Abiogenesis

[scrappy]

And the price of quote mining is loss of credibility.

What a shallow accusation!

 

That statement does not have the meaning you think it does...

So, what meaning do you think it has?

 

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.

I'm talking about biological life. Perhaps prebiotic life forms managed their structural/informational tasks thru stereochemistry. I don't reject that. But when abiogenesis managed to whelp a living organism it had to have a genetic code. I know of no organism, present or past, that existed without genes.

 

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.

This is purely true belief on your part. What do you have, other than hopeful speculation, to back it up.

 

The overall larger point is basically, DNA is NOT A COMPUTER.

No one here ever said it was.

 

There is no "code" whatsoever, it does not carry information in the sense that a computer does (whether anaalog or digital).

Who said anything about a computer? I didn't.

 

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...

But nobody at least not me, claimed any such thing.

[Reaper]

What a shallow accusation!

 

It's not, because I read that essay several times over. That statement in no way applies to what we are discussing here any way you look at it.

 

I'm talking about biological life. Perhaps prebiotic life forms managed their structural/informational tasks thru stereochemistry. I don't reject that. But when abiogenesis managed to whelp a living organism it had to have a genetic code. I know of no organism, present or past, that existed without genes.

 

And that has already been explained to you, several times on several threads. RNA can act as both an enzyme and store information. Did you even read any of the links provided over the past few months?

 

This is purely true belief on your part. What do you have, other than hopeful speculation, to back it up.

 

How about you start by reading a biology textbook. Or if that seems like too much work, read this webpage on Talk Origins: http://www.talkorigins.org/faqs/abioprob/

 

 

No one here ever said it was.

Who said anything about a computer? I didn't.

But nobody at least not me, claimed any such thing.

 

Yes you were, don't try to dodge it. You were using computer terminology to describe what DNA does and can do. I was merely demonstrating that it doesn't work that way.

 

Besides which, this nitpick really is nothing more than a red herring on your part, don't evade the subject.

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For those of you who actually want to learn something, rather than promote an ideology, here are some more good links on the subject:

 

http://exploringorigins.org/

 

http://www.pnas.org/content/97/23/12503.full?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=biochemical+cycles&searchid=1119837712082_3423&stored_search=&FIRSTINDEX=0&journalcode=pnas

 

http://www.livescience.com/animals/060609_life_origin.html

 

http://genetics.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Hanczyc_and_Szostak_2004_COChemBio.pdf

 

 

Here is a very good article on the subject for layman:

http://student.science.uva.nl/~jckastel/html/abiogenesis.pdf

 

And here is another good article, which details how RNA can be made from simple reactions:

http://www.nature.com/news/2009/090513/full/news.2009.471.html

 

The last one is important because it proves once and for all that RNA molecules aren't "too complex" to form by themselves under certain conditions, especially conditions that certainly existed when Earth was young. You need a subscription to read it though.

Edited June 4, 2009 by Reaper
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[granpa]

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?

 

the sequence of nucleotides.

[iNow]

I'm talking about biological life. Perhaps prebiotic life forms managed their structural/informational tasks thru stereochemistry. I don't reject that. But when abiogenesis managed to whelp a living organism it had to have a genetic code. I know of no organism, present or past, that existed without genes.

 

"Prebiotic life," or "protobionts" exhibit many characteristics of living organisms, but are not, by definition, alive since one of the requirements for life is generally their ability to replicate via DNA/RNA.

 

That problem you have with it all is a semantic one, not a catastrophic or theory disproving one.

 

Here's where your logic fails... and fails miserably. You're not only continually asserting that you accept protobionts as a possible precursor to life, but then in the next breath you are contradicting yourself and asserting that it's impossible for life to start from protobionts since they don't have genes.

 

Now, those were not your exact words, I stipulate that, but a close reading of your posts makes clear that my summary of your logic is quite accurate, and that your logic is internally inconsistent.

 

With that said, you simply can't have it both ways. You either accept protobionts as a possible precursor or life, or you do not.

 

 

Scientists think that the protobionts are the evolutionary precursors of prokaryotic cells. Protobionts may be originated as an array of microspheres of diverse organic and inorganic compounds enclosed by lipidic membranes. Proteins, carbohydrates, lipids, and other organic substances were the most important autocatalytic organic compounds. Water was a very important factor in the assembly of the protobionts' endoplasm. After this event, several microspheres could self-organize into organelles that were able to perform specific functions; for example, lysosomes, peroxysomes, vacuoles, etc.

