Abiogenesis Update

[Skeptic Ginger]

I had a reason to review the current state of the science of abiogenesis recently and it seemed worth sharing.


2009:The Origin of Life
A case is made for the descent of electrons

In this article we present a view gaining attention in the origin-of-life community that takes the question out of the hatchery and places it squarely in the realm of accessible, plausible chemistry. As we see it, the early steps on the way to life are an inevitable, incremental result of the operation of the laws of chemistry and physics operating under the conditions that existed on the early Earth, a result that can be understood in terms of known (or at least knowable) laws of nature. As such, the early stages in the emergence of life are no more surprising, no more accidental, than water flowing downhill….

…Since 1953, we have found many of the same simple organic molecules in meteorites, comets and even interstellar gas clouds. Far from being special, then, the simplest of the molecules we find in living systems—life’s building blocks—seem to be quite common in nature…
…The next major advance came in the early 1980s, when Thomas Cech and Sidney Altman showed that some RNA molecules can act as enzyme-like catalysts. The frozen-accident argument was then replaced by a suggestive scenario in which something like RNA was assembled by chance, and was then able to fill twin roles as both enzyme and hereditary molecule in the run up to life…..

…Networks of synthetic pathways that are recursive and self-catalyzing are widely known in organic chemistry, but they are notorious for generating a mass of side products, which may disrupt the reaction system or simply dilute the reactants, preventing them from accumulating within a pathway. The important feature necessary for chemical selection in such a network, which remains to be demonstrated, is feedback-driven self-pruning of side reactions, resulting in a limited suite of pathways capable of concentrating reagents as metabolism does. The search for such self-pruning is one of the most actively pursued research fronts in Metabolism First research.
…At the very core of metabolism—the starting point for the synthetic pathways of all biomolecules—is a relatively simple set of reactions known as the citric acid cycle (also called the tricarboxylic acid cycle or the Krebs cycle). The cycle involves eight molecules, each a carboxylic acid (a molecule containing —COO groups). In most present-day life forms on Earth, the citric acid cycle operates to break organic molecules down into carbon dioxide and water, using oxygen to produce energy for the cell—in effect, ”burning” those molecules as fuel….The cycle can also operate in the opposite direction, taking in energy (in the form of high-energy electrons) and building up larger molecules from smaller ones….

…The important pattern to appreciate is that the primordial cycle provides the stability and starting materials that make an age of selection possible. We think it was at the transition to this stage that geochemistry began to take on the features of replication and selection recognized by Darwin as distinctive of life. After such an age has begun, it can maintain the complexity and diversity needed to explore for refinements—in efficiency, in adaptation to the geological environment or in specialized division of labor within communal systems. The same pattern repeated itself when the environment was changed by the accumulation of a destructive toxin—oxygen—that was produced by primordial organisms as a waste product. As they adapted, organisms did not abandon the reductive citric acid cycle, which we believe was the unique foundation for biosynthesis. Instead they acquired the ability to run the cycle in reverse, extracting energy from the breakdown of molecules similar to those the cycle formerly produced.

The science of our origins is moving right along. The Talk Origins page on abiogenesis was apparently last updated in 2001. The evolution deniers cite Talk Origins claiming there is no mechanism for 'selection' before the first complete organisms. But it appears there is evidence for a purely non-organic chemical 'selection' process that preceded RNA molecules and replication.

The authors of the above citation compare the problem to investigating the highway system. If you just took the current form, you might investigate asphalt, cars, oil and so on. Or you could instead start with mechanisms of movement and transportation. Then you might move on from walking to trails to horses and vehicles and roads and then to the highway system.

Instead of approaching the problem of abiogenesis by trying to find the mechanisms of replication, some scientists are looking at the chemical processes within the cell and looking for the pathway those process might have been involved in creating the first organic molecules. From there the line of inquiry is then to look at what might have happened next.

 

[Taffer]

Thanks, Skeptic Ginger (when did you change your name?), interesting stuff. I always enjoy your posts on this subject.

 

[JoeTheJuggler]

But it appears there is evidence for a purely non-organic chemical 'selection' process that preceded RNA molecules and replication.

The way I've often thought of it is if vessicles form and trap a bit of water and other molecules inside, they're already "selecting" for molecules that are more abundant. Some molecules will be more abundant based on non-organic chemical processes. (This might explain why amino acids are fairly ubiquitous.)

Of course, once you get a self-replicating molecule, that process would swamp selection based on those other processes.

I think the line between life and non-life will become blurrier and blurrier. It's all really just chemical/mechanical processes. There's nothing magical about life.

 

[John Hewitt]

I had a reason to review the current state of the science of abiogenesis recently and it seemed worth sharing.


