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Old 12-17-2007, 07:32 AM
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First Life On Earth, Debate: Abiogenesis vs Creationism

This is an informal debate, posting is restricted to the participants.

Jerrwickey will affirm the following statement,

"The likely hood of the existence of a process, not yet discovered, but of currently understood strictly chemical activity, unaided by some unspecified extra natural force, which resolves to produce a minimal genetic based organism, approaches zero."

Mister Agenda will rebut.

This debate was originally issued as a challenge by jerrywickey. Mister Agenda has accepted Jerry's challenge and is prepared to take the position of rebuttal. Jerry and Agenda, along with the input of many other FC members, have hashed out the above statement and are ready to proceed with the debate across a mutually agreed time line. You can read these discussions in the thread Rrrrready to Rrrrrumble! Evo. vs Creo.

If anyone besides Jerry and Agenda would like to contribute to the debate, you are more than welcome to set up camp and assist one or the other. Just create a new thread in which you can discuss the ongoing debate. Current discussions and commentary about this debate can be found here, Debate discussion and commentary.
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Old 12-18-2007, 02:37 AM
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This will by my first post for the debate. Many thanks to Kyman for his supporting role in moderating our debate. And I feel confident of Mister Agenda's competence.

I will present the first argument in affirmation of the statement that:

"The likely hood of the existence of a process, not yet discovered, but of currently understood strictly chemical activity, unaided by some unspecified extra natural force, which resolves to produce a minimal genetic based organism, approaches zero."

While this statement is a little "egg head," creationist should be routing for me. I am affirming this statement which simply says "The very first stages of life on earth could not have started by any unaided chemical activity." I do not intend to suggest or describe in any way what manner of extra natural force might have been involved. Only that it is not any currently understood principle. And that it could not have been the theory most commonly referred to as "evolution" namely that life arose by accident of chemistry and once having taken root, evolved into the many forms we see today.

This first part of the debate will deal exclusively with the first step, that of the formation of first life. After concession of one party or the other, we may elect to continue to argue the process by which we see all the many forms of life today. And that second portion will begin with a separate from the above but related statement.

To successfully pursued anyone of the above statement, I will have to show that no natural chemical activity could have produced a minimal genetic organism. If no natural chemical activity could reasonably lead to a minimal genetic organism, and since we observe the existence of minimal in addition to very complex genetic organisms, then obviously science must investigate other forces which must have been applied in the origin of these organisms which do not abide by the currently accepted natural laws of physics and chemistry. I do not propose to suggest any possible source for these forces, only that these forces are not described by our current understanding of the natural laws of physics and chemistry.

To accomplish this I will ask Mister Agenda four questions. I presume he will likely agree on at least three. He and I will probably argue about the last one and perhaps one of us will concede. If not, he will then ask me questions of his own construction.

The following questions are explained in greater detail further below, both to define my use of any term in question by Mister Agenda, and to provide persuasive explanation for interested readers. Terms in bold will be repeated below and the explanation will follow.


==================
The minimal biologic organism conclusively could not have been first life. Current research proposes the minimal organism consists of a system of 214 protein coding genes, a ribosome with matching genetic translation code and a polymerase protein system. The 64 codon to 20 amino acid translation code alone, let alone the other components of this system are far too complex to have first arisen with out predecessor. Evolution poses that multiple steps prior to any such organism must have existed. And that genetic based organisms must necessarily have arisen from some first replicator which was pre biotic.

Question number 1

The "first replicator " could not have required the assistance of complex proteins or organic molecules to achieve replication. Do you agree?

(for the definition I am using for the terms and for explanations and descriptions of a minimal organism, genetic material, ribosome and polymerase systems, first replicator molecule read below)

Question number 2

All current life on earth however, shares many identical sequences with the minimal organisms. The likelihood of these identical sequences arising by coincidental parallel multiple evolutionary pathways is not reasonably likely. Do you agree?