 

Gradually, some segments of the external membrane would invaginate for forming membranous organelles, like endoplasmic reticulum and Golgi apparatus. First protobionts would not have a nucleus membrane (nuclear envelope); consequently, they could be identified like prokaryotes.

 

Mitochondria and chloroplasts could develop soon after as vagile and self-sufficient protobionts, which specialized in obtaining energy directly from the environment.

 

 

As for how it went from that to RNA replication, review Reaper's links in the post above and you should be good to go.

 

 

http://en.wikipedia.org/wiki/Protobiont

A protobiont is an aggregate of abiotically produced organic molecules surrounded by a membrane or a membrane-like structure. Protobionts exhibit some of the properties associated with life, including simple reproduction, metabolism and excitability, as well as the maintenance of an internal chemical environment different from that of their surroundings. It has been suggested that they are a key step in the origin of life on earth. Experiments by Sidney W. Fox and Aleksandr Oparin have demonstrated that they may be formed spontaneously, in conditions similar to the environment thought to exist on an early Earth. These experiments formed liposomes and microspheres, which have membrane structure similar to the phospholipid bilayer found in cells.

Edited June 4, 2009 by iNow

[scrappy]

the sequence of nucleotides.

Are you saying that ribozymes had genes? Even before a genetic language was invented? Wow! I'd be very interested in learning about them.

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Here's where your logic fails... and fails miserably. You're not only continually asserting that you accept protobionts as a possible precursor to life, but then in the next breath you are contradicting yourself and asserting that it's impossible for life to start from protobionts since they don't have genes.

This is crazy! Either you haven't been pay attention or you don't know what you're talking about.

[granpa]

http://en.wikipedia.org/wiki/RNA

Ribonucleic acid (RNA) is a type of molecule that consists of a long chain of nucleotide units.

 

it is the exact sequence of nucleotides that give the ribozyme its properties.

[Mokele]

Thread temporarily locked.

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Thread unlocked.

 

Everyone play nice, and cut the infighting. If you have a problem, report the post and we will deal with it.

[granpa]

if you look at the structure of rna you will see that it consists of flat plates stacked on top of each other. I'm of the opinion that the original nucleotides (whatever they were) were flat, aromatic, hydrophobic in the center, and hydrophilic on the outside. there was probably only 2 types of bases and they probably hydrogen bonded together (somehow) to form a base pair.

 

thats my unstudied opinion and you can take it for what its worth.

[scrappy]

Are you saying that ribozymes had genes? Even before a genetic language was invented? Wow! I'd be very interested in learning about them.

Ribonucleic acid (RNA) is a type of molecule that consists of a long chain of nucleotide units.

 

it is the exact sequence of nucleotides that give the ribozyme its properties.

I’m fine with that. But you haven’t yet explained how a prebiotic RNA’s nucleotides could assemble as genetic information before there was a genetic code.

[Mokele]

I laid out an entire hypothetical transitional sequence for you in post #44.

 

If it started out with ribozymes and nothing else' date=' 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.[/quote']

[scrappy]

I laid out an entire hypothetical transitional sequence for you in post #44.

I think that’s possible, as I said in post #46:

 

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.

Your hypothetical scenario doesn’t seem too far-fetched to me; it’s reasonable to assume that the extant digital genetic code had stereochemical precursors. But I still don’t see how you can call any of those stereochemical precursors “genes” unless there was a digital genetic language for encoding the genetic information.

 

What we are talking about here, IMO, is the key aspect of abiogenesis: genetic digitization. I'm saying that abiogenesis cannot be effectively understood until we know more about how a genetic language evolved. There are several good hypotheses, and all of them are of interest to me. As one astute poster here already said: understanding abiogenesis is more challenging than understanding the Big Bang. This is why I'm still suspicious of a "frozen accident." In truth, we still don't know for sure that abiogenesis was NOT a "one off." And we still don't even know if it happened here on Earth.

[granpa]

you mean how did this primitive pseudo-rna molecule replicate (assemble) before the first ribozymes evolved? presumably it replicated spontaneously due to the hydrogen bonding of the base pairs. obviously the nucleotides themselves had to already exist in large numbers. explaining this is the hard part. I think comets deposited huge amounts of water and organic molecules on the early earth. maybe they came from there.

 

 

if that is not what you are asking then I simply have no idea what you mean.

 

ribozymes are pure rna so once you have rna replication its a simple matter for ribozymes to evolve.

