Abiogenesis

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I find it amazing that a plant can take the light from a nearby star and through a series of complex photoelectric/chemical mechanisms produce the raw materials for animal bodies to produce glucose; thus allowing you to post on these boards.

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Plants don't "produce the raw materials for animal bodies to produce glucose". Plants produce the glucose themselves and then animals eat plants (or other animals that have eaten plants) and thereby acquire the presynthesized glucose.

Has abiogenesis been observed? No.What is the evidence for it? Depends on your definition. Some people use logic such as the following:1) when the universe began there was no life
2) there is life now
Therefore, life must have arisen from nonlife somehowThat logic leaves open a wide range of mechanisms for abiogenesis, including the supernatural. Although the above argument is used sometimes, it should be rejected as it misuses the term abiogenesis (after all, in that sense, even YECs would accept abiogenesis).So the simple fact that we know there is life now should not be used as evidence that abiogenesis occurred (i.e., in the scientific sense: spontaneously).There is no empirical evidence that life can arise from non-life, but there is circumstantial evidence that it can. That is, there is evidence that can be used as a basis for extrapolation. For example, as some mentioned, living organisms don't contain any "mysterious" elements - they contain the same elements found in inorganic substances; and all aspects of life can be fully described using only the "laws" of natural sciences; finally, origin of life experiments have had limited success in creating possible pathways from non-life to life (there is no complete pathway known, just various bits and pieces of various paths that are assumed to be linked by yet-unknown processes).[This message has been edited by DNAunion, 03-07-2004]

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Finally, DNA can exist outside a living cell although it degrades with time -- no longer has the mechanic doing tune-ups ... but it is not the minimum requirement for abiogenesis to have occurred.

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So far so good...

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Viruses use an abbreviated RNA that hi-jacks the cell mechanism to replicate its nefarious (to us) messages.

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Which requires DNA. The host cells wouldn't be alive without their DNA, and without living host cells viruses couldn't "replicate".Second, there's no consensus as to whether or not viruses are alive.

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Then we get to prions like the ones that cause mad cow disease, which are even less 'complete' than viral RNA ...

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But since prions are not living, they're an irrelevant example.

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DNAunion: Which requires DNA. The host cells wouldn't be alive without their DNA, and without living host cells viruses couldn't 'replicate'.

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Do we know the mechanisms of viruses outside a host environment re survival and replication? Are there conditions that would allow replication?

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Yes we know them, and not they cannot. Here's a bit on viruses.

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Viruses are obligatory intracellular parasites — that is, they absolutely require living host cells in order to multiply. (Microbiology: An Introduction: Sixth Edition, Gerard J Tortora, Berdell R Funke, and Christine L Case, Benjamin Cummings Publishing, 1998, p360)

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"Viruses are not cellular and cannot independently perform metabolic activities. They do not have the components necessary to carry on cellular respiration or to synthesize protein and other molecules. All living organisms contain both DNA and RNA, but a virus contains either DNA or RNA, not both. Viruses can reproduce, but only within the complex environment of the living cells they infect. ... Viruses have genetic information that can force the host cell to replicate the viral nucleic acid and to synthesize the capsid and envelope components. The genetic information in a virus can take over the translational and transcriptional mechanisms of the host cell." (Biology: Fifth Edition, Eldra Pearl Solomon, Linda R Berg, & Diana W Martin, Saunders College Publishing, 1999, p482)

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Viruses are subcellular parasites that are incapable of a free-living existence but invade and infect cells and redirect their synthetic machinery toward the production of more viruses. Viruses cannot carry on all of the functions required for independent existence and must therefore depend for most of their needs on the cells they invade. (The World of the Cell: Third Edition, Wayne M Becker, Jane B Reece, and Martin F Poenie, Benjamin/Cummings Publishing, 1996, p104)

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A virus is a small parasite that cannot reproduce by itself. Once it infects a susceptible cell, however, a virus can direct the cell machinery to produce more viruses. (Molecular Cell Biology: Fourth Edition, Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell, W H Freeman & Co., 2000, p191)

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Also, see my long quote in the next part.

