one paper that got the most media attention (the attacks on the global warming "hockey stick") or the methodology of hundred-year-old experiments (the anti-relativity people who obsess on Michelson-Morley and the Sobral eclipse), as if these are all that really matter.

On the other hand, one advantage of being precise about distinctions between subdisciplines is that the sloppy use of these terms is a useful social marker: someone who talks about the Big Bang or abiogenesis as part of evolutionary theory is probably some sort of creationist, or somebody who's been listening to them. It takes away their advantage of surprise.

Matt,

Everything in your post makes sense, except:
"someone who talks about the Big Bang or abiogenesis as part of evolutionary theory is probably some sort of creationist, or somebody who's been listening to them."

First, PZ proposed to see "biogenesis as the study of chemical evolution is a natural subset of evolutionary theory", and he is a professional biologist. (I will admit he has been listening to creationists a lot. But I can't see he is impressed by them. :-)

Second, how do we draw a line between abiogenesis and the rest of evolution, or between prebiotic and biotic systems? To avoid being sloppy?

As you yourself said, evolution isn't disproved because it takes on abiogenesis. Instead, the study may strengthen it.

Finding Faith in Evolution

In a wide-ranging conference that covered topics as diverse as Aristotle, spindle fibers in cell division and Augustine's interpretation of Genesis, speakers at a conference at Florida Southern College on Friday explored the controversy over evolution in American society.
.
Their conclusions: The evidence for evolution is overwhelming; there is no conflict between belief in God and Charles Darwin's theory of evolution; and intelligent design does not qualify as science.

Two of three isn't bad.

What to think? The message seems to be that religionists shouldnt be afraid to accept science, but a lot of the reasoning I cannot agree with.

I would lump together most of the story from the big bang on as part of the subject of self-organizing systems. I would disagree with Matt McIrvin that the people who try to use "evolution" for this broad category are necessarily creationists. The conflation can also occur out of enthusiasm for wanting to tie these things together.

Personally, I think that the phrase "Theory of Evolution" is reasonably restricted for historical reasons to what happened after the first living thing existed. Natural selection as it occurs in living things is a kind of self-organizing system, but it's a particularly powerful one worthy of its own name. It assumes that systems are reproducing and have a robust self-encoding. This is largely absent from the earlier steps.