 

if this pseudo-rna molecule could replicate and evolve then it was a living organism and therefore not pre-biotic. maybe you are referring to a time even before that? fire can replicate but cant evolve so its not alive. perhaps there was some kind of even simpler pre-biotic rna-like molecule that could replicate (like fire) but the molecules carried no information. perhaps they grew at the ends and then split in two rather than forming the second molecule along their length due to base pair hydrogen bonding (like modern rna does).

 

you might also find this interesting:

http://en.wikipedia.org/wiki/PAH_world_hypothesis

Edited June 6, 2009 by granpa

[Theophrastus]

I'ld like to say that if anyone is beginning to examine the concepts of abiogenisis, they ought to look at the famous Urey- Miller experiment, in which a mixture of gases like ammonia, hydrogen, methane and the like, that would have been prevalent in prebiotic conditions (simulating the atmospheric conditions hypothesised in the era), were subject to electrical discharge, simulating lightning, which given the violent conditions in the atmosphere at the time would not have been uncommon.

After a weeks time, Urey and Miller analysed the contents of the mixture, which surprisingly, due to various chemical processes contained substancial amounts of amino acids (the majority, in the form of glycine, however, 21 others were also formed), and resulting compounds, due to further intermolecular reactions, and in varying the conditions slightly, in repeated experiments, were capable of producing a variety of organic molecules, such as nucleic acids, sugars and fats. Just something interesting for everyone to look into, in light of heated debate.

I'm actually quite sorry I haven't read all of the links (to this folly I'ld attribute a lack of time), as I've read a few and they're quite interesting. Just as a note, this experiment was done in 1953! Already, over 50 years ago there was indication of the possibility of abiogenisis, so it would be interesting to see how research has progressed.

I'm also a bit annoyed of these metaphors and the like, being used for DNA. DNA, I find is not digital or the like, but rather a chemical means for reproduction. It serves its purpose through chemical processes and reactions, not some magical method in which it takes the role of some manner of blueprint, or model.

Edited June 6, 2009 by Theophrastus
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[granpa]

I dont think that anyone believes dna is magic. digital just means not analog. the bases form a base four coding system. each base encodes 2 bits of information. thats clearly digital.

 

if the early rna precursor had only 2 bases then it would have encoded 1 bit of information per base. also clearly digital. why scrappy thinks that it wasnt or couldnt have been digital is beyond me. the only requirement is that they naturally form pairs. in modern rna the base pairs form hydrogen bonds with each other.

Edited June 6, 2009 by granpa

[Mokele]

it’s reasonable to assume that the extant digital genetic code had stereochemical precursors. But I still don’t see how you can call any of those stereochemical precursors “genes” unless there was a digital genetic language for encoding the genetic information.

 

Why not? Why does the definition of a gene *require* that tRNA be involved? Just because that's what we see today? That's like saying birds are defined by lacking teeth, just because all the extant lineages are toothless.

 

You're confusing what's around today with what's actually necessary, functional, and possible.

 

What we are talking about here, IMO, is the key aspect of abiogenesis: genetic digitization. I'm saying that abiogenesis cannot be effectively understood until we know more about how a genetic language evolved.

 

I disagree - I think codons, the use of tRNA, etc. happened *after* the origin of life, and that organisms prior to that innovation were already "true life" by any reasonable definition.

 

I agree that it's an interesting question, but I disagree that it's necessary for life, and that organisms before it were somehow "not alive" just because they didn't do things exactly our way.

 

Mokele

[scrappy]

digital just means not analog.

Would it be fair to say that digital a "message" requires a code for storing the information, while an analog "message" does not?

 

if the early rna precursor had only 2 bases then it would have encoded 1 bit of information per base. also clearly digital. why scrappy thinks that it wasnt or couldnt have been digital is beyond me.

Well, extant life, as we know it, requires codons, comprising 3 bits of information (a 4^3 coding geometry). This structure enables a genetic alphabet, and thus a language. If you are saying that this coding geometry evolved from a simpler one that engaged stereochemistry instead of digit code I can go along with this, partly. But I'm puzzled about how any early coding geometry could have worked if it was entirely stereochemical. I could see maybe a 2-bit "codon" at first that functioned stereochemically to inform the union of two AAs to make a primitive polypeptide. What I can't see, though, is how that "codon" carries any digital information in the form of a code with a geometric alphabet.

 

Where did that come from?

[granpa]

whats an AA?

 

it sounds like you just need to read up on base pairing.