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DNAunion: Second, there's no consensus as to whether or not viruses are alive.

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the definition of life is a tough one indeed. Do a google on [definition life] and there is a lot of reading with no clear end in sight. Morales gives it a pretty good whack (but too much about too little) at: Psychozoan: The Definition of Life

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Here are some statements that directly address the question of are viruses living.

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In contrast to bacteria, viruses do not consist of cells. Biologists consider them to be nonliving particles. (Biology: Fifth Edition, Eldra Pearl Solomon, Linda R Berg, & Diana W Martin, Saunders College Publishing, 1999, p481)

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The question is sometimes asked whether or not viruses are living. The answer depends crucially on what we mean by living, and it is probably worth pondering only to the extent that it helps us more fully understand what viruses are — and what they are not. The most fundamental properties of living things are motility, irritability (perception of, and response to, environmental stimuli), and the ability to reproduce. Viruses clearly do not satisfy the first two criteria. Outside their host cells, viruses are inert and inactive. They can, in fact, be isolated and crystallized almost like a chemical compound. It is only in an appropriate host cell that a virus becomes functional undergoing a cycle of synthesis and assembly that gives rise to more viruses.

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Even the ability to viruses to reproduce has to be qualified carefully. A basic tenet of the cell theory is that cells arise only from preexisting cells, but this is not true of viruses. No virus can give rise to another virus by any sort of self-duplication process. Rather, the virus must subvert the metabolic and genetic machinery of the host cell, reprogramming it for synthesis of the proteins necessary to package the DNA or RNA molecules that arise by copying the genetic information of the parent virus.

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It is only in the genetic sense that one can think of viruses as living at all. Another fundamental property of living things is the capability of specifying and directing the genetic composition of progeny — an ability that viruses clearly possess. It is probably most helpful to thing of viruses as quasi-living, satisfying part but not all of the basic definition of life. (The World of the Cell: Third Edition, Wayne M Becker, Jane B Reece, and Martin F Poenie, Benjamin/Cummings Publishing, 1996, p105)

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The question of whether viruses are living organisms has an ambiguous answer. Life can be defined as a complex set of processes resulting from the actions of proteins specified by nucleic acids. The nucleic acids of living cells are in action all the time. Because viruses are inert outside of living host cells, in this sense they are not considered to be living organisms. However, once viruses enter a host cell, the viral nucleic acids become active, and viral multiplication results. In this sense, viruses are alive when they multiply in the host cells they infect. Depending on one’s viewpoint, a virus may be regarded as an exceptionally complex aggregation of nonliving chemicals, or as an exceptionally simple living microorganism. (Microbiology: An Introduction: Sixth Edition, Gerard J Tortora, Berdell R Funke, and Christine L Case, Benjamin Cummings Publishing, 1998, p360)

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And on to prions...

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DNAunion: But since prions are not living, they're an irrelevant example.

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Again they are able to replicate within a system.

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A printed page is also able to replicate within a system : just put it into a photocopier. Of course, we realize that the paper is not what is doing the replication. Same with a prion.A prion CANNOT replicate itself. It absolutely relies upon normal cellular processes to produce a specific protein — only then can the prion come along and simply convert that normal, preexisting protein into a prion. Without DNA, RNA, ribosomes, tRNA, enzymes, etc. there would be no normal protein for the prion to then simply convert.There is no clear consensus as to whether or not viruses are living, but there is a clear consensus that prions are not.[This message has been edited by DNAunion, 03-20-2004]

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I don’t think you are looking at this with a fully open mind.

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I don't think you are looking at this with a fully educated mind.

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The evidence to date is that viruses do not replicate on their own within the environments that we know about. The absence of evidence is not evidence of absence however,

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Facts are evidence. Viruses do NOT and CANNOT replicate themselves. That's basic BIO101 stuff. Now YOU have an open mind and reread what I posted from the several undergraduate biology texts.

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and does not rule out that a certain environment may exist wherein viruses could replicate.

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Sure...inside of living host cells! A virus is analogous to a printed page: they both require something completely separate and far more complex to do the work necessary to "replicate themselves".

