Abiogenesis

[foodchain]

I think you have all kinds of conceptual problems with this idea. I mean what are the speeds of the unknown chemical processes that were occurring in the pre-biotic world? Taking into account life evolved on earth, and not on every planet must have something to do with all of that. I mean some of the speeds could have been hundreds of years, humanity cannot conduct such experiments to reflect natural processes like that yet, so sorry. I mean we also could be thinking of experiments that need thousands of years or whatever to actually occur. So beyond that I think another issue you have to deal with is evolution, being biochemistry is highly similar, such as with DNA, amino acids, so on, why are we not all just exactly the same organism. In short life can evolve, if an RNA first life form existed in the past, it does not mean such could not have been evolved from, with simple example just being the role RNA plays currently, DNA, or evolution to chromosomes for instance only requires to produce more fitness right? So in short all of that could have been “eroded” by evolution to a certain extent.

 

Just that fact we can’t do it yet meant the earth was flat at some point. Evolution, or biological evolution has support from broad field terms like the biosciences, not just biology, the evidence is simply to empirically staggering. Beyond that how can abiogenesis be anything but the most simple if not scientifically plausible process for life on earth to occur.

[lucaspa]

I know that at the university I'll be attending in the fall, there is none going on.

 

How is abiogenesis viewed by the scientific community? Is there much abiogenesis research going on in universities?

 

Which university are you attending?

 

Abiogenesis is viewed as being almost certain. There is, however, quite a wide range of theories on how abiogensis can happen. There is the Protein First theory, Fox's protocells, RNA World, and the Hypercycle theory.

 

There is little funding and few funding sources for abiogenesis research. NIH does not fund it (concentrating mostly on research related to understanding life that already exists). That rules out the major funding of biological research in the USA. NASA used to fund abiogenesis research, but NASA's research budget has been severely cut over the last decade or so. There is some funding thru

 

I see Gerald Joyce had an article in a recent issue of Science showing a system of 2 RNA molecules that catalyzed each other's synthesis. But if you go to PubMed and enter "RNA, world" as your search term, you are going to get over 20 articles published just this year on that abiogenesis theory.

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wherein the digital information of genes just spontaneously occurred somehow—“Poof!”—amongst the chemical analogues.

 

Scrappy, once again you are confusing "directed protein synthesis" with abiogenesis. Directed protein synthesis is where you have genes that code for specific proteins.

 

No one is saying you get that by "poof". You need to abandon that strawman. We've given you one paper that outlines a route from the RNA world of RNA acting as enzymes to build proteins to directed protein synthesis. In doing a PubMed search for Seraph on RNA world I just came across two recent papers proposing a different route to directed protein synthesis:

 

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17540026 Look at this one carefully. It discusses how the "digital code" arose. Not "poof", but very slowly.

 

Here's the second one:

 

"1: Orig Life Evol Biosph. 2009 May 26. [Epub ahead of print]

 

A Specific Scenario for the Origin of Life and the Genetic Code Based on

Peptide/Oligonucleotide Interdependence.

 

Griffith RW.

 

Department of Biology, University of Massachusetts Dartmouth, North Dartmouth,

Massachusetts, 02747, USA, rgriffith@umassd.edu.

 

Among various scenarios that attempt to explain how life arose, the RNA world is currently the most widely accepted scientific hypothesis among biologists. However, the RNA world is logistically implausible and doesn't explain how translation arose and DNA became incorporated into living systems. Here I propose an alternative hypothesis for life's origin based on cooperation between simple nucleic acids, peptides and lipids. Organic matter that accumulated on the prebiotic Earth segregated into phases in the ocean based on density and solubility. Synthesis of complex organic monomers and polymerization reactions occurred within a surface hydrophilic layer and at its aqueous and atmospheric interfaces. Replication of nucleic acids and ranslation of peptides began at the emulsified interface between hydrophobic and aqueous layers. At the core of the protobiont was a family of short nucleic acids bearing arginine's codon and anticodon that added this amino acid to pre-formed peptides. In turn, the survival and replication of nucleic acid was aided by the peptides. The arginine-enriched peptides served to sequester and transfer phosphate bond energy and acted as cohesive agents, aggregating nucleic acids and keeping them at the interface."

[scrappy]

lucaspa,

 

Thanks for that ref. by Wolf and Koonin. They come mighty close to addressing the issue of “poof,” but they call it a “frozen accident.” I think they are asking the very same question I’m asking: How do get from stereochemistry to digital code, especially one with a 4^3 geometry, in a natural system? Maybe it was built up slowly and there was no frozen accident. Maybe it was an emergent property that came on incrementally. That seems to be the prevailing opinion in the field of abiogenesis hypotheses. I’m certainly not against it. I just think it assumes too much, at least without challenge, to count on such an extraordinary emergent property so blithely.