This is a very important question. I will draw on your answer later. Answer very thoughtfully. I do not want to win by deceit or trickery. If there is a notable exception, please feel free to agree but with a caveat for that named exception.

Evolution supposes that some in-organic FIRST replicator molecule arose at some point in the distant past. The characteristics of this first replicator must have been: 1) arising with out the aid of complex organic molecules, 2) it must catalyze production of an identical molecule or if involved in the reaction, the reaction must produce at least two identical molecules AND 3) it must copy, with fidelity any mutations which occur in the molecule.

Question number 3

Do you agree with these 3 characteristics of the first replicator molecule?

It is only by this last characteristic, that the possibility of this first replicator to "grow" into a more complex molecule and later the first minimal organism is possible.

Unlike organic molecules, which are nearly limitless in possible number and complexity, the number of in-organic molecules are finite and are well cataloged and while considerable in number, are strongly limited by the facts that there are only about a 100 elements as building blocks and the interaction of these elements is well understood and is limited by well understood principles of in-organic chemistry.

As such The theory of evolution supposes that this first replicator molecule must have arisen by the well understood principles of natural, in-organic chemistry operating on about 100 atomic elements

The study of these atomic relationships is called chemistry. Chemistry has cataloged very nearly every common non organic molecule, or attainment of atoms. We understand them well. The very complex functionality of proteins makes chemistry very complex. But in-organic chemistry is far simpler. Modern science can predict with incredible accuracy nearly every possible in-organic molecule.

It is from these in-organic molecules we will need to design our first replicator molecule. Since no organic molecules could have been present.

But modern scientific investigations have not yet produced a single example of a self replicating molecule which is capable of displaying the above essential characteristic of such a first replicator.

Question number 4

Are you able to show this debate, even a "theory" describing a "possible" "candidate" for such a molecule which must spontaneously arise?

If you are unable to demonstrate even the plausible chemical parameters of such a molecule,

given the well understood chemical engineering principles describing in-organic chemistry,

and given the far simpler and better understood chemical principles of in-organic chemistry,

and given the utilization of any atmospheric conditions which such chemical engineers may deem most conducive to such a molecules first rise,

and given the availability of any elements or simple in-organic molecules which such chemical engineers deem most conducive to such a molecules first rise....

If you are unable to demonstrate this with all these advantages, I ask you to concede the debate.





FOLLOWING ARE DEFINITIONS AND EXPLANATIONS OF THE ABOVE QUESTIONS listed by terms in bold face above.



minimal biologic organism / genetic material, ribosome and polymerase systems

A minimal genetic organism is that simplest of organisms which is capable of commandeering ambient material and energy and synthesizing its own components. And doing so by means of instructions contained in genetic sequences of nucleotide.

Any genetic system consists of three items. (Bear with me. This description is long. It is to my benefit to make readers fully aware of the complexity of contemporary genetic based life. But to be sure, this complexity alone DOES NOT prove that it could not have arisen by only un-natural means.)


1 Polymerase Protein system --

Proteins are made of a chain of amino acids. Each amino acid is about 10 to 20 atoms in size and exhibits very specific chemical properties. These amino acids bind to each other in specific ways and when they are arraigned in a certain but finite number of sequences, the combined chemical properties of the amino acids working in concert cause amazing functionality.

The most complex of these protein systems is the Ribosome. The best way to describe this complex protein system is to call it a micro machine made up of individual atoms which work together to undulate, move and manipulate long strings of mRNA in its work to produce more proteins under the specific instructions given to it by DNA.

Another important protein system is the Polymerase system. This system of proteins acts to identify the location of the next protein coding genetic sequence along the long DNA strand, which the Ribosome is next to produce. It then copies this portion of DNA to mRNA and makes it available to any proximate Ribosome for translation to a new protein for which the DNA codes.

