Abiogenesis

[olivergringold]

This is my first post, so feel free to label me as a n00b or flame me to your heart's delight. I'm going to take the opportunity afforded by my first post to ramble unendingly, and more specifically to the ends of naming the basic components of what the first unicellular organism needed to have to kickstart evolution and, given an old Earth, name a plausible way in which that may have formed without relying entirely on chance. Ready? Too bad.

The cell's main feature is its DNA, or deoxyribonucleic acid. This is a sequence of four different chemicals: adenine [A], thymine [T], guanine [G], and cytosine [C], which are held in a chain by a linking phosphate "backbone." Since A and T naturally bond chemcially, and G and C as well, DNA forms in a double-helix shape, with each side of the helix being the chemical opposite of the other (As become Ts, etcetera). This all being obvious and boring, all a First Organism would need is a long phosphate chain and high concentrations of adenine, thymine, guanine and cytosine in the general vicinity.

Obviously, though, for life to occur it's just not that simple. The chemicals need to bond with the phosphate chain, and there needs to be an "energy" source for the DNA to split and replicate, to permit variation. An experiment attempting to replicate this was carried out, which resulted in proteins. This was not a success, however, as said proteins were not capable of creating, or even being classified as, life. Consider, however, an old Earth:

The spinning of the Earth's core has generated a magnetic field preventing many of the sun's ultraviolet, X-Ray and Gamma Rays from penetrating into the Earth's atmosphere, and the upper layers of magma begin to cool. High concentrations of water condense in the crevices between the crusts, and violent electric storms frequently bombard the planet. All of the chemicals required to give rise to life are already there, and the energy required to bond them is available in abundance. Still, however, the odds of all the right chemicals happening to be in the same place at the right time are none that any wise person would bet on. Consider, though, that chance may not be the only factor at play.

Vines are often known to travel up the stems of plants in a perfect spiral shape. This is a very fascinating phenomenon, as nobody would suspect that lurking in the DNA is an instruction for the vine to travel in such a fashion. How on Earth (no pun intended) could it be occurring by chance? Indeed, however, it is not. The vine is simply distributing its weight. According to the known laws of physics, the most efficient way for a lengthy object to distribute its weight as it moves upwards is to travel in a spiral. The vine doesn't know this any more than Newton's apple "knew" about the gravity controlling it. Still, though, the organism is not only bound by its DNA, but also by the world around it.

A and T, as well as G and C, combine without any external intervention during cell reproduction. When faced with each other, the connection is instantaneous as a result of the chemical constructions of their bonds. Just as the physics may control the plants, here it is the chemistry which controls the cells. I posit, then, that it is plausible, if not outright likely, that because many of the chemicals involved were already predisposed to creating chemical bonds, the probability of abiogenesis occurring on an Old Earth extends well beyond that of pure chance.

What does all of this mean? Absolutely nothing, save for my being an exceptionally pretentious and lengthy writer. There's no known way for us to turn the clock back and see what our planet really was like in its infancy, and recent studies about the laws of causation suggest that we may never know precisely how abiogenesis happened on Earth, if not in general. Though, in closing, for all those who purport Intelligent Design and preach that God must have been He Who Turned On Evolution, remember that it only had to be possible, not likely, and that it only had to happen once.

[Confused]

Welcome.

Abiogenesis is still a very questionable theory. I think you might find people whe strongly agree it is possible and those who won't. But if I am reading your post right, you are saying that it did happen, but we may never be able to go far enough back in history to see precisely how it happened.

First: did it happen? And second, how?
http://en.wikipedia.org/wiki/Abiogenesis

Classical notions of abiogenesis, now more precisely known as spontaneous generation, held that complex, living organisms are generated by decaying organic substances, e.g. that mice spontaneously appear in stored grain or maggots spontaneously appear in meat.
However, experimental scientists continued to decrease the conditions within which the spontaneous generation of complex organisms could be observed. The first step was taken by the Italian Francesco Redi, who, in 1668, proved that no maggots appeared in meat when flies were prevented from laying eggs. From the seventeenth century onwards it was gradually shown that, at least in the case of all the higher and readily visible organisms, the previous sentiment regarding spontaneous generation was false. The alternative seemed to be omne vivum ex ovo: that every living thing came from a pre-existing living thing (literally, from an egg).
Then in 1683 Antoni van Leeuwenhoek discovered bacteria, and it was soon found that however carefully organic matter might be protected by screens, or by being placed in stoppered receptacles, putrefaction set in, and was always accompanied by the appearance of myriad bacteria and other low organisms. As knowledge of microscopic forms of life increased, so the apparent realm of abiogenesis increased, and it became tempting to hypothesize that while abiogenesis might not take place for creatures visible to the naked eye, at the microscopic level, living organisms continually arose from inorganic matter.

We could dwell further into alternative theories such as Haldanes biopoesis, or Ureys primordial soup. But overall, it is currently not possible to prove or disporve abiogenesis which is why it is a very debated topic still. Hoyle calculated that the chance of obtaining the required set of enzymes for even the simplest living cell was one in 1040,000.

The problem with most critics of abiogenesis falls into 4 main categories:

http://www.talkorigins.org/faqs/abiopro ... html#Space

1) Probability as mentioned by Hoyle: facts: Firstly, the formation of biological polymers from monomers is a function of the laws of chemistry and biochemistry, and these are decidedly not random.