 

My biggest problem is trying to understand how nature can reduce its physical analogues to digital information, which involved inventing a genetic alphabet with an elegant geometry. It must have happened somehow, of course, and maybe slowly rather than in a poof. But I know of no other occasion in natural history where such an incredible thing occurred.

 

From Wolf and Koonin:

Thus, the translation system might have evolved as the result of selection for ribozymes capable of, initially, efficient amino acid binding, and subsequently, synthesis of increasingly versatile peptides. Several aspects of this scenario are amenable to experimental testing.

 

This gets things going in the right direction, I think. Thanks for helping to educate me on what’s happening. “Selection for ribozymes” definitely interests me. Not bad!

 

Among various scenarios that attempt to explain how life arose, the RNA world is currently the most widely accepted scientific hypothesis among biologists. However, the RNA world is logistically implausible and doesn't explain how translation arose and DNA became incorporated into living systems. Here I propose an alternative hypothesis for life's origin based on cooperation between simple nucleic acids, peptides and lipids. Organic matter that accumulated on the prebiotic Earth segregated into phases in the ocean based on density and solubility. Synthesis of complex organic monomers and polymerization reactions occurred within a surface hydrophilic layer and at its aqueous and atmospheric interfaces. Replication of nucleic acids and ranslation of peptides began at the emulsified interface between hydrophobic and aqueous layers. At the core of the protobiont was a family of short nucleic acids bearing arginine's codon and anticodon that added this amino acid to pre-formed peptides. In turn, the survival and replication of nucleic acid was aided by the peptides. The arginine-enriched peptides served to sequester and transfer phosphate bond energy and acted as cohesive agents, aggregating nucleic acids and keeping them at the interface."

Well, I like this all right. "Families of codons"? (I would have guessed adenine instead.) Where do you think the stereochemistry ended and the digital alphabet began? There was a huge emergent property in there somewhere.

 

Good luck with your work; it looks quite interesting.

 

We’re both in the business of predicting emergent properties, and that’s a very risky business indeed.

[granpa]

A blueprint bears a drawing, an analogue, of the structure to be built. There is no such blueprint in the arrangement of nucleotides on a nucleic acid molecule; there is only digital code for that structure. This is the essence of my point: somewhere in the course of abiogenesis the information needed to make proteins was transferred from a stereochemical process ("Tinkertoy" chemistry) to one of digital encoding with a 4^3 geometry. Digital codes DO NOT resemble the structures they inform; they are NOT analogues of proteins, they are code that has to be transcribed and translated for implementation.

 

And by merely arguing this point I am accused of trolling and threatened with suspension. My, oh, my! What a scientific forum this is!

 

tinkertoy chemistry? stereochemical process? what are you talking about? what do you think preceded the 'digital' codes that exist now? most scientists think the rna world came first. thats definitely digital.

 

you are accused of trolling because you are misrepresenting the views of others. I've never heard of anyone that thinks that dna is a 'blueprint' in the sense that you are suggesting.

[scrappy]

tinkertoy chemistry? stereochemical process? what are you talking about? what do you think preceded the 'digital' codes that exist now? most scientists think the rna world came first. thats definitely digital.

I’ll be very interested in learning how prebiotic chemicals in the RNA world were “definitely digital.”

 

you are accused of trolling because you are misrepresenting the views of others. I've never heard of anyone that thinks that dna is a 'blueprint' in the sense that you are suggesting.

 

To say that a gene is a “blueprint” of a protein is a huge misnomer. A blueprint:

 

 

bears an analog representation of the structure to be built. A blueprint is nothing like what a gene is; indeed it’s even a very poor metaphor for a gene. Instead, a gene is purely digital information. To wit:

 

From R. Dawkins’ River Out Of Eden (1995, p. 19):

 

Genes are pure information—information that can be encoded, recorded and decoded, without any degradation or change of meaning. Pure information can be copied and, since it is digital information, the fidelity of the copying can be immense.

 

This is a legitimate scientific debate. Just calling your opponent a troll doesn’t win you any points. I could make the same claim about you and be just as wrong.

[granpa]

you obviously arent serious. you are trying to make me look foolish by baiting me into a ridiculous argument.

 

the literal meaning of 'blueprint' and its metaphorical use are completetly different.

 

once again I ask you what do you think came before the digital world? nobody I know of believes that there was ever such a world as you are describing. chemistry simply doesnt work that way. the rna world came first and rna is clearly digital.

