How one defines life influences origin view?

[Generally Rational]

It occurred to me in my post to the "Why do you believe naturalism to be the best explanation for our existence" thread, that how one defines life might influence what mechanism one sees as being most important in its origin.

I think it has influenced biologist and geneticist Jack Szostak, but more on that below.

http://www.jbsdonline.com/mc_images/category/4317/2-szostak-jbsd_29_4_2012.pdf

You might favor "Genes First" because you see as most important the self-replication through DNA of current surviving descendants of an unbroken chain of replicators that has lasted billions of years. How those replicators have managed their energy use every moment during all that time is incidental.

You might favor "Metabolism First" if you see the ability to manage energy as being what separates living from not living. Life that manages energy and increases entropy around itself while perpetuating order within is still living even if it never replicates. The cost of never replicating is that the life is most likely to leave no evidence of its existence. A replication system has to be evolved to have sentient descendants around to discuss the origin question.

This was written as a rebuttal to Szostak:

http://www.science20.com/gadfly/jack_szostak_and_origin_life-87085

My own view is that biochemists (and geochemists and even chemists and physicists) have more to contribute to the discussion of life substantially before LUCA than biologists do. Biologists would contribute more by doing an exhaustive comparison of bacteria and archaea to pin down the nature of LUCA so we have a fixed target for figuring out how that stage was reached.

Oh, yes, if how I worded the comparison paragraphs didn't make it clear, I've become a committed Metabolism Firster under the influence of the biochemist Nick Lane. Apparently, the physicist and BBC documentary series host Brian Cox has also since he put so much effort in explaining the concept in the first episode of "Wonders of Life".

I would really be interested in cogent rebuttals, particularly if you have read "Life Ascending" or "Power, Sex, Suicide" or any of the other pertinent literature.

 

[ynot]

Q - What came first, the chicken or the egg?
A - Neither, it was the chegg.

 

[aggle-rithm]

Metabolism probably came first, many, many times. It took some form of replication to allow it to become an ongoing thing.

IMHO.

 

[Dancing David]

Metabolism, as in set catalyzing sets

 

[ehcks]

Metabolism, as in set catalyzing sets

Isn't the set itself the gene? The first self-replicating molecules were their own genetic code? Or is that stretching the definition of "gene?"

 

[Generally Rational]

Metabolism probably came first, many, many times. It took some form of replication to allow it to become an ongoing thing.

IMHO.

Exactly. The only "It only had to happen once" thing is much more sensible in the context of a continuous ongoing system.

The declaration that "metabolism first" does not allow for evolution was premature.

http://www.sciencedaily.com/releases/2010/01/100108101433.htm

What was evolving was decreasing dependence on the system for resources and catalysis. As has been pointed out by quite a few people, increasing independence of the system would have allowed precursors to LUCA to exist in more marginal parts of the system with less competition.

RNA World(s) existed, but were contained in places like the *many* alkaline hydrothermal vents systems that would have existed, or perhaps some other area with ongoing geochemistry for which strong evidence has not yet been discovered.

I'm not saying we know definitely how anything exactly happened, but the general outline emerges once you assume a geochemical system, complete with the proton gradient life depends on today, kicked off the start of a chemical evolution towards LUCA.

 

[Dancing David]

Isn't the set itself the gene? The first self-replicating molecules were their own genetic code? Or is that stretching the definition of "gene?"

I would call it a stretch, because the crucial step is containment of SCS in the lipid layer or something like a cell wall, that can be maintained by the SCS.

Otherwise they just kind of disperse and clump together randomly.

 

[Dinwar]

I'm not saying we know definitely how anything exactly happened, but the general outline emerges once you assume a geochemical system, complete with the proton gradient life depends on today, kicked off the start of a chemical evolution towards LUCA.

Just wanted to point out that LUCA can't be assumed to be the first life. It's certainly very early in life, but it's equally almost certainly not the first. LUCA is Last Universal Common Ancestor. That means that it's the LAST one; there could be innumerable previous common ancestors.

This same error crops up when discussing Mitochondrial Eve. ME isn't the first human, and isn't even generally considered to be anywhere close to it. She's merely the LAST human from which we all descend. She was around humans, had human ancestors, had human relatives, and if you went back in time to meet her you'd never be able to identify her. She's merely unique in a statistical sense. Same with LUCA. There was almost certainly life before LUCA, life all around LUCA, and if you saw LUCA on a microscope slide you'd never know. It's only statistics that make LUCA special, not circumstances.