2009:The Origin of Life
A case is made for the descent of electrons

The science of our origins is moving right along. The Talk Origins page on abiogenesis was apparently last updated in 2001. The evolution deniers cite Talk Origins claiming there is no mechanism for 'selection' before the first complete organisms. But it appears there is evidence for a purely non-organic chemical 'selection' process that preceded RNA molecules and replication.

The authors of the above citation compare the problem to investigating the highway system. If you just took the current form, you might investigate asphalt, cars, oil and so on. Or you could instead start with mechanisms of movement and transportation. Then you might move on from walking to trails to horses and vehicles and roads and then to the highway system.

Instead of approaching the problem of abiogenesis by trying to find the mechanisms of replication, some scientists are looking at the chemical processes within the cell and looking for the pathway those process might have been involved in creating the first organic molecules. From there the line of inquiry is then to look at what might have happened next.

Could you please give the source of these quotations.

 

[Cainkane1]

If it happened here it happened elsewhere. Who wants to go to Europa with me?

 

[TheDoLittle]

If it happened here it happened elsewhere. Who wants to go to Europa with me?

No, thanks. As an American, I can't imagine staying at the ultimate hostile Europian Hostel!

 

[blobru]

Could you please give the source of these quotations.

The line-break might've caused a glitch in the OP's. Here's the fixed link:

Origin of Life: A case for the descent of electrons.

 

[Skeptic Ginger]

The line-break might've caused a glitch in the OP's. Here's the fixed link:

Origin of Life: A case for the descent of electrons.

Thanks. I usually check my links but not always.

 

[Skeptic Ginger]

The way I've often thought of it is if vessicles form and trap a bit of water and other molecules inside, they're already "selecting" for molecules that are more abundant. Some molecules will be more abundant based on non-organic chemical processes. (This might explain why amino acids are fairly ubiquitous.)

Of course, once you get a self-replicating molecule, that process would swamp selection based on those other processes.

I think the line between life and non-life will become blurrier and blurrier. It's all really just chemical/mechanical processes. There's nothing magical about life.

What I found especially interesting was the trend in the attack on evolution theory by the IDer/Creationists. Since their attacks are always "that's impossible" rather than evidence based, I have read a few times now that because natural selection can't occur until you have a life form, abiogenesis is impossible.

But I see natural selection pressures as not specifically related to a living organism surviving to reproduce. Rather, I view natural selection as anything that amplifies a gene sequence. It seems a no brainer you might also have selection pressures amplifying an inorganic molecule in transition to creating an organic one, amplifying the organic molecule in transition to becoming replicating RNA and so on.

 

[Skeptic Ginger]

Thanks, Skeptic Ginger (when did you change your name?), interesting stuff. I always enjoy your posts on this subject.

Thanks for the compliment. My name was getting confused with another forum member so I changed it.

 

[JoeTheJuggler]

But I see natural selection pressures as not specifically related to a living organism surviving to reproduce. Rather, I view natural selection as anything that amplifies a gene sequence. It seems a no brainer you might also have selection pressures amplifying an inorganic molecule in transition to creating an organic one, amplifying the organic molecule in transition to becoming replicating RNA and so on.

I agree.

We shouldn't transfix on survival and death of organisms as the sole objects of selection. (Simple archaebacteria don't really die anyway, since the result of cell division for them are two "daughter cells" that replace the one parent cell.)

Instead, I think the emphasis should be on relative abundance. I like to think of a vessicle trapping stuff in water as the selector that gives you a random sample of the relative abundance of molecules in the water.

When the vessicle grows to a microtubule and then breaks off ("reproduces") the more abundant molecules will again be selected. But that's just a convenient way of thinking about it for me. You could say the same thing about any random sample of the water even without anything like a proto-cell.

I think we'll find that there is no hard and fast line between abiotic chemistry and life. And I think this blurring is also why there won't likely be a newspaper headline saying "Life on Mars Discovered" (unless, of course, we find something readily recognizable, like a cell with organelles) or "It's Certain: There Is No Life on Mars". Instead we'll just get more and more confident in one or the other conclusion.

ETA: And the ID/Creationist argument you mentioned is at heart an argument from ignorance. Just because we once didn't know how non-life could evolve into life (that is, how evolution works on non-biotic chemistry) doesn't in any way support their explanations.

 

[Soapy Sam]

... it appears there is evidence for a purely non-organic chemical 'selection' process that preceded RNA molecules and replication.

SG-
Given the carboxylic acids obviously are organic chemicals in the strict sense, you might want to find alternatives to the highlighted phrase for use with creationists. They're confused enough already. In fact, avoiding the word "organic" altogether is usually a timesaver when discussing abiogenesis.

 

[Skeptic Ginger]

SG-
Given the carboxylic acids obviously are organic chemicals in the strict sense, you might want to find alternatives to the highlighted phrase for use with creationists. They're confused enough already. In fact, avoiding the word "organic" altogether is usually a timesaver when discussing abiogenesis.

