The Origin of Life

[Jose]

The abiogenesis story nonetheless follows the same rules as the rest of science. We gather information--data, observations, etc--from the world. We then develop models to explain the observations. The rules are that we can't invent things for which there are no data. ... If we stick with facts--hard evidence from geochemistry and from experimental chemistry--we're kinda stuck with current ideas for the origin of life. We may be dissatisfied that we don't have a complete story yet, but that doesn't justify the response that so many people have: throw out everything we know, in favor of magical stories that emerged in a pre-scientific age.

But abiogenesis does exactly that. It invents a mechanism that explains the creation of life to fit with the theory of cosmogenesis even though there is absolutely no data to support it and ignores the masses of data that debunk it. ... Hard evidence from intensive experimentation suggests that life does not originate in this way at all. There is no evidence that biological/living processes can evolve from non-living self replicating molecules and all the data suggests that they do not. By all means believe it if you must but it isn't science.

The above exchange illustrates the basic issue. The Origin-of-Life researchers have lots of data and lots of ideas, but no absolute proof of a particular mechanism by which life certainly arose from plain old chemistry. The anti-evolution folks insist that the physical origin of life (as opposed to special creation) is hogwash, a flight of fancy for which there are no facts. They use this to claim that evolution is impossible, although "evolution" is what life does after it exists, not before.

Questions for Debate

1. Are there data and ideas? Are they valid? What is the current status of Origin-of-Life research?
2. What, if anything, has been debunked?
3. Is it valid to pretend that a chemical origin of life is impossible until it's been re-constructed in the lab, with a complete description of every step? We don't require this level of certainty for medical research; why require it for this?

__________________
Use a small broom for the corners.

[Jose]

Thank you all! This is going to be fun.

Let me throw into this a couple of things.

1. The first quasi-living things were much simpler than what now exists. It is necessary to keep this in mind, especially if we are to start making probability calculations. The relevant probability is not that of producing a bunch of present-day proteins, but of producing a much simpler self-replicating entity.

2. Current studies indicate that the most fundamental pieces of living things are RNA molecules. An enzyme like RNAse P, which cuts pre-tRNA molecules into mature tRNAs, is one molecule of RNA and one molecule of protein. The protein can be replaced entirely with a high salt concentration. The enzyme is actually the RNA molecule. Tom Cech's self-splicing RNA from Tetrahymena was the first of these catalytic RNA molecules to be verified. Since then, RNA catalysis has become pretty standard. Even the multi-protein ribosome, which is what assembles proteins, has a catalytic RNA. The proteins, like that of RNAse P, seem to be mere modifiers.

That is: what we see now is a world in which DNA is the information repository, and proteins are the "normal" machines. But, you don't need proteins to have catalysis of chemical reactions. RNA will do it. You don't need DNA to have information. RNA will do it.

Current thinking is that the first self-replicating thingies were RNA molecules, or things like them. Assembly of nucleotides has been shown to be catalyzed by the surface of clay particles. I bet we'd all agree that the early earth is likely to have had clay. Self-replicating RNAs, lurking in little pools or somewhere, could start things off--without any of the complexity required for assembling membranes or DNA, and without the confusion of transcribing DNA into RNA, and then translating it.

Another recent proposal is that DNA was an innovation of a virus-like thing, and got added to the mix well after the establishment of the "RNA world." Because DNA is more stable than RNA, it would be selected for where stability is helpful. But it would not be selected for where stability is not helpful, and where the flexibility of RNA molecules is more useful. DNA would make a great repository, or library of information. RNA would go out into the world and "do stuff." That's pretty much what we have now, with a couple of additional bits thrown in.

-----

So: what about thinking in terms of the first things being fairly simple self-replicating RNA molecules, and all that extra complexity that we see now being added incrementally?

[Grumpy]

PRIMITIVE LIFE

Self-Reproducing Molecules

Reported by MIT Researchers

By Eugene F. Mallove

News Office

A significant step toward understanding the origin of life may have been
made by a group of MIT researchers. Led by Professor Julius Rebek, Jr.
of the Department of Chemistry, they have created an extraordinary self-
replicating molecular system that they say might be regarded as a
"primitive sign of life."

