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Which came first, the proteins or the DNA?

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Stephanos
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0 posted 07-10-2003 01:59 PM       View Profile for Stephanos   Email Stephanos   Edit/Delete Message      Find Poems   Click to visit Stephanos's Home Page   View IP for Stephanos

Since we have been discussing naturalistic evolution, I wanted to bring up another consideration. (I hope I'm not out of order here Ron.  I know this isn't a bilogy forum.  But this is loosely related to cosmology right?     )


Random mutation and natural selection is Darwin's proposed mechanism for changes, big and small.  Small changes (microevolution) are not in doubt.  Finch beaks change within a species, as well as the color of moth wings.  But the bigger changes, such as the development of larger systems, have not been proven to have happened via the Darwinian way, they have been inferred to have happened that way.  So there are problems with this theory, as suggested by certain biochemists.  But let's say we accept that, returning to those problems later ...

Natural selection requires reproduction to work.  It can only fuction where genetic mutations can be passed on.  But there is a huge gap which lies between inorganic chemistry and genetic replication, that cannot be explained by natural selection.  This is the gap I want to discuss.  How did inorganic chemicals find their way to replication and reproduction?  In answering,  remember that Darwin is out of his jurisdiction on this one.  

All cells are made up of proteins.  Proteins are made up of amino acids.  These amino acids (20 different types) fit together in highly specified chains.  If a chain is in the right sequence, it folds up on itself and forms a protein.  The protein provides a very specified shape, and functions literally as a machine part.  Either functional or structural, proteins make up almost the entire cell.  They are also indispensibly involved (along with DNA & RNA) in making other proteins.  So in order for reproducing cells to exist, it seems proteins must have existed before.  But how?  


Dean H. Kenyon once wrote a book called "Biochemical Predestination" which theorized that proteins might have once been formed by the innate chemical properties of attraction found in amino acids.  But science has concluded that there are no such properties.  Amino acids do not (in fact) come together like magnets.  They are formed according to genetic assembly instructions, found in DNA.  Kenyon has since debunked his theory, and has become an advocate of intelligent design.  

This seems to me to be quite an impasse for the theory of naturalistic evolution.  Some may say the journey is small from non-organic chemistry to replication, but many think it is anything but small.  I was just wondering if any of you might have any ideas about this.  I am no scientist, just an interested lay person.  So anything added would be a learning experience for me.

Some have suggested that precursors existed, like lone RNA and then DNA which were able to make proteins.  But the complex process and the accompanying proteins required for these molecules to make proteins, make this claim seem highly improbable if not impossible.  

Here is an interesting quote...

"it requires an absolutely dazzling array of proteins to split the DNA and make RNA which is then used to make proteins via inordinately complex processes.
So, you need a really well-designed set of proteins etc etc in order to use and maintain the DNA. If these don't exist, the DNA is useless. If the DNA is useless, you can't code for proteins. It's like the chicken and the egg, really.
The more you look at the complexity of biochemical systems in living cells, the harder it gets to understand how any of it could have survived without the rest of the system already being in place.
"


Any ideas?

Stephen.





[This message has been edited by Stephanos (07-10-2003 02:15 PM).]

Toad
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1 posted 07-10-2003 03:52 PM       View Profile for Toad   Email Toad   Edit/Delete Message      Find Poems  View IP for Toad


Perhaps we’re missing another link.

Natural selection itself may hold a clue to how the chicken and egg paradox you describe came about.

Imagine a big machine that builds bigger and better machines, to help it the big machine builds little engines that manufacture useful parts for the bigger and better machines. The little engines are modified to improve their manufacturing ability and speed up the production line. The improvement cycle continues until the little engines are so adept they can even manufacture themselves and in time can do so at a rate that far outstrips production of the bigger and better machines. At that point the little engines are totally self-sufficient and virulent reproducers, if they are in direct competition for raw materials with the bigger machines natural selection would dictate that the small engines would proliferate and the bigger machines would become extinct. If, after such an extinction, an observer looked at the little engines he'd probably scratch his head and start muttering something about chickens and eggs.

My point is that a now extinct third participant on the grassy knoll at the birth of evolution is a plausible scenario, whether it holds truth or not is open to debate and speculation. My guess is that A. G. Cairns-Smith may be on the right track.
http://originoflife.net/takeover/
Stephanos
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2 posted 07-10-2003 04:50 PM       View Profile for Stephanos   Email Stephanos   Edit/Delete Message      Find Poems   Click to visit Stephanos's Home Page   View IP for Stephanos

"Imagine a big machine that builds bigger and better machines, to help it the big machine builds little engines that manufacture useful parts for the bigger and better machines. The little engines are modified to improve their manufacturing ability and speed up the production line. The improvement cycle continues until the little engines are so adept they can even manufacture themselves and in time can do so at a rate that far outstrips production of the bigger and better machines. At that point the little engines are totally self-sufficient and virulent reproducers, if they are in direct competition for raw materials with the bigger machines natural selection would dictate that the small engines would proliferate and the bigger machines would become extinct. If, after such an extinction, an observer looked at the little engines he'd probably scratch his head and start muttering something about chickens and eggs."


In the real world, machines are made by intelligent designers.  But let's say that a big machine does produce smaller machines which in turn make parts to be used by the bigger machine in making other big machines.  What you are describing is a process of reproduction ... in which natural selection may be considered.  But what I am talking about is a different scenario.  It is about what happened before reproduction.  Cellular reproduction, and even the production of proteins needs proteins already present, along with some kind of code like RNA or DNA.  But to get to that point you cannot use Darwin at all.  So Natural selection cannot explain the chicken and the egg problem.