Being in the infectious disease field and not in the molecular chemistry field, such distinctions are not a concern to me. Most people (assuming biochemists are in the minority) may know organic and inorganic as names. The lay public if they have at least pondered abiogenesis, are likely to know one needs to go from inorganic to organic to living organisms. I doubt many people have much interest in the details of the molecules.

I agree with you that accuracy is important. I often distinguish between a "challenge dose" of Hep B vaccine vs a "booster dose" of vaccine even though the vaccine dose itself is the same. But I do that because I have a goal in mind. I don't want to add to the erroneous belief one needs Hep B vaccine booster dose and I know people recall things differently years after the fact. I'm hoping by calling it a "challenge dose" years later people will not have modified their memories and come to believe booster doses are needed. So I'd expect to speak the details correctly, for example, if I were talking to biochem students. But I don't see why such a detail would ever matter to a lay person simply pondering the evidence for or mechanism of abiogenesis.


So I'll accept your advice if you would please explain to me the specific goal you have in mind. Confusing Creationists further isn't clear to me without a bit more specifics. Technical correctness can sometimes get in the way of effective communication. A lot of skeptics/science types don't understand that concept and see technical errors as very important when such errors may not be depending on the folks you are communicating with.


Dang, my edit disappeared. Trying again....

I would think molecular details matter when you are communicating with a group like biochem students. But I don't think such pedantic issues matter if you are merely communicating with laypersons contemplating abiogenesis.

 

[Skeptic Ginger]

duplicate deleted

 

[Sideroxylon]

What I found especially interesting was the trend in the attack on evolution theory by the IDer/Creationists. Since their attacks are always "that's impossible" rather than evidence based, I have read a few times now that because natural selection can't occur until you have a life form, abiogenesis is impossible.

But I see natural selection pressures as not specifically related to a living organism surviving to reproduce. Rather, I view natural selection as anything that amplifies a gene sequence. It seems a no brainer you might also have selection pressures amplifying an inorganic molecule in transition to creating an organic one, amplifying the organic molecule in transition to becoming replicating RNA and so on.

It's been a while since I read 'The Selfish Gene', but didn't Dawkins describe selection working on crystals?

Thanks for the posts - I'm enjoying the read.

 

[bokonon]

Skeptic Ginger -

Our "DNA - Proof of God?" thread over in R&P is becoming more sciencey and less philosophical, so I thought I'd see if maybe it might make more sense to continue it here. I re-read the article you linked, and I understand how, if that line of inquiry turns out to provide a comprehensive explanation for abiogenesis, it might be possible to find life beginning fairly commonly throughout the universe.

Even in that article, though, the authors write

Whereas most scientists believe, on the basis of Cech and Altman’s work, that life went through an early RNA-dominated phase (dubbed “RNA World”), the “RNA First” scenario has again a quality of frozen accident.

Certainly, even more extreme versions of "frozen accident" have not been falsified. It remains on the table as a viable hypothesis, though it is not an especially promising direction for research, and I doubt many scientists today are pursuing it.

Of RNA First or Metabolism First, I'd place my money on MF too, but even there one has to propose a way to get from metabolism to RNA. That's a big step. Simply proposing MF can provide a possible framework, but the devil is still in the details.

What if a critical step requires a very rare substrate, which surfaced like a diamond four billion years ago and then was once again subsumed? That scenario, or dozens of others like it, could make life a rare and unlikely occurrence, even if MF turns out to be the method used (and I think that's likely).

I'm not even sure if any researcher has managed to get a Krebs cycle working outside a cell, and it would seem to me that that would be a necessary first step toward validating the MF framework. If anyone else is more informed, a link would be much appreciated.

 

[Skeptic Ginger]

I posted an answer in the other thread before reading your post here, so take that one as applying to a different aspect of the discussion.

In the meantime, I found this fascinating article that I believe contributes a lot to the abiogenesis questions, including some facts about viruses I was totally unaware of.

Astrobiology Field Reports: Are Canadian Lake Structures Biological or Chemical?

Okay, cool, you may be thinking. Advanced DNA work done in the field. But why viruses? Surely no-one thinks viruses are building the Pavilion Lake microbialites.

"Viruses amplify life," Suttle says. "For every living organism that you find, there's many, many more viruses that infect that organism." On average, there are a million bacteria in a milliliter of water. And 10 million viruses.

What's more, although the genome of an individual virus is relatively small, "Collectively, viruses probably have about 90 percent more genetic information than we find in the three domains of life" combined, Suttle says. Let's go over that again: 90 percent of the genes found in viruses are not found in cellular organisms.

