Abiogenesis

fair enough (only an A???) ahahahaaaWhile I agree that abiogenesis has not been accomplished experimentally, I will not be surprised when it happens.

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The thing is, although we can make the conditions right to make the building blocks of life right before our eyes, has anybody actually created a LIVING cell from the building blocks of life? Untill I hear it's possible to create artificially, I'll have to say I can't see abiogenesis occuring naturally, and I think that's fair.

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Even if life is created in the lab, it is still not PROOF (as in ultimate proof) that life arose via a precise mechanism. 3.5 billion years is a long time ago, and any models that we create are tentative and will not tell us the specifics of how life arose on Earth.On the other hand, if self replicators do form spontaneously, then the possibility of life arising naturally is possible. Current research is getting closer and closer, but questions will remain. What it comes down to for me is the God of the Gaps fallacy. Natural mechanisms have been found for almost every natural phenomena previously ascribed to dieties. Hanging your faith on a dieties presence in natural phenomena is probably not the best route to take, because that gap in knowledge may be closed and your faith with it. I don't see how abiogenesis lowers the wonderment of life on the planet, but to some it may. Oh well, at least we live in a world where we can discuss these lofty questions.

"Even if life is created in the lab, it is still not PROOF (as in ultimate proof) that life arose via a precise mechanism. 3.5 billion years is a long time ago, and any models that we create are tentative and will not tell us the specifics of how life arose on Earth."That's a really good point: Just because something can happen doesn't mean it did. Guess that's something that both sides of the debate need to keep in mind.As for when (and if) we can create life from non-life, keep in mind that using a bunch of instruments and setting everything just right to prove that abiogenesis can occur naturally, without intelligent intervention is... kind of redundant. I'm NOT saying that such a success would invalidate natural abiogenesis, it's just that it wouldn't guarantee that its too often. But then again I guess one could argue that given enough time anything happens and so on.Either way, it won't effect my faith because I believe God plays by his own rules(chemical rules in this case) and created us through MOSTLY non-miraculous means. Then again, the materials would probably gather near or on the surface of the soil, and we were created from the 'Dust of the Earth'... but that's another speculation, and a whole other thread.

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Wanna feel God? Step onto the wrestling mat and you'd be crazy to deny the uplifting spirit.

hmmm

"Even if life is created in the lab, it is still not PROOF (as in ultimate proof) that life arose via a precise mechanism. 3.5 billion years is a long time ago, and any models that we create are tentative and will not tell us the specifics of how life arose on Earth."

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That's a really good point: Just because something can happen doesn't mean it did. Guess that's something that both sides of the debate need to keep in mind.

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It would be proof that life can originate when the conditions of the experiment occur in the real world. Of course it will not be proof of how it actually happened, as there is (still) a lot of debate about what the conditions were like on earth at that time.What I would expect to see, is that once a self replicating element has been achieved, that a number of similar experiments would follow using different conditions --- if for no other reason than to see how easily life could evolve on other planets: what are the limiting factors?And as the number of extra-solar planetary systems has sky-rocketed since the discovery of the first one, I would expect to see many successful experiments using many varieties of conditions.That is a prediction based on the way science works and the innate inquisitiveness of humans.Enjoy.

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As for when (and if) we can create life from non-life, keep in mind that using a bunch of instruments and setting everything just right to prove that abiogenesis can occur naturally, without intelligent intervention is... kind of redundant.

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If we have to intelligently measure the distance from the Earth to the Sun, does this mean that that distance was intelligently made? Nope. With respect to abiogenesis, even if the CONDITIONS were intelligently controlled, the resultant self replicators would be considered natural and not the product of intelligence. Another example, is ice intelligently created because you stick water in your freezer? Obviously not. If conditions and reactants set up by an intelligence is reasonably close to what we would expect in a natural early earth environment then the results can be considered indicative of what we would expect in nature. This type of rule is adhered to throughout science, and in the biological sciences especially.An example of possible intelligently made self replicators would be a step by step synthesis. An analogous procedure is drug manufacturing where each step in the synthesis is controlled to such a degree that the chances of this compound naturally occurring in the quantities seen in synthetic manufacturing is quite low. It is the step by step procedure that is the problem. Equating this to self replicators, it would be like creating a 3 million base genome and controlling the sequence base by base. Non-intelligently produced self replicators must have a large dose of randomness, and this must be reflected in the methodology.Argh, turned 30 last month and already I am getting long winded. I'll probably start repeating myself any minute now. And I'll probably start getting long winded too.

Agreed. However, I did state just after the end of that quote that it doesn't make the experiment irrelevant in the least.

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Wanna feel God? Step onto the wrestling mat and you'd be crazy to deny the uplifting spirit.

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

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Again they are able to replicate within a system.The [bottom up] question of abiogenesis is not life but the first replicator.The [top down] question of abiogenesis is what is the absolute simplest possible form of life. Dissecting DNA down to an absolute minimum for bacteria to still qualify as life brings us very close to virus type stuff at this point though controversy ensues.A professor at school mentioned the difference between practical and theoretical:

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Take a boy and a girl and stand them 10 feet apart. Every second, halve the distance between them. theoretically they never touch, but they get close enough for all practical purposes.

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the [top down] and [bottom up] approach is like that.

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we are limited in our ability to understand
by our ability to understand

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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]

I don’t think you are looking at this with a fully open mind. 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, and does not rule out that a certain environment may exist wherein viruses could replicate. That environment could be something closer to a primordial environment or one of the extremophiles type or depend on a random input of energy in a pre-bio soup. It is also possible that the viruses have lost mechanisms where they have found easier mechanisms to use from cells than from their [original development], even though that [original mechanism] may have differed significantly from modern cell biology. This would mean that they are not devolved bacteria but a separate form of life, perhaps one entirely based on RNA. ... we don't know. As mentioned regards prions, the development of a replicator is a relatively necessary first step whether it can be classed as [life by some definition or other] or not, even if that replicator uses a clay or crystal structure to form a molecular production [not so much Xerox as Widget building] machine. Perhaps "replicator" is the wrong word and we should be looking for "implicators" ("imps" for short?) first. Then one could look for how "imps" can be incorporated into proto-cell structures where they start to turn out product to maintain the proto-cells without necessarily replicating themselves.

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we are limited in our ability to understand
by our ability to understand

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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).

I would like to know where you found information on the self assembly of ribose or deoxyribose. If the sugar glucose is assembled in living things and if ribose and deoxyribose, especially ribose, can't self assemble then you have a very difficult problem with abiogenesis. I think it is very ironic that something simple enough to happen accidently has baffled the scientific community for hundreds of years. I would think if life arrose on it's own with no help then it should be very easy to duplicate. Yet with all our intellegence and advancements it still remains tantilizingly out of reach.

Diamonds also arise on their own. Do you think that they are easy to duplicate?Don't conflate "natural" with "simple", please. The universe is quite capable of great complexity on it's own.

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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).