Metabolism First Hypothesis

[Furrowed Brow]

OK. I’ll not pretend. Most of what follows I’ve lifted from Scientific American June 2007 from an article by Robert Shaprio “A simpler Origin for Life” pp 25-31.

Since the work of Stanley Miller in 1953 it is known that amino acids can be created “in a test tube”. However amino acids are far less complex than the nucleotides that form DNA. And DNA has never been created in a test tube.

A further hurdle is that DNA provides the code for protein construction, but the information contained in DNA requires proteins to retrieve and copy its information. This is a chicken and egg problem.

The solution to the chicken and egg is RNA. A simpler form of nucleotide. RNA can sometime take the form of a double helix, and sometimes it can ferry information like a protein. However RNA is still a nucleotide and has never been created in a test tube.

Each RNA contains 10 carbon atoms, nitrogen, and oxygen, atoms from the phosphate group, and they are all bound together in a precise three dimensional form.

There are thousands of ways these atoms could come together to form alternative nucleotides to RNA, and millions of alternative molecules that are not nucleotides. Shapiro uses a golf analogy. The odds against the formation of RNA are akin to a ball finding its way around all 18 holes of a golf course dues to natural causes. Not impossible, just highly improbable.

Life certainly does not seem destined if the odds are so high against. Shapiro quotes Jaques Monod

The universe was not pregnant with man. Our number came up in the Monte Carlo game.

Shapiro discusses the small molecule alternative. Rather than RNA coming first, there are small molecules that work together as a metabolism. There are five requirements for the metabolism first hypothesis. However two formulations are offered.

1/ Energy source is required
2/ Released energy must drive a chemical reaction
3/ There must be a network of chemical reactions to permit adaptation
4/ The network must draw material into itself faster than it loses material
5/ No information storage molecule is required.

1/ A boundary is needed to separate life from non life.
2/ An energy source is needed
3/ A coupling mechanism must link the release of energy to the organisation process that sustains life.
4/ A chemical network to permit adaptation
5/ The network must grow and reproduce

One weakness of the metabolism first hypothesis is the lack of research and lab work. However, if the metabolism first hypothesis is correct then life would not rely on a single improbable event to get going.

I like the metabolism first hypothesis. I think it will probable take over from the RNA first hypothesis.

However there are some interesting implications. The RNA first hypothesis requires a massive improbability, which in itself is not very Darwinian. However , if it were true, we should perhaps expect to find ourselves alone in the universe. The RNA hypotheses then does not seem inconsistent with a creator.

The metabolism first hypothesis implies we got to RNA the long way, in small steps, by the way of small molecules coming together to produce the function of a metabolism. As metabolisms adapted and evolved, things became more complex, until self replications proper arrived. This route does not require massive improbabilities, in fact it implies the universe be pregnant with life. So perhaps we should not expect to be alone.

Ok. Do you think the metabolism first hypothesis is plausible? Is it going to be a greater challenge to creationism than the RNA first hypothesis?

[ST88]

Ok. Do you think the metabolism first hypothesis is plausible? Is it going to be a greater challenge to creationism than the RNA first hypothesis?

I must be late to this party, because I was under the assumption that [what is now described as 'metabolism first'] was the prevailing theory. Spontaneously occuring RNA seems preposterous. Not the least reason of which is because even if you get RNA from a random system, you still have to have the randomly produced enzyme decoder ring to do anything with it.

However, there is nothing that says the universe must be "pregnant" with life even if metabolism-first is true. It's still true that -- under the theory -- conditions must be just right in order for this to happen, and it must happen over a million to billion year/s timespan during which any of your garden-variety cataclysms could stop the process from happening, perhaps permanently. I don't think old-earth creationists have anything to worry about, and young-earth creationists surely won't be halted in their tracks by such news. Even if we could produce the correct reactions that lead us from proton soup to algal mass, all that really proves in a YEC hermeneutic is that we are able to do such a thing.

Some observations that may expose my thoughts on this subject (and are just off the top of my head, so rip it up...):
Of the first formulation:

4/ The network must draw material into itself faster than it loses material

This doesn't sound like it's necessary. What does the system care if it's losing material faster than it can draw it in? All that's required is for the correct sequence of events to happen.

Of the second formulation:

1/ A boundary is needed to separate life from non life.