For example, "Other lifeforms only have double-stranded DNA. Viruses have double-stranded DNA, single-stranded DNA, positive-sense single-stranded RNA, negative-sense single-stranded RNA, double-stranded RNA. They have every possible combination of nucleic acids for passing along genetic information." They're quite versatile.

So if you want to look for life on another world, you'd do well to learn how to hunt for viruses, Suttle suggests. "They're like a biosignature for other living organisms."

Work on the smallest number of genes needed to make up a life form have used viruses. I think they are down to 9 genes. But in general, viruses are viewed as needing cells to replicate. But that doesn't mean it was always so. Nor does it mean that viruses don't exist which replicate without parasitic activity. It could just be that viral pathogens or viruses that have come to our attention use cells to reproduce.

This research suggests that maybe there are trillions or more viruses out there that replicate outside of cells. Maybe there are RNA fragments still around that we've yet to detect which reflect a step in the abiogenesis process and we just didn't know about yet.


This companion story was also interesting but less directly so regarding the abiogenesis process:

What Do You Call a Microbialite?.

 

[shadron]

The way I've often thought of it is if vessicles form and trap a bit of water and other molecules inside, they're already "selecting" for molecules that are more abundant. Some molecules will be more abundant based on non-organic chemical processes. (This might explain why amino acids are fairly ubiquitous.)

Of course, once you get a self-replicating molecule, that process would swamp selection based on those other processes.

I think the line between life and non-life will become blurrier and blurrier. It's all really just chemical/mechanical processes. There's nothing magical about life.

This kind of reminds me of cdk007's video about simulating clock evolution. The very first clocks that just happen to come together at random are simple pendulums; Once there is a mechanism for them to work against the randomness of their lives they immediately take over the environment they are in. cdk007 points out, as sort of an after-thought, that each of the stages of improve clocks takes over very quickly from the previous stage, and the possibility of finding "transitional" clocks (those with the improved works but not yet as accurate as older clocks) in any kind of fossil strata of any transitional age would be exceedingly small.

cdk007's video about this is here:

 

[Skeptic Ginger]

....
Certainly "frozen accident" would not be inevitable. RNA First would probably not be inevitable. Metabolism First might or might not be inevitable, but the burden of proof is on the one making the positive claim, and in my opinion the evidence is nowhere near there.

And until the real answer is known, it may still turn out to be "none of the above".

If you'd prefer to continue this conversation in your "Science and Technology" thread, we can do that. As I said when I revived it today, the recent discussion here has seemed to center less on philosophy than on science.

I'm not familiar with the "frozen accident".

I'm convinced abiogenesis was inevitable given the composition and conditions on our planet at the time it occurred, and, think it is inevitable that said conditions are not unique to our planet. I think it is much more likely that abiogenesis is not so unique as to be a one time event in the entire Universe.

I fail to see why the default position is superior, that unless demonstrated otherwise, we should go with the one time event. Since I reject magical and god explanations for reasons I've defended in other threads, we can say that abiogenesis occurred once. But once again, it seems most rational thinkers consider only the narrow point of view that this is all the information we can put into our conclusion basis.

How many other events in the Universe have we observed that were one time events? I can't think of any.

The composition of the planets and other bodies in the Universe is fairly consistent. Why shouldn't that support the conclusion that a one time abiogenesis event is much less likely than that we should find the conditions and events to not be a one time event?

 

[bokonon]

I'm not familiar with the "frozen accident".

It's mentioned on page 2 of your original link:

The essential legacy of the Primordial Soup was twofold: It simplified the notion of the origin of life to a single pivotal event, and then it proposed that that event—the step that occurred after the molecules were made—was a result of chance. In the standard language, life is to be seen, in the end, as a “frozen accident.” In this view, many fundamental details about the structure of life are not amenable to explanation. The architecture of life is just one of those things.

I fail to see why the default position is superior, that unless demonstrated otherwise, we should go with the one time event.

"Law of parsimony" and that's where the evidence points today.

There is no indication that life arose more than once on earth. All terrestrial life uses DNA for reproduction and as a template for protein synthesis. All proteins are built from left-handed amino acids; all cells use right-handed sugars for energy.

There is no evidence that life arose outside of life on earth. Products of metabolism which would suggest photosynthesis are not seen in the spectrographs of any of the heavenly bodies we've analyzed.

Simply assuming abiogenesis happened elsewhere is more than a leap of faith, it's a hop (simple chemical reactions are all that's required for abiogenesis / invariably result in abiogenesis), skip (those chemical reactions are found on other planets), and a jump (those planets are sufficiently like earth to allow life to form) of faith.

How many other events in the Universe have we observed that were one time events? I can't think of any.

We don't know of any other Earth-like planets. No other planets in our solar system have a single large moon, or an atmosphere which contains water vapor. I'm a one-time event; so are you.