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That environment could be something closer to a primordial environment...

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So there were living host cells in the primordial environment to replicate the viruses?

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... or one of the extremophiles type...

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Extremophiles are living - they're cellular.

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... or depend on a random input of energy in a pre-bio soup.

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A random input of energy in a pre-bio soup? Pretty naive. Besides, if you're switching to talking about a self-replicating RNA molecule then do so..don't try to call it a virus.[This message has been edited by DNAunion, 03-21-2004]

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If I remember last midterm correctly, DNA only exists in living cells.

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Better would be to say that DNA is produced only in living cells (as someone already did, one could nit pick your statement and say that DNA can exist outside of living cells).

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One thing I want to know is how non-life can change into life without DNA?

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How about using the other important nucleic acid, RNA? That’s one of the main theories: at some point RNA alone served both the informational and catalytic functions associated with life.

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DNA's pretty complicated, kind of has the 'irreducible complexity' thing to it.

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A misuse of the term irreducible complexity (a term that seems to be assigned by someone to just about anything more complex than water!).

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Even if this 'non-living organism', if you will, suddenly started making DNA, it'd take a long time for even part of DNA to be completed, and from what I know about irreducible complexity, even if something has DNA it just doesn't think that far into the evolutionary future.

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A self-replicating RNA would be the organism. OOL researchers (and any rational and objective person) would be completely satisfied if a prebiotically plausible process were found that could produce a self-replicating RNA molecule able to undergo evolution.

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Not only that, but DNA is made up of proteins and acids.

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DNA is made by proteins, but is not made up of proteins. Nucleic acids (DNA and RNA) are made of individual units called nucleotides, which are linked together in a chain. Each nucleotide consists of three parts:1) a nitrogenous base (adenine, guanine, cytosine, and either thymine (DNA) or uracil (RNA))
2) a pentose (5-carbon sugar: deoxyribose (DNA) or ribose (RNA))
3) a phosphate groupOOL researchers have had success in making most or all of the individual components under prebiotically plausible conditions. The problems arise at higher levels (joining the three parts together to form nucleotides, getting the nucleotides to link together into polymers, and getting the particular polymers that could participate in some kind of mutation/selection process).

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I would like to know where you found information on the self assembly of ribose...

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In OOL-related experiments, ribose has been produced more than one way. There are some problems with these methods though: the prebiotic plausibility of the processes can be questioned, the wrong type of ribose is produced, or ribose is swamped out by many other sugars. Also, both enantiomers are formed in equal amounts (which leads to the problem of enantiomeric cross inhibition...but that's are the polymerization level).

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DNAunion: Facts are evidence. Viruses do NOT and CANNOT replicate themselves. That's basic BIO101 stuff. Now YOU have an open mind and reread what I posted from the several undergraduate biology texts.

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AbbyLeever: ... Only when every environment in all the pasts have been eliminated can you come close to making an absolute statement of that type.

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Wrong. Science can and does make claims based on what is known, all the time.Now, by your reasoning, we can't say that a star can't just turn into a cat or a computer overnight. After all, just because we've never seen it occur doesn't mean we can come close to ruling it out. Gee, there are all those billions of billions of stars out there...anything is possible! Right?Science knows of reasons why a star can't just turn into a computer, and also why a virus can't replicate itself.

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AbbyLeever: Of course Bio101 levels sometimes simplify things so as not to introduce too much at once ... you might want to try xenobiology 101 ... it may help.

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Nope, your evidence didn’t help at all. In fact, the word VIRUS doesn’t even appear once on the page you linked to![This message has been edited by DNAunion, 03-23-2004]

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DNAunion: Extremophiles are living - they're cellular.

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AbbyLeever: sorry I thought you would understand I was talking about extremophile environments not the extremophiles themselves.

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So you’re claiming that if we put viruses in extremely salty, or extremely acidic, or extremely high pressure, or similar extreme conditions that they would then be able to self-replicate? Your support for this Nobel Prize-worthy "finding"?

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Notice that only a little while ago biologists were saying that life couldn't exist in such extreme conditions. Then they found it. Your argument against viruses is the same logic: we haven't seen it therefore it can't be true ... a limited argument.