My point is, LUCA almost certainly had undergone a period of evolution. How long is unknown, but LUCA and abiogenesis aren't related, outside of the fact that abiogenesis needed to occur for LUCA to exist.

The first self-replicating molecules were their own genetic code?

Depends on your definition of "genetic". If you mean "genes", then you're begging the question. If you mean the old definition (dealing with hereditary), then possibly. There are non-DNA/RNA self-replicating molecules. And I mean that as, we have them today, we can see them in the lab, or even die from some of them if we don't cook our food well enough. It's not unlikely that similar molecules were around back at the beginning.

Q - What came first, the chicken or the egg?

I once answered this question in depth. Short answer? The egg. Depending on your definition of "egg", it's by anywhere from 200 million years to over half a billion years.

Otherwise they just kind of disperse and clump together randomly.

Not necessarily. Certain crystals (like clays and calcite) can, due to the arrangement of the atoms, concentrate the proper molecules. It's one proposed mechanism for how life adapted to only use molecules of a certain orientation--that orientation dictates which crystal facets the molecule will be attracted to.

 

[yomero]

At the ''Naturalism etc..'' thread I tried to address Gibhorn's reservations on a naturalistic origin of life:

_______________________________________________________________________________
[QUOTEYomero]There are several competing hypotheses on the origin of life. Any of them demonstrates that the first organisms on earth could arise by entirely natural means. One is the very legitimate ''RNA World'' explanation, accepted today by a large number of scientists. On the Sept. 2009 issue of Scientific American there is an article by Alonso Ricardo and Nobel prize winner J.W.Szostak titled ''The Origin of Life on Earth.'' Google ''Ricardo and Szostak origin of life on earth,'' it should come as the first result. The article is so well written and easy to read that a layman may understand it. Thus, I feel emboldened to attempt a summary.

In other posts Gibhor has correctly pointed out that proteins are essential for DNA's functioning. Those proteins are manufactured acccording to sequences in DNA. This apparent circular paradox disappears when we consider that another genetic molecule, RNA, can form spontaneously. RNA can replicate, carry genetic ''information'' and act as a catalyst.

RNA consists of a long string of nucleotides composed of a sugar (ribose), a phosphate and a nucleobase (A,G,C and T). Although ribose and the nucleobases can independently assemble spontaneously, there is a problem in that an independent ribose molecule is unstable. It won't combine with a phosphate and a base to form a nucleotide. John Sutherland et al found in 2009 a possible solution to ribose's inestability. Rather than attempting to combine a separate ribose, a separate base and a phosphate, they started by mixing cyanide, acetylene and formaldehyde along with phosphate. This produced a small stable molecule, 2-aminooxazale which can be considered as a fragment of a nucleobase combined with a fragmment of a sugar. An accumulation of those molecules and further chemical reactions would form a molecule with a complete sugar and a complete base. This process will form nucleotides of different varieties, but exposure to UV light destroys the ''incorrect'' types, leaving the ''correct'' ones. Minerals present in clay would then facilitate the linking of these nucleotides leading to the formation of long strands of RNA.

When a strand of RNA is free from the clay, it and water are encapsulated by a membrane formed by fatty acids. This can be considered a proto-cell. On a relatively cool environment, the chain of nucleotides inside the proto-cell forms its complementary chain from free nucleotides entering it. The double helix is now formed. By convection, the proto-cell reaches a warmer enviroment. Heat causes the strands of RNA to separate. The membrane increases its volume as it incorporates new lipid molecules, and divides into 2 daughter proto-cells, each with its copy of RNA. A portion of RNA will not go to form the helix. Some of it will fold into complex shapes and act a a catalyst (ribozyme) to speed up reproduction, to facilitate the intake of nutrients and to strengthen the membrane.

The next step would be the formation of proteins according to ''instructions'' present in the sequence of nucleobases on RNA. Ribosymes could have catalyzed those reactions. (My opinion: A sequence that codifies for a more efficient protein that aids in the survival of the proto-cell will reproduce more, and pass on that ''information'' to its daughters.) Proteins are more efficient catalysts than ribozymes and took over their work. These proteins are then able to control the manufacture of DNA which is more stable than RNA.