It is not life itself, of course, but it is a kind of molecular model of
how self-replicationÑa most fundamental life processÑcan occur.

In work recently reported in the Journal of the American Chemical
Society, Professor Rebek and his coworkers, Tjama Tjivikua, a graduate
student from Namibia, and Pablo Ballester, a visiting scientist from
the University of Palma in Mallorca, Spain, described the creation of an
extraordinary self-replicating molecular system.

Ordinarily, it takes the complex biochemical machinery of a cell to
reproduce protein molecules. The building blocks of life simply don't
replicate themselves by themselves they need helpÑlots of itÑfrom
enzymes and above all from information carried in DNA and RNA.

How the whole business of molecular replication got started has been and
remains one of the central mysteries of the origin of life. The origin
of life is a classic "chicken-and-egg" dilemma. In the presumed
molecular evolution on primitive Earth, what came first, proteins or the
nucleic acids RNA and DNA? And remember that the enzymes necessary to
make proteins are themselves proteins, where did they come from?

Amazingly, the laboratory-made molecule that Professor Rebek and his
colleagues have created can reproduce itself without the "outside"
assistance of enzymes. As such, and because of its specific
constitution, the molecule embodies some of the "template" qualities of
a nucleic acid, and some of the structural qualities of a protein.

The researchers say in their paper, "At best, this can be regarded as a
primitive sign of life; at the very least, the system offers a bridge
between the information of nucleic acids and the synthesis of amide
bonds. It should be possible to design systems capable of peptide
[protein] synthesis on a nucleic acid backbone and thereby provide
models for events that occurred some time ago." That "some time ago"Ñin
case you missed it in the understated scientific proseÑis four billion
years ago on primitive Earth.

Technically, the self-replicating compound made by the MIT group is
called an amino adenosine triacid ester (AATE). This molecule was
initially formed by reacting two other molecules. [

The AATE replicates by attracting to one of its ends anester molecule,
and to its other end an amino adenosine molecule. These molecules react
to form another AATE. The "parent" and "child" AATE molecules then break
apart and can go on to build still more AATE molecules.

Professor Rebek's research is a continuation of work he began at the
University of Pittsburgh. Professor Rebek has been on the MIT faculty
since the spring of 1989. His work is supported by the National Science
Foundation.

http://web.mit.edu/newsoffice/tt/90/may09/23124.html

Sorry for the cut and paste but this was a short article that covers this very subject.

Grumpy

[achilles12604]

Several of those issues you are discussing (the initial ones), have already been solved. For example, when it comes to amino acids, they will form naturally in many atmospheres that have methene, with the addition of electricity. The Urey-Miller experiments showed that quite conclusively.

Actually their experiments were based on CHON not methane. Also, they had very specific amounts of each and added a very specific amount of energy to the system. I'm not sure why you think their experiment had methane. Perhaps you are aware of a source I am not. Everything I have read about their experiment only included very specific mixtures of CHON and some organic compunds.

Indeed, when NASA sent a probe to Titan, which has an atmosphere they think is similar to the early earth, the number of complex organic compounds that were in the atmosphere amazed them. I believe they expected some, but not at the levels that were found. Therefore, amino acids are very likely in the atmosphere that is thought to be the early earth.

Again what is your source and how accurate are they in this ussumption.

Here are a few problems with you just saying this.

http://www.technologynews.info/001335.html

The probe lost 18 years of data because of error at Nasa
The data they did collect was full of holes and patchy

I'm not saying that you are wrong. In fact I would expect there to be amino acids in other parts of space. But did you check you source before posting this information. That Probe was all but useless. Just keeping you honest.

Then, another piece of the puzzle is that amino acids will link togather on an exposed quartz crystal face to form simple proteins.

Amino acids will link anywhere to form protiens. This is what they do...

Again I am not disputing that amino acids linked to form DNA. In fact if they hadn't I wouldn't be typing would I. My point is that for the hundreds of links to just happen to be correctly assembled into a DNA strand which could create a self-replicating molecule, without any guidance and within just a few million years of when they could because of the surroundings, suggests someone assisting them.