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So you believe that a star can turn into a computer overnightright? That conclusion follows from the same logic you’re using against me.

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AbbyLeever: The question was (and is) whether something else can provide the missing elements that are currently provided by living cells to allow {viruses or close cousins} to reproduce. Could that have been how the first replicators worked.

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Oh no, that’s not the question at all. You made flawed statements about viruses and prions specifically, and I pointed out the problems with those statements of yours. Now you’re trying to slyly move the goal posts.As I said, if you are going to SWITCH to discussing self-replicating ribozymes then do so, but don’t try to call them viruses.[This message has been edited by DNAunion, 03-23-2004]

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AbbyLeever: Your denial of possibilities is quite amusing.

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No, it's your overactive imagination that's amusing.

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AbbyLeever: At some point in the search for the beginning of life you will have to get out of the cell as we know it ...

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And where did I say otherwise? Nowhere. You're confused.[This message has been edited by DNAunion, 03-23-2004]

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LizardBreath: In order to get an agreed upon context you need an infusion of intelligence...

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That's where we disagree (I'm talking about the origin of life, which your analogy addresses).The key is INFORMATION, not intelligence. While I agree that a large amount of information would be needed for an RNA to replicate itself, I don't agree that it would require a God or ETI's to supply that information.

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LizardBreath: In other words, even if the DNA could create itself through random chance and time, what is this stuff supposed to do with itself once it comes into being without some force guiding it's implementation?

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Just what life today does...reproduce. That's the primary function of life...to produce more of itself.[This message has been edited by DNAunion, 03-23-2004]

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Black: If abiogenesis were possible, we would expect to observe certain things. We would be able to predict that certain things were possible, namely:

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(1) Amino acids could form naturally
(2) Amino acids could link together (as peptides) and reproduce naturally
(3) RNA could form from amino acid chains (peptides)
(4) RNA would need neither DNA nor protein to catalyze its own replication

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These are what's predicted. We now know all these things can happen.

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We do? Let's look at them one at a time.

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(1) Amino acids could form naturally

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Correct.

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(2) Amino acids could link together (as peptides) and reproduce naturally

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This has never been demonstrated. If you believe it has, please post your support.

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(3) RNA could form from amino acid chains (peptides)

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RNA is not even made of amino acids...it's made of nucleotides.

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(4) RNA would need neither DNA nor protein to catalyze its own replication

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That's the theory. No prebiotically plausible experiment has accomplished this.The only actually supported point you have is that amino acids can form naturally. The rest is theory, not fact demonstrated by experiments carried out under prebiotically plausible conditions.

Go back and look and you will see that I have not made errors, and if you claim I have, they you are wrong.You continue to reject logic and science...not my problem.[This message has been edited by DNAunion, 03-24-2004]

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AbbyLeever: one last chance to think:
where do viruses come from?

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Uhm, how is that any kind of last chance when it is the FIRST time you asked me that question?Here, let me give it a try.One last chance to think AbbyLeever: what's the difference between the lysogenic and lytic cycles?[This message has been edited by DNAunion, 03-24-2004]

Okay, let me sum up these exchanges. Although your original point was correct, your two supports for that point were both flawed. I agreed with your point, but exposed the flaws in your support.Let's go back to the original.

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DNAunion:

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AbbyLeever: Finally, DNA can exist outside a living cell although it degrades with time -- no longer has the mechanic doing tune-ups ... but it is not the minimum requirement for abiogenesis to have occurred.
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DNAunion: So far so good...

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AbbyLeever: Viruses use an abbreviated RNA that hi-jacks the cell mechanism to replicate its nefarious (to us) messages.
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DNAunion: Which requires DNA. The host cells wouldn't be alive without their DNA, and without living host cells viruses couldn't "replicate".

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Second, there's no consensus as to whether or not viruses are alive.

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AbbyLeever: Then we get to prions like the ones that cause mad cow disease, which are even less 'complete' than viral RNA ...
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DNAunion: But since prions are not living, they're an irrelevant example.

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