The result would be a modern cell with DNA ''codifying'' for proteins and capable of mostly faithful replication; proteins carrying out the cell's functions and a selective membrane enclosing the cell.

The authors do not claim that this is the absolute truth. They present one hypothesis of how the origin of life could have started. None of the steps mentioned was pulled from a magician's hat, all of them have been shown to be possible naturally. Perhaps this wasn't the way life started. But this article proves there are natural paths that could lead to the origin of life.
________________________________________________________________________________

[/QUOTE]

That was the way I understood the Ricardo and Zsostak article. In my layman's perspective, the article offers very convincing support for the ''RNA first'' hypothesis. What does anyone else think? Laymen or scientists.

 

[Generally Rational]

Just wanted to point out that LUCA can't be assumed to be the first life. It's certainly very early in life, but it's equally almost certainly not the first. LUCA is Last Universal Common Ancestor. That means that it's the LAST one; there could be innumerable previous common ancestors.

It may surprise you that I knew all that. It was not an error. It was incomplete.

My assumption has always been that whatever geochemical system, be it an alkaline hydrothermal vent system or something else, that brought forth life had LUCA as its LAST dependent. Bacteria and Archaea were the ones stopped depending on it for anything but raw resources, and eventually not even that.

I was/am assuming an ever increasing complexity of cooperative chemical systems leading up to LUCA, and that includes genetic mixing as well as competition.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC148579/

"However, several core components of the bacterial replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic replication apparatus. This is in sharp contrast to the principal proteins involved in transcription and translation, which are highly conserved in all divisions of life."

Lane suggests that the current life-form LUCA most resembles is a retrovirus, which is about as complex a life-form you can have with genetic system at least partly composed of RNA, given RNA's instability compared to DNA.

Certainly this view covers where viruses come from without invoking reductive evolution.

 

[Generally Rational]

That was the way I understood the Ricardo and Zsostak article. In my layman's perspective, the article offers very convincing support for the ''RNA first'' hypothesis. What does anyone else think? Laymen or scientists.

One, RNA first is an elaboration on Genes first, since the first genes were most certainly contained in RNA.

Two, it is not actually probable for the entire ocean to become an RNA world, nor is it necessary. Countless RNA Worlds could have formed inside the geochemical systems that would have supplied the free energy necessary for the unending battle against entropy.

But it is certainly true that whatever the origin it was not necessary for any supernatural being to have any part in it.

 

[Loss Leader]

As you define it above, genes are a thing but metabolism is a process. So, I'd expect the process came first.

 

[Dinwar]

It may surprise you that I knew all that. It was not an error. It was incomplete.

Not really. It's just that I thought the issue deserved to be explained in a bit more detail.

My assumption has always been that whatever geochemical system, be it an alkaline hydrothermal vent system or something else, that brought forth life had LUCA as its LAST dependent.

Possibly. But it's not something I'm willing to assume without substantially more evidence than I've seen. Mitochondrial Eve wasn't the last generation in Africa, and there's no reason to suspect that she was the last generation before people began to move out of Africa. Given that horizontal gene transfer is far easier for single-celled organisms, it's entirely plausible that LUCA occurred well after that final step in the origin of life.

Certainly this view covers where viruses come from without invoking reductive evolution.

I'm not sure why you think that's beneficial. Reductive evolution is not uncommon--parasites frequently undergo it. Also, if you're right and LUCA was both the last of the ancestral form of life and it was essentially a virus, how did the virus procreate? They can't do so without a host. Also, why does all life except certain viruses have DNA? If LUCA was RNA-based I'd expect at least a few RNA-based organisms to be running around (viruses don't necessarily count--again, reductive evolution is a viable pathway for evolution).

 

[yomero]

One, RNA first is an elaboration on Genes first, since the first genes were most certainly contained in RNA.

Two, it is not actually probable for the entire ocean to become an RNA world, nor is it necessary. Countless RNA Worlds could have formed inside the geochemical systems that would have supplied the free energy necessary for the unending battle against entropy.

But it is certainly true that whatever the origin it was not necessary for any supernatural being to have any part in it.