Let's say there is a machine that makes parts necessary for the building of other machines like itself.  Let's also say that these parts are integral and necessary in the actual making of the parts themselves.  Let's also say that there has been no observed process in which these parts have been made, other than by the highly specified machine.  

This is the situation we have with protein production.  DNA and RNA are useless without accompanying proteins ... especially the ribosome.  So they are powerless to produce proteins without proteins present.  And yet they are the only known means to produce proteins.  Even if we suggest an earlier self replicating RNA, how did it make proteins without the ribosome (which is made of proteins)?  The only speculative answer I have heard is that the earliest proteins may have come together by the chance joining of amino acids.  When the immense improbability of that is brought out,  (And it really is immense) the time factor is usally given, that anything can happen over billions and billions of years.  This may be true, or it may not, but it is not exactly science, it is conjecturing.  It is also faith in time, perhaps of the same degree that some have faith in God.  


The first parts (proteins) cannot be said to have been produced by a reproductive machine, because the machines themselves are comprised of these parts.  Yes there can be speculation and hypothesis, but in science, hypothesis must be tested, or it remains speculation.  And no doubt, any mechanism here that explains "how" it happened cannot be the Darwinian mechanism, because again it is dependent upon reproduction.


Stephen.

[This message has been edited by Stephanos (07-10-2003 04:55 PM).]

Local Rebel
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3 posted 07-11-2003 12:05 AM       View Profile for Local Rebel   Email Local Rebel   Edit/Delete Message      Find Poems  View IP for Local Rebel

"In the real world, machines are made by intelligent designers"

um... as an old machine designer let me just say thanks -- but -- I've never seen one with an intelligent design... hehe.. just playin with you stephen... carry on.
Stephanos
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4 posted 07-11-2003 01:53 AM       View Profile for Stephanos   Email Stephanos   Edit/Delete Message      Find Poems   Click to visit Stephanos's Home Page   View IP for Stephanos

LR,

Yeah my last lawn mower seems to confirm what you're saying.  Let me revise my theory.  

The theory of Rev-pollution perhaps?

Don't throw tomatoes.  I still have a day job.

Stephen.
Brad
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5 posted 07-11-2003 11:29 PM       View Profile for Brad   Email Brad   Edit/Delete Message      Find Poems  View IP for Brad

This essay explains where we are as of 1997:
http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html
Brad
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6 posted 07-12-2003 04:54 PM       View Profile for Brad   Email Brad   Edit/Delete Message      Find Poems  View IP for Brad

Uh, anybody who understands chemistry molecular biology better than I do, please feel free to correct this. I'm just trying to rewrite what I've read as simply as possible without using too much jargon.

Okay, let's start with what we know:

A.

1. We know that the bases of DNA and RNA nucleotides can be found in a pre-biotic atmosphere.

2. We know that amino acids, the building blocks of proteins, can also be found in a pre-biotic atmosphere.

3. The actual amounts of these molecules are dependent on the composition of the pre-biotic atmosphere, and that's still controversial.

B.

1.We know that nucleo-tide bases interact and form carbon crystals (RNA crystals, DNA comes later). Crystals are molecular structures that can replicate the same structure over and over again. This is a chemical process, no need to worry about intent.

2. We know that amino acids can come together and form rudimentary protein-like substances that have a little catalytic ability. That is, when they interact with nucleotides, they provide energy for longer strings of those carbon crystals.

3. The problem is that nucleotides are expensive, they take lots of energy to form the complex chains that we see in even the most rudimentary signs of life (even present day viruses, a judgement call whether you want to call them alive or merely complex crystals).  

So the trick is how we get from here to there or rather from there to here.

One possibility is clay.

Clay is composed of silicon crystals or silicates. These silicates absorbed the rudimentary carbon crystals, stabilizing them in a framework that allowed carbon crystals to grow more complex. Again, no intent is necessary.

So, now we have increasingly complex RNA molecules that replicate themselves (about as big as the smallest viruses today), but that's all they do. Remember we're still talking about crystals.

Ah, but we still have those protein-like amino acid structures around too. Get these two together and what's called a hyper-cycle appears. I see it as a kind of chain reaction whereby the protein-like structures enhance the complexity of the basic RNA (for that is what proteins do) and the RNA in turn enhances the production of proteins. At first, however, this is done indirectly over a very complex chain of events -- I don't know the sequence of events for this to take place.

At some point, the most stable form of RNA and the simplest form of protein merge so that a fragment of the protein is actually in the RNA sequence.And now you have RNA dictating the protein sequence, making it ever more complex and allowing for it to in turn become more complex as a result of the ever increasing complexity and efficiency of the protein.

No life yet, but an evolutionary process nonetheless.

The point, however, doesn't get us away from the Intelligent Design problem. It's still there and reading Dempsky's response in the other thread, he's quite willing to place Intelligence anywhere in the process -- including a fine tuner of physical laws.

For what we don't know is why physical laws work the way they do and not in some other way. We don't know why (not how) proteins have the effect they do on RNA, why they catalyze chemical reactions.

But then we don't know why matter should have mass either or why gravity obeys the inverse square law (apparently there is a theory in quantum mechanics for that so I'll just say I don't have a clue as to why gravity obeys the inverse square law).

  


serenity blaze
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7 posted 10-08-2007 02:28 PM       View Profile for serenity blaze   Email serenity blaze   Edit/Delete Message      Find Poems  View IP for serenity blaze

 
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