[Kaeroll]

I'm actually quite sorry I haven't read all of the links (to this folly I'ld attribute a lack of time), as I've read a few and they're quite interesting. Just as a note, this experiment was done in 1953! Already, over 50 years ago there was indication of the possibility of abiogenisis, so it would be interesting to see how research has progressed.

Indeed... there's a group in my university working on it, the head of which showed me a summary of the past half-century of work in the area. It was a while back and I don't have a copy unfortunately, but it showed (amongst other things) that it is possible to stereoselectively form all the RNA nucleosides stereoselectively from "first principles", as it were (i.e. inorganic matter, such as phosphate, ammonia, etc). Current work focuses on self-assembly of RNA oligomers and the like.

[scrappy]

Why not? Why does the definition of a gene *require* that tRNA be involved? Just because that's what we see today? That's like saying birds are defined by lacking teeth, just because all the extant lineages are toothless.

Are you saying that were organisms in the past that didn’t require genes? If so, what support do you have for this? We’re talking about living organisms. I can’t imagine a living organism without genes, digital genes. But I might agree that dead organisms don’t have any.

 

You're confusing what's around today with what's actually necessary, functional, and possible.

Such as? And how would you know?

 

I disagree - I think codons, the use of tRNA, etc. happened *after* the origin of life, and that organisms prior to that innovation were already "true life" by any reasonable definition.

 

agree that it's an interesting question, but I disagree that it's necessary for life, and that organisms before it were somehow "not alive" just because they didn't do things exactly our way.

You’re going to have come up with something pretty good here to convince me that there ever were any living organisms that lacked genes.

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whats an AA?

 

it sounds like you just need to read up on base pairing.

"AA" is a common abbreviation for "amino acid."

Edited June 6, 2009 by scrappy
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[Mokele]

Are you saying that were organisms in the past that didn’t require genes? If so, what support do you have for this? We’re talking about living organisms. I can’t imagine a living organism without genes, digital genes. But I might agree that dead organisms don’t have any.

 

I bet you can't imagine a fish with jaws like a pair of serrated scissors, or an animal with five eyes, but they existed.

 

I've explain this to you repeatedly - you cannot simply assume that what exists today is the only possibility. And each time, you acknowledge it, and then within a week completely forget it and bring up this tired old argument.

 

You agreed that my hypothesized series of events is "plausible". By any definition of "life", even an organism which just has ribozymes and stores their sequences on DNA is "alive" - it can metabolize, grow, reproduce, mutate, maintain homeostasis, respond to stimuli, etc. It could presumably do anything a modern living organism can do. It would be alive by any currently accepted definition, but would have lacked "genes" in the sense you describe them (though I also disagree with that definition, and would consider the information in the DNA that's transcribed into ribozymes to be "genes").

 

Of course, I can't point to a living organism that does it, but you also cannot prove that it's not possible. Your entire premise rests on the idea that what is currently alive is the only possibility, and has been repeatedly and amply refuted.

 

You want to claim that the definition of "life" requires tRNA and codons, then cite a peer-reviewed paper claiming that.

[granpa]

if you stick a short rna strand in a vial with a bunch of nucleotides it will AFAIK spontaneously replicate itself and its sequence of nucleotides because nucleotides spontaneously pair up. if some of those strands were to fold up and were to act as ribozymes that helped it somehow to replicate then you would have life.

 

But I'm puzzled about how any early coding geometry could have worked if it was entirely stereochemical. I could see maybe a 2-bit "codon" at first that functioned stereochemically to inform the union of two AAs to make a primitive polypeptide. What I can't see, though, is how that "codon" carries any digital information in the form of a code with a geometric alphabet.

 

this really makes no sense. you have a misconception about something but I cant quite figure it out. we've all told you repeatedly what you need to know and you have ignored us. I dont know what more we can do.

[scrappy]

I bet you can't imagine a fish with jaws like a pair of serrated scissors, or an animal with five eyes, but they existed.

Sure, if they had genes just about anything was possible (read Dawkins’ Unweaving the Rainbow). What would be impossible is for your fishes with scissor-like jaws to exist without genes.

 

You agreed that my hypothesized series of events is "plausible". By any definition of "life", even an organism which just has ribozymes and stores their sequences on DNA is "alive" - it can metabolize, grow, reproduce, mutate, maintain homeostasis, respond to stimuli, etc.