2 Ribosome --

A very complex system of proteins which acts to "read" and "translate" each of the 64 possible arraignments of each codon of a genetic sequence into one of the 20 or so amino acids. A few of these amino acids occur in nature by random. But most do not occur naturally. They are synthesized only by the functionality of complex proteins which are built by Ribosome under the specific instructions of the DNA sequence coding for proteins whose purpose is to synthesis these crucial building blocks of life.

(It is important to note that even though many of these building blocks of life could not have been available when life first arose because they are a product of life already living, this DOES NOT prove that amino acids which do not occur naturally were required by first life. It is theorized that the later more complex amino acids were designed by the evolutionary process to answer specific evolutionary pressures.)

As each amino acid is selected according to the Ribosome's "interpretation" of the codon, it is attached to the previous amino acid, until a peptide sequence is produced of often hundreds of amino acids in length. The last codon of every protein coding genetic sequence ends with one of these three arraignments of three of the four nucleotides. Thymine, guanine, adenine or Thymine, adenine, adnenine or Thymine, adenine, guanine.

Once this termination or stop codon is encountered by the Ribosome, it releases the growing peptide chain of amino acids and the chemical functionality of the peptide is now entirely subject to the complex chemical arraignments of its atoms.

3 DNA --

which stores among other things, instructions to assemble complex molecules called proteins. It stores them by utilizing small molecules of 15 or fewer atoms each, called nucleotides. These nucleotide bind to each other in two long strands which compliment each other.

Each strand is made of four different nucleotides Adenine, 15 atoms in size, Guanin, 18 atoms, Cytosine 12 atoms in size, and Thymine 15 atoms. Uracil replaces Thymine in the transcription process but this is unimportant to this discourse. These nucleotides are arraigned and translated in groups of three, called, codons, by the activity of a complex system of proteins called a Ribosome. Each codon represents one of 64 possible combinations of these four nucleotides.

As you read this description of genetic machinations, each of the three refer to the other two. You did not understand the whole process until you read all three. In the same way, it is obvious that all three systems must not only be present together but that the genetic translation code that the Ribosome uses to translate new proteins and the translation table utilized by the DNA instructions must be identical. Should two different translation codes arise in Ribosome which evolved independently of each other, a strand of DNA which codes for functional proteins under the translation code of one Ribosome will code for nonsense under the other.

All life on earth utilizes a single translation table, except for a few exceptions mostly involving begin and terminate codons. (I am throwing a bone to my adversary here. Since this seems to suggest a common origin and connection between all species on a basic chemistry level.)

DNA alone does nothing. If contained in a seed, it would simply sit there and rot. It merely stores the building instructions for proteins. Likewise the Ribosome is useless alone, with out the instructions describing which amino acids to put together and in what order. And the proteins themselves can accomplish a lot by themselves. But again, they will wear out and can not be replaced with out the Ribosome and DNA instructions to build more. All three must work together.

The current work on minimal organisms show that it seems to require a few less than 250 protein coding genetic sequences to provide all the required functions of allowing for replication, energy acquisition and nutritional acquisition. Each of the 214 protein coding genes are about 100 to 400 codons or 1200 nucleotides long. That represents a molecule of about 18000 atoms. Plus the approximately 50,000 atoms of the Ribosome and Polymerase protein systems which are required to be assembled and operating prior the production of the first protein described by the genetic instructions of this minimal organism. Obviously, if anyone is going to be persuaded that this minimal organism arose by natural process, there must have been a simpler, much simpler first step.

Sources for further study
http://www.pubmedcentral.nih.gov/art...?artid=1488858
http://arjournals.annualreviews.org/...v.genom.1.1.99



pre biotic / organic molecules / in-organic molecules

There exist in-organic and organic molecules. There are only a few more than 100 stable elements and only a fraction of these are available in sufficient number for the production of naturally occurring molecules. The number of possible arraignments which can occur spontaneously with out biological aid or catalysis is quite small compared to organic molecules, the number of which is incalculable, since DNA could carry the instructions to build molecules of any size and complexity.