The timeframe from when the earth was cool enough to begin to allow cells and life, to when there was life emerging was almost zero. (well a few million years but that is really zero on a comsic scale. Given the insaine complexity and the numbers of strands which all had to be assembled perfectly (one or two combinations off in any place and the whole thing fails), life appeared much to quickly to be due to random chance.

Going to Mits post, the card analogy. This would be like being given a deck of cards and you had to assemble the cards into one of a few possible combinations. Lets say since the possibilities of combinations within DNA is something times ten to the whatever power (4 to the 400,000 unless I am wrong) and the possibile hands that would have worked are somewhere aroung 10 to the 51, I am working from memory right now so my numbers may not be exact, this leaves a HUGE possibility of incorrect parings. Using the card analogy, this would be like telling the shuffeler to get ace through 2 in every suit. This is the only one that will work.

Now given enough time and repetitions I am sure that someday the would have all added up. But since life appeared very quickly as soon as it was possible, this would be like giving the shuffler a half hour deadline to complete this task.

Now do you understand what I am getting at.

You and I agree that life was probably going to happen sometime. However, the fact that it happened so quickly after earth was capable of sustaining life is what makes me believe there was intelligence behind the quick springing of life.

If you don't think so then get a deck and shuffle for 1 half hour. Tell me if it comes up Ace through 2 suited in that half hour without you helping by placing the cards in order.


As a final thought, I am not a believer in the God of Gaps. I do not think that God must have done whatever we can not yet explain. I am saying that the odds of it all happening so quickly and perfectly point to intelligent assistence. Just because we can understand the how . . . Doesn't mean God didn't do it.

[Grumpy]

achilles12604

Several problems with your post.

1. The first known life appeared at 3,8 billion years. Since the Earth is 4.5 billion years old, that is multi HUNDREDS of millions of years for these things to get going.

2. A complex molecule IS NOT REQUIRED, just replication. As I posted in my last post, these things have been shown through experiment to require only ONE amino acid paired with only ONE acid analase to start the process. Surely you would not argue that such a simple molecule would be unlikely given the amino acids are already made and delivered by comet!!!

3. To you 10 ^? is a big number, but to nature that many combinations could occur in a single cubic mile of earth(which has 10^? cubic miles of topsoil to work with, plus uncounted miles^3 of crust), add in a few HUNDRED million years and suddenly your big number becomes a near certainty. AND IT ONLY HAS TO OCCUR ONCE.

By the way is CH3, also part of CHON. And a reducing atmosphere doesn't have any free o2

Grumpy

[Grumpy]

achilles12604

Several problems with your post.

1. The first known life appeared at 3,8 billion years. Since the Earth is 4.5 billion years old, that is multi HUNDREDS of millions of years for these things to get going.

2. A complex molecule IS NOT REQUIRED, just replication. As I posted in my last post, these things have been shown through experiment to require only ONE amino acid paired with only ONE acid analase to start the process. Surely you would not argue that such a simple molecule would be unlikely given the amino acids are already made and delivered by comet!!!

3. To you 10 ^? is a big number, but to nature that many combinations could occur in a single cubic mile of earth(which has 10^? cubic miles of topsoil to work with, plus uncounted miles^3 of crust), add in a few HUNDRED million years and suddenly your big number becomes a near certainty. AND IT ONLY HAS TO OCCUR ONCE.

By the way methane is CH3, also part of CHON. And a reducing atmosphere doesn't have any free o2

Grumpy

[micatala]

Going to Mits post, the card analogy. This would be like being given a deck of cards and you had to assemble the cards into one of a few possible combinations. Lets say since the possibilities of combinations within DNA is something times ten to the whatever power (4 to the 400,000 unless I am wrong) and the possibile hands that would have worked are somewhere aroung 10 to the 51, I am working from memory right now so my numbers may not be exact, this leaves a HUGE possibility of incorrect parings. Using the card analogy, this would be like telling the shuffeler to get ace through 2 in every suit. This is the only one that will work.

pa

[micatala]

Going to Mits post, the card analogy. This would be like being given a deck of cards and you had to assemble the cards into one of a few possible combinations. Lets say since the possibilities of combinations within DNA is something times ten to the whatever power (4 to the 400,000 unless I am wrong) and the possibile hands that would have worked are somewhere aroung 10 to the 51, I am working from memory right now so my numbers may not be exact, this leaves a HUGE possibility of incorrect parings. Using the card analogy, this would be like telling the shuffeler to get ace through 2 in every suit. This is the only one that will work.