Why do we need a line between life and non-life? Is it possible to even identify this line with what we know now? This seems like a life-fro-pomophric fallacy or something like that. It's based on a deconstruction of the polymer chain event leading up to recombination and finally to reproduction -- a piece of information that is irrelevant to the process, but only helps us to describe it.

[otseng]

Do you think the metabolism first hypothesis is plausible?

Well, I'm glad at least it's being recognized that a spontaneous generation of RNA is not possible. And my guess is that just as RNA first was embraced and discarded, that metabolism first will also have the same fate. But, time will eventually tell as more research is made on this.

[Furrowed Brow]

Some observations that may expose my thoughts on this subject (and are just off the top of my head, so rip it up...):
Of the first formulation:

4/ The network must draw material into itself faster than it loses material

This doesn't sound like it's necessary. What does the system care if it's losing material faster than it can draw it in? All that's required is for the correct sequence of events to happen.

Of the second formulation:

1/ A boundary is needed to separate life from non life.

Why do we need a line between life and non-life? Is it possible to even identify this line with what we know now? This seems like a life-fro-pomophric fallacy or something like that. It's based on a deconstruction of the polymer chain event leading up to recombination and finally to reproduction -- a piece of information that is irrelevant to the process, but only helps us to describe it.

On point 1/ Shapiro says

Life is distinguished by its degree of organisation, yet the second law of thermodynamics requires that the universe move in a direction in which disorder, entropy, increases, A loophole, however, allows entropy to decrease in a limited area, provided that a greater increase occurs outside the area.

I think what the metabolism first hypothesis attempts to abstract the basic functions that are necessary for life. For there to be life it is necessary that a unit or organism disobeys the second law locally. A characteristic that will distinguish it from its surroundings. Therefore there has to be some kind of boundary.

As for point 4/ this is a requirement for reproduction. Simply put an organism needs to grow before it divides. Otherwise you haven’t got reproduction, you just have a smaller bounded area than you had before. The implication is that there will probably be a size/complexity threshold below which functionality is lost.

Well, I'm glad at least it's being recognized that a spontaneous generation of RNA is not possible.

Not “not possible”

The chances against are immense..

That's not quite "not possible"

However the article contains a response from Steven Benner an RNA- first researcher.

The sugar ribose, the R in RNA, provides an object lesson in how a problem declared “unsolvable” may instead merely be “not yet solved”. Ribose long remained “impossible” to make by periodic synthesis…because it contains a carbonyl group - a carbon atom twice bonded to an oxygen atom.

…if borate…and organic compounds abundant in meteorites are mixed and hit with lightening, good quantities of ribose are formed from…and the ribose does not decompose.

The fact that such a simple solution can be found for a problem declared “unsolvable” does not mean that the first form of life definitively used RNA to do genetics. But it should give us pause when advised to discard avenues of research simply because some of their problematic pieces have not yet been solved.

I suppose for guys like Benner the objective is to find the solution, and the solution once found may be a lot simpler, and a lot more probable than the 18 hole golf course analogy suggests.

However, even if the likes of Benner discover how RNA was zapped into existence, I suspect there will be small molecules performing the function of a metabolism prior to hesitance of RNA.

[otseng]

Well, I'm glad at least it's being recognized that a spontaneous generation of RNA is not possible.

Not “not possible”

The chances against are immense..

That's not quite "not possible"

In my book for "a ball finding its way around all 18 holes of a golf course due to natural causes" would be classified as not possible.

But, I guess if given enough time, anything could be probable.

[ST88]

On point 1/ Shapiro says

Life is distinguished by its degree of organisation, yet the second law of thermodynamics requires that the universe move in a direction in which disorder, entropy, increases, A loophole, however, allows entropy to decrease in a limited area, provided that a greater increase occurs outside the area.

I think what the metabolism first hypothesis attempts to abstract the basic functions that are necessary for life. For there to be life it is necessary that a unit or organism disobeys the second law locally. A characteristic that will distinguish it from its surroundings. Therefore there has to be some kind of boundary.

This is a different definition for "life" than I have seen before, because I believe it is currently controversial whether viruses constitute life. But then viruses would have to be a later development, later than prokaryotes at least. If we can define life as a "network" of molecules that defies the second law, I would think that opens up whole new area of what life might be.

In order to maintain this view, however, I would have to submit that non-life polymer material reproduction is possible just through happenstance. I suppose if a carbon chain in some chemical/micro-physical way attracted enough material to produce an identical carbon chain alongside it -- and then for some reason let it go into the ether -- that could be reproduction without life. But that's pure speculation.

