Calilasseia: 78 Papers on Abiogenesis

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Re: Calilasseia: 78 Papers on Abiogenesis

#141  Postby byofrcs » Jan 10, 2012 2:19 pm

rainbow wrote:
byofrcs wrote:
rainbow wrote:What has that paper to do with Abiogenesis?

Do you know what abiogenesis means ?

Yes.
Please answer my question.


You know the answer; understanding abiogenesis is finding the pathway out from chemistry and back from biology. This is working back from biology. It clearly states that is showing how so-called complexity can be evolved in molecular machines.
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Re: Calilasseia: 78 Papers on Abiogenesis

#142  Postby Rumraket » Jan 10, 2012 2:42 pm

byofrcs wrote:
rainbow wrote:
byofrcs wrote:
rainbow wrote:What has that paper to do with Abiogenesis?

Do you know what abiogenesis means ?

Yes.
Please answer my question.


You know the answer; understanding abiogenesis is finding the pathway out from chemistry and back from biology. This is working back from biology. It clearly states that is showing how so-called complexity can be evolved in molecular machines.

I have to say I don't think this is particularly relevant to abiogenesis either. Sure, we can work back through evolution, but only until a certain point. That point is the remaining remnants of the RNA world and how it came about, or even if it was the first genetic system, isn't obvious by any stretch. The article you link "just" talks about how a multi-protein molecular machine evolved, once a DNA-based genetic system is in place. Don't get me wrong, it's an extremely interesting article, but I don't see how gene-duplication followed by cooptation and subfunctionalization of coded proteins explain anything about how the first self-replicating protobiont came into existence.

A much more interesting paper on that subject, and just as new, is this one:
http://www.biology-direct.com/content/7/1/1/abstract
Evolution before genes
Vera Vasas, Chrisantha Fernando, Mauro Santos, Stuart Kauffman and Eors Szathmary
Biology Direct 2012, 7:1 doi:10.1186/1745-6150-7-1
Published: 5 January 2012

Abstract (provisional)
Background
Our current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate') of chemicals that predated fully-fledged cell-like entities seems to be farfetched to most scientists today. However, this is exactly the kind of scheme we propose for how Darwinian evolution could have occurred prior to template replication.

Results
We cannot confirm previous claims that autocatalytic sets of organic polymer molecules could undergo evolution in any interesting sense by themselves. While we and others have previously imagined inhibition would result in selectability, we found that it produced multiple attractors in an autocatalytic set that cannot be selected for. Instead, we discovered that if general conditions are satisfied, the accumulation of adaptations in chemical reaction networks can occur. These conditions are the existence of rare reactions producing viable cores (analogous to a genotype), that sustains a molecular periphery (analogous to a phenotype).

Conclusions
We conclude that only when a chemical reaction network consists of many such viable cores, can it be evolvable. When many cores are enclosed in a compartment there is competition between cores within the same compartment, and when there are many compartments, there is between-compartment competition due to the phenotypic effects of cores and their periphery at the compartment level. Acquisition of cores by rare chemical events, and loss of cores at division, allows macromutation, limited heredity and selectability, thus explaining how a poor man's natural selection could have operated prior to genetic templates. This is the only demonstration to date of a mechanism by which pre-template accumulation of adaptation could occur. Reviewers This article was reviewed by William Martin and Eugene Koonin.

This paper seems to constitute a much needed first step in trying to elucidate how and if autacatalytic sets(which is extremely relevant to many forms of metabolism-first scenarios) can undergo darwinian evolution. Hitherto produced research seemed to have hinted that the types tested, couldn't, but now it seems there are some interesting mechanics at play that will allow it to work anyway, among them is the requirement of compartmentalization(which, I might add, is supplied by the hydrothermal, metabolism-first, Iron-Sulfur version of abiogenesis I have alluded to at various other places).
I can't wait to see what comes up next, given this final remark by the author in response to one of the reviewers:
Authors’ response:
An understanding of the kinds of chemical organization that could sustain heredity is logically anterior to the problem of the stability of such organizations. We are planning to investigate the selective origin of template replication within such a framework in the near future. We also think that the origin of the genetic code is a considerably later step (as advocated by one of the authors): an interim (albeit dirty) RNA world must have prevailed, simply as a consequence of the opportunistic nature of evolution by natural selection.
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Re: Calilasseia: 78 Papers on Abiogenesis