Now given enough time and repetitions I am sure that someday the would have all added up. But since life appeared very quickly as soon as it was possible, this would be like giving the shuffler a half hour deadline to complete this task.

Now do you understand what I am getting at.

I understand the point. I think we need to get down to some precisely determined numbers to decide how probable or improbably this is, even under the assumption of equally likely outcomes.

My point in my previous post which I perhaps didn't say very well was that getting a functional DNA (or smaller RNA or whatever self-replicating type of sequence we might consider) may be a lot more probably than Ace through 2 arranged in suits. For example, it might be that any sequence where the gap between adjacent cards is less than 5 would work. This would be a huge number of combinations. If, for example, there are 40 factorial 'functional sequences' out of the 52 factorial total possibilities, then the probability of getting a functional sequence goes up from 1 out of roughly 10^68 to 1 out of roughly 10^20. This is still of course quite small, but many orders of magnitude better than the first calculation.

If the entire earth could perform only 1 million 'shuffles' per second (say by having 10 million people take 10 seconds for each shuffle), it would take about 3 million years to perform 10^20 shuffles. Thus, one could obtain a fairly high probability of hitting any pre-determined functional arrangement in a fairly short amount of time.

In addition, one other issue that I have not seen dealt with is whether all of these sequences are equally likely to occur. In general, all of these sorts of calculations that I have seen assume this. However, it may be that some sequences, because of the structure of the molecules, are more likely to occur than others. Sort of like certain cards having an "affinity" for being close together (the 2's tend to attract each other for example, or the spades tend to attract each other). If the chemistry determines that at least some of the functional sequences (or even subsequences of what turn out to be longer functional sequences) are more likely to occur than 'random' then you can pretty much throw these calculations out the window, at least until you get some reasonable estimates on the relative likelihood of the possible sequences.

In my view, until this is done, any calculations purporting to show that "event A is practically impossible or at least extremely unlikely in the given time frames" where A is some sort of chemical combination process resulting in a self-replicating molecule are essentially worthless.

[Goat]

Several of those issues you are discussing (the initial ones), have already been solved. For example, when it comes to amino acids, they will form naturally in many atmospheres that have methene, with the addition of electricity. The Urey-Miller experiments showed that quite conclusively.

Actually their experiments were based on CHON not methane. Also, they had very specific amounts of each and added a very specific amount of energy to the system. I'm not sure why you think their experiment had methane. Perhaps you are aware of a source I am not. Everything I have read about their experiment only included very specific mixtures of CHON and some organic compunds.

Indeed, when NASA sent a probe to Titan, which has an atmosphere they think is similar to the early earth, the number of complex organic compounds that were in the atmosphere amazed them. I believe they expected some, but not at the levels that were found. Therefore, amino acids are very likely in the atmosphere that is thought to be the early earth.

Again what is your source and how accurate are they in this ussumption.

Here are a few problems with you just saying this.

http://www.technologynews.info/001335.html

The probe lost 18 years of data because of error at Nasa
The data they did collect was full of holes and patchy

I'm not saying that you are wrong. In fact I would expect there to be amino acids in other parts of space. But did you check you source before posting this information. That Probe was all but useless. Just keeping you honest.

Then, another piece of the puzzle is that amino acids will link togather on an exposed quartz crystal face to form simple proteins.

Amino acids will link anywhere to form protiens. This is what they do...

Again I am not disputing that amino acids linked to form DNA. In fact if they hadn't I wouldn't be typing would I. My point is that for the hundreds of links to just happen to be correctly assembled into a DNA strand which could create a self-replicating molecule, without any guidance and within just a few million years of when they could because of the surroundings, suggests someone assisting them.

The timeframe from when the earth was cool enough to begin to allow cells and life, to when there was life emerging was almost zero. (well a few million years but that is really zero on a comsic scale. Given the insaine complexity and the numbers of strands which all had to be assembled perfectly (one or two combinations off in any place and the whole thing fails), life appeared much to quickly to be due to random chance.