But you’re confusing “alive” with biological life. Even a virus would not be alive by your wiki definition, but it still has genes. I still maintain that biological life didn’t start until the genes showed up. If you know of any existing or historical forms of biological life that lacked genes please post you evidence. But remember that genes require a digital code with an alphabet as a format for their information storage system.

 

As far as biological life on Earth is concerned there is only one life form. If you think there were other biological life forms before abiogenesis you need to support your hypothesis with something more than a statement like “you cannot simply assume that what exists today is the only possibility.”

 

Of course, I can't point to a living organism that does it, but you also cannot prove that it's not possible.

You want me to prove a negative when you can’t even prove a positive?

 

ou want to claim that the definition of "life" requires tRNA and codons, then cite a peer-reviewed paper claiming that.

We’ve been all over this. If you want to call a prebiont a biological life form then go ahead and be wrong. Show me a peer-reviewed paper that claims that a single molecule can be a biological organism.

[granpa]

all you need is 2 nucleotides that form a base pair and you can have self replicating rna and ribozymes. the rna would carry genetic information. the genetic information would be the sequence of its nucleotides. this sequence would be carried over to its offlsring.

 

this is simple and self evident and I cant understand why you are having trouble understanding it.

 

there is another thread where someone is asking where such a molecule would get the energy to replicate itself. is that what you are asking? hydrogen bonds (like those between base pairs) are very weak. they arent even 'real' chemical bonds. they form spontaneously between inert molecules. waves splashing on shore during a storm would probably be sufficient to break them.

 

I suspect that the original nucleotides were entirely held together by hydrogen bonds. no chemical bonds at all (except within the nucleotide itself of course). thats what I was getting at here:

if you look at the structure of rna you will see that it consists of flat plates stacked on top of each other. I'm of the opinion that the original nucleotides (whatever they were) were flat, aromatic, hydrophobic in the center, and hydrophilic on the outside. there was probably only 2 types of bases and they probably hydrogen bonded together (somehow) to form a base pair.

 

thats my unstudied opinion and you can take it for what its worth.

 

A kind of pseudopolymer

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basically, the bases already spontaneously form base pairs by means of weak hydrogen bonds. there is no need for a 'code' (which from your postings I gather you think involves some elaborate mechanism involving transfer rnas and codons)

Edited June 7, 2009 by granpa
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[scrappy]

To me, at least, the emergence of the genetic code was the necessary trick nature had to pull off to make abiogenesis happen. My driving question has been: Why is the genetic code universal? Why is there only one kind of life? The answer, I think, must connected somehow to abiogenesis (and not to the capricious idea that the first life form ate up all of its competitors.).

 

So, it seems relevant here in this discussion on the various theories on abiogensis to differentiate “The Stereochemical Theory” from “The Frozen Accident Theory,” and do this with respect to the evolution of the genetic code. I rather like the way Francis Crick did this in his 1968 paper The Origin of the Genetic Code (J. Mol. Biol. 38, pp. 369-370):

 

[The Stereochemical Theory] states that the code is universal because it is necessarily the way it is for stereochemical reasons. Woese has been the main proponent of this point of view (see Woese, 1967). That is, it states that phenylalanine has to be represented by UUU/C, and by no other triplets, because in some way phenylalanine is stereochemically “related” to the two codons. There are several versions of this theory. We shall examine these shortly when we come to consider the experimental evidence for them.

 

[The Frozen Accident Theory] states that the code is universal because at the present time any change would be lethal, or at least very strongly selected against. This is because all organisms (with the possible exception of certain viruses) the code determines (by reading the mRNA) the amino acid sequences of so many highly evolved protein molecules that any change in these would be highly disadvantageous unless accompanied by many simultaneous mutations to correct the “mistakes” produced by altering the code.

 

This accounts for the fact that the code does not change. To account for it being the same in all organisms one must assume that all life came from a single organism (more strictly, from a single closely interbreeding population). In its extreme form, the theory implies that the allocation of codons to amino acids was entirely a matter of “chance.”

Since then there has been a lot of interesting discussion on the molecular aspects of abiogensis, but, IMO, not enough on the digitally coded aspects of it.

[granpa]

either that or transfer rna's and protein synthesis could simple have been accidental byproduct of rna replication

 

it seems entirely reasonable to me to suppose that rna, at some point, learned to replicate itself using (preassembled) nucleotide triplets. this might have been more efficient for any number of reasons.

 

the amino acid may have been added to the triplet simply to help the replication machinery to identify it.

Edited June 7, 2009 by granpa