In-organic molecules tend to be less than 20 atoms in size. Even crystals and other regular atomic structures repeat in units of less than 10 atoms. But organic molecules start at 20 atoms even for the simple amino acid tryptophan. Organic molecules range upward in size to well over 200,000 atoms, each arraigned specifically, atom by atom, according to sequences of genetic instructions, as recorded in DNA. The complexity and size of these complex molecules is unlimited.

This complexity and size do not alone preclude the natural formation of these complex molecules with out the aid of ribosomal molecular manipulation guided by genetic instructions. But these complex molecules, even the small simple ones do not occur with out such aid for specific, and well understood chemical rules.

While a particular atomic arraignment might be stable once the atoms are placed, due to valance shell considerations, ionic attractions and repulsions and other esoteric considerations, chemists are certain that many of these complex molecules could never come together with out genetic assistance. It is important to note that this does not alone preclude "evolution."

The theory of evolution supposes that complex organic molecules were not necessary for the first replicator to arise.

To be sure there are many possible inorganic molecules. But the number is finite and well cataloged, due to the well understood nature of the simpler arraignments

If you look around your surroundings right now, ninety percent of what you see is made of organic molecules. The dies in your clothing, the fabric itself, the fibers in the carpet the paint on the walls the cellulose in the ceiling tiles, if you look outside you will see bushes, trees, grass. You will be hard pressed to find a single example of a molecule which is not organic. Strictly defined for the purpose of this debate, organic is any molecule which is produced by the activity of proteins. While an in-organic molecule is a molecule which occurs naturally with out the aid of protein activity. In a world before any genetic activity, only in-organic molecules would be available for any pre-life chemistry

Water H2O is an in-organic molecule, others are CO2, (both water and carbon dioxide are often produced by biological activity But each also occur naturally therefore for the purposes of this discourse, I regard them as in-organic or pre-biotic.) Others are SO2, He, CO, S2, Cl2, N2, H2 CH4. These are ones likely available for use by first replicators. There are many more, thousands in fact, but the number is finite.

You see that a large in-organic molecule might be Sodium thiocyanate, NaSCN. This inorganic molecule is only 4 atoms in size and occurs with out the aid of any biologically process. But the simplest of organic compounds such as tryptophan C11H2N2O2 This simplest of organic molecules is 17 atoms in size and does not occur naturally. Organic molecules often top 40,000 atoms in size and are most often produced with perfect fidelity. Every atom is in a specific place.

There are only a few more than 100 stable elements and only a fraction of these are available to naturally occurring molecules. The number of possible arraignments which can occur spontaneously with out biological aid or catalysis is nothing compared to organic molecules, the number of which is incalculable, since DNA could carry the instructions to build molecules of any size and complexity.

While an organic molecule has atoms arraigned in a chemically stable configuration, it does not naturally occur because there is no chemical mechanism which allows the atoms to find that stable configuration. Organic molecules require the catalytic activity of other complex proteins to overcome the chemical obstacles which work to prevent the organic arraignment from forming. Once the catalytic function of the organic protein produces the arraignment, the organic molecule remains stable. O2, the oxygen that we breath, does not occur naturally. In a pre-biotic world any small amount of O2 would be immediately bound by C or H to form water or carbon dioxide. The immense biologic production of O2 over overwhelms the natural, inorganic processes which bind free di-atomic oxygen. And therefore we can breathe. There are only so many in-organic molecules.

Current science understands well the properties of atoms as they bind to each other. We understand very well why the element hydrogen likes to bind to itself and becomes di-atomic hydrogen. We understand well, why hydrogen almost never exists as a single atom. We understand that a single hydrogen atom, at liquid water temperatures and pressure simply will not remain alone.