Going to Mits post, the card analogy. This would be like being given a deck of cards and you had to assemble the cards into one of a few possible combinations. Lets say since the possibilities of combinations within DNA is something times ten to the whatever power (4 to the 400,000 unless I am wrong) and the possibile hands that would have worked are somewhere aroung 10 to the 51, I am working from memory right now so my numbers may not be exact, this leaves a HUGE possibility of incorrect parings. Using the card analogy, this would be like telling the shuffeler to get ace through 2 in every suit. This is the only one that will work.

Now given enough time and repetitions I am sure that someday the would have all added up. But since life appeared very quickly as soon as it was possible, this would be like giving the shuffler a half hour deadline to complete this task.

Now do you understand what I am getting at.

You and I agree that life was probably going to happen sometime. However, the fact that it happened so quickly after earth was capable of sustaining life is what makes me believe there was intelligence behind the quick springing of life.

If you don't think so then get a deck and shuffle for 1 half hour. Tell me if it comes up Ace through 2 suited in that half hour without you helping by placing the cards in order.


As a final thought, I am not a believer in the God of Gaps. I do not think that God must have done whatever we can not yet explain. I am saying that the odds of it all happening so quickly and perfectly point to intelligent assistence. Just because we can understand the how . . . Doesn't mean God didn't do it.

Oh, ye of 'it's not the bilbe so I am skeptical of it'

http://www.nature.com/nature/journal/v4 ... 04349.html

[achilles12604]

achilles12604

Several problems with your post.

1. The first known life appeared at 3,8 billion years. Since the Earth is 4.5 billion years old, that is multi HUNDREDS of millions of years for these things to get going.

But you are not allowing for the hundreds of million years it would require for the earth to cool and then form an atmosphere. This is estimated at around 500 million years which once again puts us to about 150-200 million years for all this complexity to come together just right. This isn't that long on a cosmic scale.

2. A complex molecule IS NOT REQUIRED, just replication. As I posted in my last post, these things have been shown through experiment to require only ONE amino acid paired with only ONE acid analase to start the process. Surely you would not argue that such a simple molecule would be unlikely given the amino acids are already made and delivered by comet!!!

No I have no problem with this whatsoever. But even RNA molecules (which is FAR more simple than DNA) need to create much more complex patterns to create cells. And without cells there is only molecules.

No matter how you get to it, a very complex set of instructions was needed for life to begin.

I know that the arguement is mutation of the molecules which eventually created more complex molecules and then eventually had enough information to assist in the creation of life. However, this is where the theory part begins because I am unaware of any experiment where a molecule was mutated enough to get life. You yourself pointed out that this process would have required hundreds of millions of years. . .

Let me see if I can get the right quote. . .

From that point it could have taken several millions(or even billions of years) before RNA showed up.

You were quite correct. Even if it was possible for mutations to build RNA and even DNA molecules, (an so far this is a theory, but for the record I have no objections) this would have certainly taken much longer than 150 million years. And mind you that we are not talking about a couple once celled organisms at 150 million years. We are talking about the whole earth covered in algea. This is really fast. Especailly since there are so many combinations that the RNA and DNA could combine into which would have created nothing.

Since it appears that the - adenine (A), thymine (T), cytosine (C), and guanine (G)- have no preference as to how they prefer to link up, wrong combinations would have been much more likely than correct ones considering how many of each needed to be in just the right place. (the card deck times a huge factor)

52 cards being put into place is a sure thing next to these all being assembled correctly by chance.

3. To you 10 ^? is a big number, but to nature that many combinations could occur in a single cubic mile of earth(which has 10^? cubic miles of topsoil to work with, plus uncounted miles^3 of crust), add in a few HUNDRED million years and suddenly your big number becomes a near certainty. AND IT ONLY HAS TO OCCUR ONCE

.

Ah yes, but then once again, it must have been a totaly sucess and also grown into algea within 150 million years. Yes the complexity and wild amount of combinations which would have yielded nothing of value do point to God. But the speed . . . it is almost like nature got it right immediatly. Remember that while there are many combinations of the adenine (A), thymine (T), cytosine (C), and guanine (G) which would have yielded good results, there were infinatly more which would have yielded nothing. Yet nature got the right ones and on their first try too.