Although the Ricardo and Szostak article is very lucidly written, there are several blank spaces in my understanding of abiogenesis. The authors mention proximity to volcanoes and the intake of nutrients through the proto-cell membrane as sources of energy. My main doubt is this: How is the ''economy'' of the energy managed? How is it stored to be used when convenient? Was there a burst of chemical activity when energy was available followed by a dormant stage? Did most of the chemical reactions take place spontaneously without need of external energy? Is ''metabolism first'' the only way out of this problem?

 

[Dinwar]

How is the ''economy'' of the energy managed?

Is there evidence that it was? This may be something that evolved later.

How is it stored to be used when convenient?

Again, this could easily be something that evolved laterr. If you're in a situation where you don't NEED to store energy, such a storage mechanism is costly and won't increase your fitness.

Was there a burst of chemical activity when energy was available followed by a dormant stage?

Not likely if life started near undersea volcanoes. It's more probable that there was a constant influx of chemical activity. The type of volcanism you get underwater is called mafic (magnesium and iron rich). That type of magma tends to ooze, rather than explode.

Incidently, this is why I tend to ignore biologists talking about abiogenesis. To understand abiogenesis, you need to understand biology, AND chemistry, AND minerology, AND volcanology (at least a bit), AND..... To be fair, I tend to ignore most paleontologists talking about this stuff, too, because they ignore the volcanology and chemistry aspects. You miss any one of these components, and you cannot build a model for how life arose. It's like building a car without pistons.

Did most of the chemical reactions take place spontaneously without need of external energy?

Depends on your definition. The issue is, phase changes require energy to at least get started; the questoin is, did that energy come from the heat of the water, or from the organisms, or from somewhere else?

Is ''metabolism first'' the only way out of this problem?

No, it's just one of the best-studied options.

 

[yomero]

Thank you for your response, Dinwar. I was guessing that the answers would be somewhat like your post. As I understand, there is still no definite model that explains the origin of life. The following years should be very interesting.

 

[Generally Rational]

Given that horizontal gene transfer is far easier for single-celled organisms, it's entirely plausible that LUCA occurred well after that final step in the origin of life.

True except the only thing Bacteria and Archaea cell membrane and walls have in common is that they're made out of lipids. Easier for that to come about if LUCA only had a simple lipid membrane to hold itself together and the two progeny developed their own more complex structure in the process of gaining independence.

I'm not sure why you think that's beneficial. Reductive evolution is not uncommon--parasites frequently undergo it. Also, if you're right and LUCA was both the last of the ancestral form of life and it was essentially a virus, how did the virus procreate? They can't do so without a host. Also, why does all life except certain viruses have DNA? If LUCA was RNA-based I'd expect at least a few RNA-based organisms to be running around (viruses don't necessarily count--again, reductive evolution is a viable pathway for evolution).

A Retrovirus needs a living host now, but if it's living a semi-autonomous existence, in say a system of vent micro-pores, it might reproduce by grabbing free amino acids.

As for switching over to being phages depending on bacteria and archaea, the latter would have been living in the vents for a good long while. There would have been plenty of opportunity to learn how. Besides, the gigantic pool of genetic material would have been waging a running battle against each for reproductive success long before that point. Hijacking another's setup might have been a tactic before there was anything as complex as the two prokaryotes.

But I'm hardly an expert. This was just the interpretation I developed while reading the first two chapters of Life Ascending, as well a few other papers.

Unfortunately, we're a long way from being able to test most of these ideas. The steps you'd have to eliminate bacteria and archaea from any large scale experiment to replicate the Hadean environment staggers the imagination.

 

[Soapy Sam]

Go to Venus.

(nb. This is a joke).

 

[Generally Rational]

Is there evidence that it was? This may be something that evolved later.

Again, this could easily be something that evolved laterr. If you're in a situation where you don't NEED to store energy, such a storage mechanism is costly and won't increase your fitness.

Hmmm, I think I'll trust the words of biochemists first.

Chemiosmosis is NOT an affectation. It's a basic foundation of life. It's dimly possible for carbon/water based life on other planets to come into being by precisely matching energy producing reactions with energy using reactions, but I think they're more likely to use gradients across a membrane and an a universal energy currency like we do even if the details will be substantially different.