 

you seem to be the only person that believes that there ever was such a thing as this 'blueprint' chemistry. yet you are accusing others of believing that life still uses it. until you mentioned it I'd never heard anyone even suggest that such a thing was even possible.

Edited June 2, 2009 by granpa

[Psycho]

There is research in the department I am studying at into the idea of panspermia and other idea, I would guess there is little research due to lack of funding, whatever you find out isn't going to be very useful apart from in an academic sense and the result of any provable science would most likely be easier achieved via another less expensive method.

 

Anything that you did find out in data mining process would only add to the available information and wouldn't be provable, due to the nature of what the research is based on.

[scrappy]

you obviously arent serious. you are trying to make me look foolish by baiting me into a ridiculous argument.

 

the literal meaning of 'blueprint' and its metaphorical use are completetly different.

Sorry, but a gene is not a "blueprint" of a protein, not literally, not metaphorically, not even allegorically.

 

once again I ask you what do you think came before the digital world?

The analog world.

 

nobody I know of believes that there was ever such a world as you are describing. chemistry simply doesnt work that way. the rna world came first and rna is clearly digital.

It is? How?

 

you seem to be the only person that believes that there ever was such a thing as this 'blueprint' chemistry.

But you're the one who brought it up.

 

yet you are accusing others of believing that life still uses it. until you mentioned it I'd never heard anyone even suggest that such a thing was even possible.

...and Hamlet said: "There are more things in heaven and earth, Horatio, than are dreamt of in your philosophy."

[granpa]

and how did this 'analog world' work in your opinion? how did it lead to life and to the digital world. how does chemstry work in this 'tinkertoy/blueprint' world of your imagination?

 

how is the rna world not digital in your opinion?

[foodchain]

tinkertoy chemistry? stereochemical process? what are you talking about? what do you think preceded the 'digital' codes that exist now? most scientists think the rna world came first. thats definitely digital.

 

Well with RNA you can have ribozymes, and what about ribosomes, which I think a eukaryotic nucleus produces just ungodly amounts of those constantly, within the nucleolus right? With a prokaryote don’t you have an unnucleated nucleoid surrounded by a bunch of free floating ribosomes?

 

My personal view is that you had parts of the earth during periods of differentiation that supported such, something like underground caves, and in that you had protobionts with all kinds of chemical mixtures going in them. Then of course equilibrium being what it is made some of these things like consumers, but when the “food” started to dry out this basically strained out all but what could find ways to keep a metabolism. This is why I find RNA handy, not only because it performs so many roles in cells, its highly similar to DNA chemically, and is found to exist still in roles occupied by enzymes. Maybe some sort of ribosome-ribozyme structures occurring within protobionts. I think the production of protein by ribosomes for instance could maybe be tied back to chemical equilibrium, and free energy of course in a system trying to obtain some level of stability, not to be to wordy. Overall I just think chemical equilibrium over geological differentiation is key in the process in regards to understanding abiogeneisis.

[granpa]

there is a lot of things I could say in response to that but since this whole thread just seems to be degenerating into nitpicking and trolling I dont want to take the chance.

 

I think you might be on the right track though. (maybe protein production was a by product of rna replication)

[scrappy]

and how did this 'analog world' work in your opinion? how did it lead to life and to the digital world. how does chemstry work in this 'tinkertoy/blueprint' world of your imagination?

 

how is the rna world not digital in your opinion?

I’m still waiting to learn how (from your post #31): “the rna world came first and rna is clearly digital.” Yes, I think it came first, but I'm not at all sure how it was digital.

 

I'll try to answer your question anyway. For the RNA world to be digital it would need to have a digital genetic alphabet, comprising nucleotides (A,G,C and T/U) as bits and codons as bytes. From there an RNA analog could carry the digital information necessary to make a protein to a ribozyme or ribosome, if there had been a genetic language to transcribe and translate. Nascent biological life, as we know, required a digital language to synthesize proteins, which was not present in the RNA world, so far as we know. As such, the real biological fun didn't start until the digits showed up.

[granpa]

the digits were the nucleotides. thas what rna is made of. the original rna may have been made of simpler molecules but they were still nucleotides. this 'alphabet' wasnt used to produce protein it was used to produce more rna. thats digital.

 

no the rna world didnt have proteins. it had ribozymes. ribozymes are simply rna molecules that act as enzymes.

[scrappy]

the digits were the nucleotides. thas what rna is made of. the original rna may have been made of simpler molecules but they were still nucleotides. this 'alphabet' wasnt used to produce protein it was used to produce more rna. thats digital.