This is why I mentioned giving the shuffeler a half hour time limit. Yes given an infinatr number of years it could happen by chance. But when limited to 1/2 hour, it is impossible for the shuffeler to hit Ace through 2 suited.

By the way methane is CH3, also part of CHON. And a reducing atmosphere doesn't have any free o2

You see this is why I failed chemistry.

My apologies. Question though . . . Does Carbon wish to combine with Hydrogen automatically? If not, then methane should only occur after a process, not be used in a process.




Oh by the way . . .

The rate of mutation is .002 pre generation for DNA. This is REALLY slow and again shows it should have taken a whole lot longer than it did. I guess we are all REALLY lucky that nature happened to get the right combinations (from litterally infinate amount of incorrect possibilities) on the first try. . .

or Maybe it was something else?

http://www.blairgenealogy.com/dna/dna101.html

One last thought . . .

Medicine and science have shown that almost every single cell containing any form of mutation, is hazardous and even life threatening. Mutations of cells in called cancer.

Just something to think about when you assume that every mutation by every molecule was for the advancement of nature. Today we see almost the total opposite. Every mutation is harmful, well that we know of today.

Just a final thought.

[ENIGMA]

From that point it could have taken several millions(or even billions of years) before RNA showed up.

You were quite correct. Even if it was possible for mutations to build RNA and even DNA molecules, (an so far this is a theory, but for the record I have no objections) this would have certainly taken much longer than 150 million years. And mind you that we are not talking about a couple once celled organisms at 150 million years. We are talking about the whole earth covered in algea. This is really fast. Especailly since there are so many combinations that the RNA and DNA could combine into which would have created nothing.

Once one has one functioning algae with plenty of food and space to expand and no predators, the near exponential growth rate resulting from these conditions allows it to quickly cover the Earth, especially with the quick generation time and the huge timescales we are talking about here.

Since it appears that the - adenine (A), thymine (T), cytosine (C), and guanine (G)- have no preference as to how they prefer to link up, wrong combinations would have been much more likely than correct ones considering how many of each needed to be in just the right place. (the card deck times a huge factor)

52 cards being put into place is a sure thing next to these all being assembled correctly by chance.

Several perfect games of Bridge (where each player has all of a suit) have occurred in regulation play (i.e. No funny stuff with the deck) despite there being profoundly less time (decades as opposed to many millions of years) and profoundly less parallel processing (only a few games of Bridge going on at once, as opposed to almost innumerable chances for combination). Also, any successful combinations (i.e. ones that can consistantly self-replicate in a fairly steady manner) inevitably persist for longer periods and propogate farther than unsuccessful combinations (ones that can't self-replicate or can only self-replicate a few times before breakdown).

3. To you 10 ^? is a big number, but to nature that many combinations could occur in a single cubic mile of earth(which has 10^? cubic miles of topsoil to work with, plus uncounted miles^3 of crust), add in a few HUNDRED million years and suddenly your big number becomes a near certainty. AND IT ONLY HAS TO OCCUR ONCE

.

Ah yes, but then once again, it must have been a totaly sucess and also grown into algea within 150 million years. Yes the complexity and wild amount of combinations which would have yielded nothing of value do point to God. But the speed . . . it is almost like nature got it right immediatly. Remember that while there are many combinations of the adenine (A), thymine (T), cytosine (C), and guanine (G) which would have yielded good results, there were infinatly more which would have yielded nothing. Yet nature got the right ones and on their first try too.

This is why I mentioned giving the shuffeler a half hour time limit. Yes given an infinatr number of years it could happen by chance. But when limited to 1/2 hour, it is impossible for the shuffeler to hit Ace through 2 suited.

Except there are very many shufflers working concurrently. Then it simply becomes a matter of how many are needed, are there any quirks in the deck that help lock successful subsets in place, and whether a deck is accepted at 31 minutes after the process has begun.

Medicine and science have shown that almost every single cell containing any form of mutation, is hazardous and even life threatening. Mutations of cells in called cancer.

Roughly every 30 minutes, on average, a random cell in your body undergoes a mutation. Care to restate?