#143  Postby rainbow » Jan 10, 2012 3:43 pm

Thanks, Rumraket.
After a short glance at the paper it appears to be purely theoretical, and no actual chemistry was carried out.
Now if they could construct such a viable core, and measure adaptation and Darwinian evolution - then we'd really have something.
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Re: Calilasseia: 78 Papers on Abiogenesis

#144  Postby Rumraket » Jan 10, 2012 3:59 pm

rainbow wrote:Thanks, Rumraket.
After a short glance at the paper it appears to be purely theoretical, and no actual chemistry was carried out.
Now if they could construct such a viable core, and measure adaptation and Darwinian evolution - then we'd really have something.

Yes, the paper is on conceptual mathematical treatment, the details of which is unfortunately a bit out of my league. The authors seem to be trying to work out why previously tested autocatalytic sets didn't seem capable of evolution, in order to find out on that basis, what could evolve.
I like the biology-direct publisher alot because you can see the discussion with the reviewer, where different points are reflected back and forth and you get a better understanding of the contents.
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Re: Calilasseia: 78 Papers on Abiogenesis

#145  Postby rainbow » Jan 11, 2012 1:33 pm

Rumraket wrote:
rainbow wrote:Thanks, Rumraket.
After a short glance at the paper it appears to be purely theoretical, and no actual chemistry was carried out.
Now if they could construct such a viable core, and measure adaptation and Darwinian evolution - then we'd really have something.

Yes, the paper is on conceptual mathematical treatment, the details of which is unfortunately a bit out of my league. The authors seem to be trying to work out why previously tested autocatalytic sets didn't seem capable of evolution, in order to find out on that basis, what could evolve.
I like the biology-direct publisher alot because you can see the discussion with the reviewer, where different points are reflected back and forth and you get a better understanding of the contents.

It is refreshingly critical of the failures of prior abiogenesis experimentation.
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Re: Calilasseia: 78 Papers on Abiogenesis

#146  Postby Rumraket » Jan 11, 2012 1:55 pm

rainbow wrote:
Rumraket wrote:
rainbow wrote:Thanks, Rumraket.
After a short glance at the paper it appears to be purely theoretical, and no actual chemistry was carried out.
Now if they could construct such a viable core, and measure adaptation and Darwinian evolution - then we'd really have something.

Yes, the paper is on conceptual mathematical treatment, the details of which is unfortunately a bit out of my league. The authors seem to be trying to work out why previously tested autocatalytic sets didn't seem capable of evolution, in order to find out on that basis, what could evolve.
I like the biology-direct publisher alot because you can see the discussion with the reviewer, where different points are reflected back and forth and you get a better understanding of the contents.

It is refreshingly critical of the failures of prior abiogenesis experimentation.

That's how science works. Failed hypotheses are discarded and new ones are tested. :thumbup:
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Re: Calilasseia: 78 Papers on Abiogenesis

#147  Postby proudfootz » Jan 20, 2012 2:22 am

Interested in abiogenesis since the record shows life began at some point after the rest.
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Re: Calilasseia: 78 Papers on Abiogenesis

#148  Postby rainbow » Jan 20, 2012 7:43 am

proudfootz wrote:Interested in abiogenesis since the record shows life began at some point after the rest.

Where exactly does the record show this?
What does 'after the rest mean'?
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Re: Calilasseia: 78 Papers on Abiogenesis

#149  Postby proudfootz » Jan 20, 2012 1:09 pm

rainbow wrote:
proudfootz wrote:Interested in abiogenesis since the record shows life began at some point after the rest.

Where exactly does the record show this?
What does 'after the rest mean'?


It's my understanding that the fossil record shows a beginning in time and subsequent development.

The rest of everything besides life is the material substrate from which life apparently sprang.
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Re: Calilasseia: 78 Papers on Abiogenesis

#150  Postby rainbow » Jan 21, 2012 8:26 am

proudfootz wrote:
rainbow wrote:
proudfootz wrote:Interested in abiogenesis since the record shows life began at some point after the rest.