But is it digital information? For that to be the case there had to be a digital language with a digital alphabet. What I'm talking about is the way proteins are informed. My only point here is the need to take notice that nature did a very remarkable thing when it stored the structural information to make a protein on a nucleic acid molecule using a digital language. That's all I'm saying. Biological life didn't show up until that happened. Yes, maybe there were protogenes in the RNA world that acted stereochemically to make proteins. Maybe is was a gradual process, as some have argued, or maybe it was a frozen accident, a mysterious emergent property that still defies understanding.

 

But we wouldn't be here talking about it if nature didn't allow such a magnificent emergent property as biological life. There was no magic in it, no godly activities. It's just that we don't know enough yet about biological life to figure out abiogenesis.

 

no the rna world didnt have proteins. it had ribozymes. ribozymes are simply rna molecules that act as enzymes.

I still think the RNA world is our best theory for abiogenesis. To me, it came with the emergence of a digital genetic language, something that is not entirely stereochemical. Instead, it has a geometric logic with a 4^3 structure that ushered in a whole new venue for molecular affairs.

[granpa]

first of all the rna world didnt need proteins. it had ribozymes. there was a digital code for producing the ribozymes. is that what you are calling 'tinkertoy/blueprint' stereochemistry? because the code was a mirror image of the resulting ribozyme? it still carried information telling exactly how to build the ribozyme. it still evolved. why you think that is somehow different is beyond me. the rna world was 'alive'. that was biological life.

 

no one but you has mentioned magic or God.

[scrappy]

first of all the rna world didnt need proteins. it had ribozymes. there was a digital code for producing the ribozymes.

There was? Please explain how.

 

is that what you are calling 'tinkertoy/blueprint' stereochemistry? because the code was a mirror image of the resulting ribozyme?

Now you're catching on, with one critical exception: there was no digital code without a digital alphabet.

 

it still carried information telling exactly how to build the ribozyme. it still evolved.

Of course. I'm asking how it evolved from stereochemistry to digital code.

 

why you think that is somehow different is beyond me. the rna world was 'alive'. that was biological life.

And why you call the RNA world "biological life" is beyond me. How do you define "biological life"?

[granpa]

I define life as having the ability to reproduce and evolve.

 

you are clearly just arguing the semantics of 'blueprint' and 'code'.

[scrappy]

I define life as having the ability to reproduce and evolve.

Don't you usually need an organism to have biological life?

 

you are clearly just arguing the semantics of 'blueprint' and 'code'.

Yes, and it's important. No person educated in biology should equate a gene with a blueprint. This is a serious misrepresentation. A gene is digital code; it's pure information, just as Dawkins said.

[Mokele]

Why couldn't RNA world have been analog, then digital?

 

If it started out with ribozymes and nothing else, it would have been "analog", much like how a prion makes new prions. But then DNA could have developed, to store the ribozyme in a 1:1 copy that's more stable. At that point, you have a 'cell' with stored information that's literally and directly translated into metabolic machinery.

 

Some experiments have indicated that codons aren't purely arbitrary, and that the corresponding amino acids preferentially bind to the DNA of the 'right' sequence. So maybe from the DNA->RNA life, you can get DNA->protein life, where the DNA is a direct reflection of AA sequence. From there, mRNA probably got involved (with proteins directly attaching to it), and from that, tRNAs.

 

Of course, that's all hypothetical, but IMHO it's plausible and there's some key experiments that support certain aspects, though of course a LOT more work needs to be done.

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Don't you usually need an organism to have biological life?

 

Isn't fulfilling the criteria (metabolism, reproduction, growth, evolution, etc.) what defines an organism? (see the perennial 'is a virus alive' debate).

 

Yes, and it's important. No person educated in biology should equate a gene with a blueprint. This is a serious misrepresentation. A gene is digital code; it's pure information, just as Dawkins said.

 

And a muscle isn't a motor and differs in a lot of very important ways, but we still talk about motor neurons, motor units, etc.

 

It's a metaphor. Whether it's a bad or good one is utterly irrelevant. You're just arguing semantics. Move on.

[granpa]

the rna strand with its associated ribozymes was the organism. why on earth do you think it doesnt constitute an organism????? (the original organism may even have been a single molecule)

 

I've already told you that NOBODY believes that dna is a literal blueprint. and nobody but you believes that anybody believes that.

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it cannot be analog. a single enzyme/ribozyme can only at most add a few nucleotides to a strand. it would take hundreds of different ribozymes to produce a single ribozyme. that obviously wont work. and if it could work, say by producing a strand of all one nucleotide then it couldnt evolve.