As for point 4/ this is a requirement for reproduction. Simply put an organism needs to grow before it divides. Otherwise you haven’t got reproduction, you just have a smaller bounded area than you had before. The implication is that there will probably be a size/complexity threshold below which functionality is lost.

This makes some sort of sense when you get down to the actual workings of the individual unit. But the fact that this is stated with respect to speed (gain is faster than loss) makes it sound suspicious.

[Furrowed Brow]

On point 1/ Shapiro says

Life is distinguished by its degree of organisation, yet the second law of thermodynamics requires that the universe move in a direction in which disorder, entropy, increases, A loophole, however, allows entropy to decrease in a limited area, provided that a greater increase occurs outside the area.

I think what the metabolism first hypothesis attempts to abstract the basic functions that are necessary for life. For there to be life it is necessary that a unit or organism disobeys the second law locally. A characteristic that will distinguish it from its surroundings. Therefore there has to be some kind of boundary.

This is a different definition for "life" than I have seen before, because I believe it is currently controversial whether viruses constitute life. But then viruses would have to be a later development, later than prokaryotes at least. If we can define life as a "network" of molecules that defies the second law, I would think that opens up whole new area of what life might be.

It seems to me the metabolism first hypothesis is an attempt to strip the concept of life down to the bear bones - and in so doing one might then stand a better chance of getting a clear view of what needs to come together, and a better appreciation of chemical interactions that might be bordering on life. With the RNA first hypothesis everything becomes focused on the creation of nucleotides. RNA provides a clear threshold but it's an all or nothing deal. Interestingly the article does not try to define how efficient a metabolism of small molecules has to be. With the metabolism first hypothesis I think the entry level of what counts as life becomes more vague. This not necessarily being a weakness of the hypothesis, but an acceptance that nature may be more fluid than our concepts that categorise nature.

Though the article does not draw the implication I'd say the 5 criteria are an attempt to draw up necessary, though perhaps not sufficient conditions for life. A bounded area that breaks the second law locally being necessary but not sufficient for life. This is "the metabolism first" hypothesis. Perhaps the collection of small chemicals performing the function of a metabolism as so defined, would if we found such an entity not look anything like life, or be something we would want to attach the ascription life. but that misses the point. It would be a collection of small molecules that functions like a metabolism.

In order to maintain this view, however, I would have to submit that non-life polymer material reproduction is possible just through happenstance. I suppose if a carbon chain in some chemical/micro-physical way attracted enough material to produce an identical carbon chain alongside it -- and then for some reason let it go into the ether -- that could be reproduction without life. But that's pure speculation.

The article is a bit short on detail in this respect. I get the impression that this is a new(ish) approach. One that has yet to recieve much research. I would not use the word speculation - I'd say its an hypothesis that requires further research.

As for point 4/ this is a requirement for reproduction. Simply put an organism needs to grow before it divides. Otherwise you haven’t got reproduction, you just have a smaller bounded area than you had before. The implication is that there will probably be a size/complexity threshold below which functionality is lost.

This makes some sort of sense when you get down to the actual workings of the individual unit. But the fact that this is stated with respect to speed (gain is faster than loss) makes it sound suspicious.

I would not get hung on this point. Put another way we could just say the bounded area must experience growth, or must increase in volume. I think it amounts to the same thing.

[QED]

If we can define life as a "network" of molecules that defies the second law, I would think that opens up whole new area of what life might be.

Don't you mean "appears to defy the second law". Your definition would seem to imply that life is non-existent! The transformation of energy from more to less usable forms is what characterizes life in general terms.

[ST88]

If we can define life as a "network" of molecules that defies the second law, I would think that opens up whole new area of what life might be.

Don't you mean "appears to defy the second law". Your definition would seem to imply that life is non-existent! The transformation of energy from more to less usable forms is what characterizes life in general terms.

Sorry, was that irony too dry?

[QED]

If we can define life as a "network" of molecules that defies the second law, I would think that opens up whole new area of what life might be.

Don't you mean "appears to defy the second law". Your definition would seem to imply that life is non-existent! The transformation of energy from more to less usable forms is what characterizes life in general terms.

Sorry, was that irony too dry?

Yes, I'm afraid it was. We have participants here who will greedily take advantage of such things.