Where exactly does the record show this?
What does 'after the rest mean'?


It's my understanding that the fossil record shows a beginning in time and subsequent development.

The rest of everything besides life is the material substrate from which life apparently sprang.


Any evidence prior to the Great Bombardment would've been destroyed. We therefore can't rely on the fossil record.
http://www.livescience.com/5426-life-su ... dment.html
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Re: Calilasseia: 78 Papers on Abiogenesis

#151  Postby proudfootz » Jan 21, 2012 9:58 am

rainbow wrote:
proudfootz wrote:
rainbow wrote:
proudfootz wrote:Interested in abiogenesis since the record shows life began at some point after the rest.

Where exactly does the record show this?
What does 'after the rest mean'?


It's my understanding that the fossil record shows a beginning in time and subsequent development.

The rest of everything besides life is the material substrate from which life apparently sprang.


Any evidence prior to the Great Bombardment would've been destroyed. We therefore can't rely on the fossil record.
http://www.livescience.com/5426-life-su ... dment.html


So the idea is that there might have been microbes that developed from non-living matter earlier than we have evidence for?
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Re: Calilasseia: 78 Papers on Abiogenesis

#152  Postby rainbow » Jan 21, 2012 11:49 am

proudfootz wrote:
So the idea is that there might have been microbes that developed from non-living matter earlier than we have evidence for?

One could consider that possibility.
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Re: Calilasseia: 78 Papers on Abiogenesis

#153  Postby proudfootz » Jan 21, 2012 4:23 pm

rainbow wrote:
proudfootz wrote:
So the idea is that there might have been microbes that developed from non-living matter earlier than we have evidence for?

One could consider that possibility.


No problem - life may have developed from non-life earlier than we have evidence for.
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Re: Calilasseia: 78 Papers on Abiogenesis

#154  Postby rainbow » Jan 23, 2012 9:52 am

Indeed.
...or not.
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Re: Calilasseia: 78 Papers on Abiogenesis

#155  Postby Landrew » Jan 24, 2012 11:42 am

It's either abiogenesis or magic. Since magic does not exist, what else could explain life?
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Re: Calilasseia: 78 Papers on Abiogenesis

#156  Postby proudfootz » Jan 25, 2012 12:03 am

Landrew wrote:It's either abiogenesis or magic. Since magic does not exist, what else could explain life?


Abiogenesis seems the most likely explanation.

If magic existed how could it be proved?

If life began by magical means, whoever did the magic trick did a good job of making it look like abiogenesis.

But what sort of magician does tricks that look like perfectly normal events?
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Re: Calilasseia: 78 Papers on Abiogenesis

#157  Postby Landrew » Jan 25, 2012 2:16 am

proudfootz wrote:
Landrew wrote:It's either abiogenesis or magic. Since magic does not exist, what else could explain life?


Abiogenesis seems the most likely explanation.

If magic existed how could it be proved?

If life began by magical means, whoever did the magic trick did a good job of making it look like abiogenesis.

But what sort of magician does tricks that look like perfectly normal events?

If magic could be proved to exist, it wouldn't be magic, would it?
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Re: Calilasseia: 78 Papers on Abiogenesis

#158  Postby proudfootz » Jan 25, 2012 2:17 am

Landrew wrote:
proudfootz wrote:
Landrew wrote:It's either abiogenesis or magic. Since magic does not exist, what else could explain life?


Abiogenesis seems the most likely explanation.

If magic existed how could it be proved?

If life began by magical means, whoever did the magic trick did a good job of making it look like abiogenesis.

But what sort of magician does tricks that look like perfectly normal events?

If magic could be proved to exist, it wouldn't be magic, would it?


That's one of the nice things about science - it encompasses everything that is shown to exist...
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Re: Calilasseia: 78 Papers on Abiogenesis

#159  Postby hackenslash » Jan 25, 2012 7:05 am

It isn't even either abiogenesis or magic. It's abiogenesis, whether by magic or other means.
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Re: Calilasseia: 78 Papers on Abiogenesis

#160  Postby rainbow » Jan 29, 2012 8:57 am

Landrew wrote:It's either abiogenesis or magic. Since magic does not exist, what else could explain life?


Not X, therefore Y - is not a compelling argument.
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