 

the whole point of the rna world hypothesis is that rna can act as both ribozyme and as the carrier of genetic information. some ribozyme was able to produce a copy of the rna molecule thereby producing both ribozymes and reproducing the organism. thats digital. if you want to call that a blueprint and not a code then thats fine with me but I still fail to see why you think thats so important.

Edited June 4, 2009 by granpa
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[scrappy]

Why couldn't RNA world have been analog, then digital?

I think that’s possible. But before anything digital could have worked there had to be a genetic language with a digital alphabet. Otherwise there would be nothing but stereochemistry to propagate information.

 

If it started out with ribozymes and nothing else, it would have been "analog", much like how a prion makes new prions. But then DNA could have developed, to store the ribozyme in a 1:1 copy that's more stable. At that point, you have a 'cell' with stored information that's literally and directly translated into metabolic machinery.

I certainly don’t rule that out.

 

Some experiments have indicated that codons aren't purely arbitrary, and that the corresponding amino acids preferentially bind to the DNA of the 'right' sequence. So maybe from the DNA->RNA life, you can get DNA->protein life, where the DNA is a direct reflection of AA sequence. From there, mRNA probably got involved (with proteins directly attaching to it), and from that, tRNAs.

Yes, from stereochemistry to digital information.

 

Of course, that's all hypothetical, but IMHO it's plausible and there's some key experiments that support certain aspects, though of course a LOT more work needs to be done.

I agree. Most of what you say here seems reasonable. Still, I don’t see biological life emerging without the code.

 

Isn't fulfilling the criteria (metabolism, reproduction, growth, evolution, etc.) what defines an organism? (see the perennial 'is a virus alive' debate).

No, not if you include evolution as a criterion for an organism. Organisms do not evolve; only populations of organisms evolve.

 

And a muscle isn't a motor and differs in a lot of very important ways, but we still talk about motor neurons, motor units, etc.

But a motor doesn’t need to be an internal cumbistion engine. Oxford Dict., for example, includes this definition of a motor: “a source of power, energy, or motive force : hormones are the motor of the sexual functions.”

[Mokele]

Still, I don’t see biological life emerging without the code.

 

But what would you call an organism that transcribed mRNA by AA binding to the actual nucleotides? Why is that not "alive" when a descendant that uses tRNAs is?

 

No, not if you include evolution as a criterion for an organism. Organisms do not evolve; only populations of organisms evolve.

 

True, mutation would be a better criterion. But then why would something that uses analog means not be alive if it metabolizes, mutates, grows, and reproduces?

 

But a motor doesn’t need to be an internal cumbistion engine. Oxford Dict., for example, includes this definition of a motor: “a source of power, energy, or motive force : hormones are the motor of the sexual functions

 

The point is it's just a metaphor, good or bad. A semantic argument is the lowest form of argument.

[scrappy]

the rna strand with its associated ribozymes was the organism. why on earth do you think it doesnt constitute an organism????? (the original organism may even have been a single molecule)

Ah, you're not serious are you? If so, you don't understand what an organisms is.

 

the whole point of the rna world hypothesis is that rna can act as both ribozyme and as the carrier of genetic information.

What genetic information?

 

some ribozyme was able to produce a copy of the rna molecule thereby producing both ribozymes and reproducing the organism. thats digital.

No, not with a coded language.

 

if you want to call that a blueprint and not a code then thats fine with me but I still fail to see why you think thats so important.

I'm going to leave it here. Good luck with your metaphors. As Schrödinger pointed out in his famous essay What Is Life?: "The price of a metaphor is constant vigilance."

[iNow]

From post #21:

 

 

you just seem to be nitpicking the arguments of others. that is definitely trolling.

 

Trust your gut, granpa.

[Reaper]

I'm going to leave it here. Good luck with your metaphors. As Schrödinger pointed out in his famous essay What Is Life?: "The price of a metaphor is constant vigilance."

 

And the price of quote mining is loss of credibility. That statement does not have the meaning you think it does...

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No, not with a coded language.

 

Why do you think there has to be some "code" involved when the first life forms emerged? It has already been demonstrated, on and on, that the first life forms needn't be that complex, like in this post.

 

All one really needs is a few self-replicating molecules, and then over time protocells and DNA will end up emerging because of Natural Selection.

 

 

The overall larger point is basically, DNA is NOT A COMPUTER. There is no "code" whatsoever, it does not carry information in the sense that a computer does (whether analog or digital). In short, it's just sequences of nucleotides that formed via the laws of chemistry, physics, and Natural Selection. And its a very crude carrier of information; to give an example, the human brain, which can be legitimately considered to be an "analog device", holds millions of times more information. Hell, I can probably design a mechanical calculator that holds more "information" than DNA...

Edited June 4, 2009 by Reaper
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