The study of these atomic relationships is called chemistry. Chemistry has cataloged very nearly every common non organic molecule, or attainment of atoms. We understand them well. The very complex functionality of proteins makes chemistry very complex. But in-organic chemistry is far simpler. Modern science can predict with incredible accuracy nearly every possible in-organic molecule.

It is from these in-organic molecules we will need to design our first replicator molecule. Since no organic molecules could have been present.


first replicator molecule

The front runner for this molecule is amino adenosine triacid ester, discovered by researchers at MIT. This molecule is in-organic by the definition I use here. And it catalyzes production of itself. But...

Sources for further study: http://w3.mit.edu/newsoffice/tt/1990/may09/23124.html

Jerry
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Old 12-18-2007, 04:25 PM
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Jerry, I will try to reward your detailed challenge with adequate responses, but will have to break them up a bit.

Thanks so much for taking the time to clarify your terms and provide definitions. It's the first thing I would have had to ask working just from your questions.
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Old 12-18-2007, 05:00 PM
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My esteemed adversary,

Be my guest. I expect this to be an intellectually pleasurable experience.

Feel free to break it up any way that you feel is convenient for your explanation.

Should we stray from the four questions I ask, I will inform you of my concern. I am sure we will keep it inbounds. And Kyman will stand by.

Jerry
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Old 12-18-2007, 05:03 PM
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OK, Jerry, it's a little confusing when you use your own definitions for things. I've gotten used to the idea that you are unable to separate the theory of evolution from abiogenesis. Now you are redefining 'organic'. Organic chemistry is a bit of a misnomer, since it was originally thought that only biological processes could produce carbon compounds besides oxides, chlorates, and the like. Not only is amino adenosine triacid ester considered by chemists to be an organic molecule, so is methane (CH4). Am I correct in concluding that by 'organic' you mean 'biological'?
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Old 12-18-2007, 05:10 PM
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If you propose alternate terms one for any molecule which can form with out the aid of protein activity and one for molecules which have very great difficulty forming with out such aid, so great as to preclude their presence in any usable manner in a pri-biotic world, I would be glad to adopt those terms.

Jerry
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Old 12-18-2007, 05:21 PM
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It is this very quality of fluidity in bio chemistry that makes this debate troublesome.

"Organic chemistry is a bit of a misnomer, since it was originally thought that only biological processes could produce carbon compounds "

To successfully consider this debate, we must agree on terminology which is more strict than convention. But I am open to any alteration of terminally, even coining a new term just for this debate, just as:

"anti-proteinesque" molecule for any molecule which is sufficiently capable of forming with out biological aid

And

"protienesque" molecule for any molecule which requires biological aid to form in any significant quantity.

Just suggestions. But it is important to make this distinction if we are to understand the first replicators.

Jerry
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Old 12-18-2007, 05:51 PM
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How about 'biotic' and 'abiotic'? Abiotic molecules are not necessarily abiological (eg, CO2 is a product of respiration but can certainly form sans metabolism). If I were to postulate, say, abiotic nucleotides I would be claiming that nucleotides (or at least certain nucleotides) can form through non-biological chemical processes.
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Old 12-18-2007, 07:34 PM
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Done!

Biotic molecules are molecules which do not readily form with out assistance, aid, catalysis, or other influence of proteins or RNA enzymes.

Abiotic molecules are molecules which readily form with out assistance, aid, catalysis, or other influence of proteins or RNA enzymes.
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Old 12-18-2007, 07:48 PM
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If you promise not to worry the term 'readily' too much, ok. I would say that abiotic molecules would have to be able to form in some quantity, so 'vanishingly rare' would not be 'readily' enough, but it would not have to be AS readily as biotic formation.

"Question number 1

The "first replicator " could not have required the assistance of complex proteins or organic molecules to achieve replication. Do you agree?

(for the definition I am using for the terms and for explanations and descriptions of a minimal organism, genetic material, ribosome and polymerase systems, first replicator molecule read below)"

Restating as "The first replicator could not have required the assistance of biotic molecules to achieve replication", I agree with this statement.

However, I do not concede the particulars of your helpful definitions, if I can show, for example, a possible 'more minimal' replicator, I do not want it disallowed on the grounds that I have conceded your definitions along with your statement. I'm not a molecular biologist, (I just have a BA in Psychology), I'm going to have to do research pretty much at each step.

Is my concession of this point acceptable with the stated caveat?
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Old 12-19-2007, 04:44 AM
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Yes, given our understanding as to the definition of "biotic" molecules and your statement:

"The first replicator could not have required the assistance of biotic molecules to achieve replication,"

We concur. I agree with this statement as well and this answers my first question with our agreement on that questions.

I understand you may retain certain points about which we may still wrangle. Such as exactly how a first replicator molecule or system of molecules may behave. and on how many of these molecules may have came into existence.

This number will actually become an important point later in this debate. This number represents an important hysteresis, the implications of which will be another thing about which we may wrangle.

But we will get to that in due time.

We have agreed on question number 1, if we agree that any chemistry that might have taken place, must have taken place in an "abiotic" environment.

I believe we have agreed on this.

I also, as you, do not hold a formal degree in molecular biology.

And of course, if I revisit our agreement on this point, you are free to remind me of your caveat in this agreement.

Jerry
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Old 12-19-2007, 02:30 PM
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Good! On to:

"Question number 2

All current life on earth however, shares many identical sequences with the minimal organisms. The likelihood of these identical sequences arising by coincidental parallel multiple evolutionary pathways is not reasonably likely. Do you agree?

This is a very important question. I will draw on your answer later. Answer very thoughtfully. I do not want to win by deceit or trickery. If there is a notable exception, please feel free to agree but with a caveat for that named exception.

Evolution supposes that some in-organic FIRST replicator molecule arose at some point in the distant past. The characteristics of this first replicator must have been: 1) arising with out the aid of complex organic molecules, 2) it must catalyze production of an identical molecule or if involved in the reaction, the reaction must produce at least two identical molecules AND 3) it must copy, with fidelity any mutations which occur in the molecule."

I agree that it is likely that all current life is descended from the first successful replicating molecules and that all life probably shares coding derived from abiotic replicators.

However, it is not necessary that there were not multiple cases of replicator origination (what are the odds? no one knows) or that our current genetic code preserves information from abiotic replicators. For example, viruses may have been involved in the transition from RNA replicators to DNA storage, and it is possible that modern RNA only superficially resembles abiotic RNA replicators. Granting these possible complicating factors though, I agree with the statement. Given your warning I feel I may be taking a wrong step, but I trust we can resolve any honest misunderstanding.

I hope to be able to engage more fully next week, providing my plans to purchase a new computer for my home materialize. Tomorrow, question 3!
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Old 12-19-2007, 07:00 PM
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Do I understand correctly? That you believe that all, every genetic based organism, on earth shares at least some of the same genetic sequences as all the others?

Or are there exceptions? Do organisms exist which have no genetic sequences in common with any other organism?

I am supposing that you agree with the first. I am just checking.

While we will probably both draw on this in the second debate, should it take place, I might draw on this agreed fact later to demonstrate a principle of Dr. Turing's work on computable tasks.

And yes, I while I want an answer before there can be any taint by the temptation of the constraints of the question, at the same time, I am not interested in pressing an answer that will not fit.

Also it is possible that I will not draw on this.

Glad you hear of the new computer. Time is not that important to me. Often it takes time to carefully consider. I don't see either of us delaying for an unreasonable time.

Jerry
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Old 12-19-2007, 07:32 PM
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I don't know of any organism with entirely unique genetic sequences, so that is my belief, provided some odd critter with unique coding doesn't turn up.
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Old 12-19-2007, 10:05 PM
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I agree. To my knowledge there are no organisms which utilize genetic material and which do not share many nucleotide sequences with other organisms.

Jerry
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