Secondly, the entire premise is incorrect to start off with, because in modern abiogenesis theories the first "living things" would be much simpler, not even a protobacteria, or a preprotobacteria (what Oparin called a protobiont [8] and Woese calls a progenote [4]), but one or more simple molecules probably not more than 30-40 subunits long. These simple molecules then slowly evolved into more cooperative self-replicating systems, then finally into simple organisms [2, 5, 10, 15, 28]. An illustration comparing a hypothetical protobiont and a modern bacteria is given below

2) The myth of the "life sequence"
Another claim often heard is that there is a "life sequence" of 400 proteins, and that the amino acid sequences of these proteins cannot be changed, for organisms to be alive.

This, however, is nonsense. The 400 protein claim seems to come from the protein coding genome of Mycobacterium genetalium, which has the smallest genome currently known of any modern organism [20]. However, inspection of the genome suggests that this could be reduced further to a minimal gene set of 256 proteins [20]. Note again that this is a modern organism. The first protobiont/progenote would have been smaller still [4], and preceded by even simpler chemical systems [3, 10, 11, 15].

As to the claim that the sequences of proteins cannot be changed, again this is nonsense. There are in most proteins regions where almost any amino acid can be substituted, and other regions where conservative substitutions (where charged amino acids can be swapped with other charged amino acids, neutral for other neutral amino acids and hydrophobic amino acids for other hydrophobic amino acids) can be made. Some functionally equivalent molecules can have between 30 - 50% of their amino acids different. In fact it is possible to substitute structurally non-identical bacterial proteins for yeast proteins, and worm proteins for human proteins, and the organisms live quite happily.

The "life sequence" is a myth.

3) They calculate/misinterpret the probability of sequential trials, rather than simultaneous trials. Fact: The synthesis of primitive self-replicators could happen relatively rapidly, even given a probability of 1 chance in 4.29 x 1040 (and remember, our replicator could be synthesized on the very first trial).

Assume that it takes a week to generate a sequence [14,16]. Then the Ghadiri ligase could be generated in one week, and any cytochrome C sequence could be generated in a bit over a million years (along with about half of all possible 101 peptide sequences, a large proportion of which will be functional proteins of some sort).

Although I have used the Ghadiri ligase as an example, as I mentioned above the same calculations can be performed for the SunY self replicator, or the Ekland RNA polymerase. I leave this as an exercise for the reader, but the general conclusion (you can make scads of the things in a short time) is the same for these oligonucleotides.

4) Another misunderstanding is that most people feel that the number of enzymes/ribozymes, let alone the ribozymal RNA polymerases or any form of self-replicator, represent a very unlikely configuration and that the chance of a single enzyme/ribozyme forming, let alone a number of them, from random addition of amino acids/nucleotides is very small.

However, an analysis by Ekland suggests that in the sequence space of 220 nucleotide long RNA sequences, a staggering 2.5 x 10112 sequences are efficent ligases [12]. Not bad for a compound previously thought to be only structural. Going back to our primitive ocean of 1 x 1024 litres and assuming a nucleotide concentration of 1 x 10-7 M [23], then there are roughly 1 x 1049 potential nucleotide chains, so that a fair number of efficent RNA ligases (about 1 x 1034) could be produced in a year, let alone a million years. The potential number of RNA polymerases is high also; about 1 in every 1020 sequences is an RNA polymerase [12]. Similar considerations apply for ribosomal acyl transferases (about 1 in every 1015 sequences), and ribozymal nucleotide synthesis [1, 6, 13].

Similarly, of the 1 x 10130 possible 100 unit proteins, 3.8 x 1061 represent cytochrome C alone! [29] There's lots of functional enyzmes in the peptide/nucleotide search space, so it would seem likely that a functioning ensemble of enzymes could be brewed up in an early Earth's prebiotic soup.

So, even with more realistic (if somewhat mind beggaring) figures, random assemblage of amino acids into "life-supporting" systems (whether you go for protein enzyme based hypercycles [10], RNA world systems [18], or RNA ribozyme-protein enzyme coevolution [11, 25]) would seem to be entirely feasible, even with pessimistic figures for the original monomer concentrations [23] and synthesis times.

While none of this actually proves abiogenesis occurred, the very premise of creationists' probability calculations is incorrect in the first place as it aims at the wrong theory. Furthermore, this argument is often buttressed with statistical and biological fallacies.

Will we ever be able to trace the origins of life back far enough to prove that this was in fact the event that began life? We are within second of what happened after the big bang for creation of the universe, with enough science, technology, and time, we may be able to prove or disprove it, but it won't be in my life.

[McCulloch]

Abiogenesis it not a theory. It is a fact. Once there was no life. Later there was life. Life must have therefore come from non-life. How it happened is still undetermined. Perhaps DNA was formed by some process from other existing chemicals or perhaps almighty God breathed life into some mud.

[olivergringold]

Abiogenesis it not a theory. It is a fact. Once there was no life. Later there was life. Life must have therefore come from non-life. How it happened is still undetermined. Perhaps DNA was formed by some process from other existing chemicals or perhaps almighty God breathed life into some mud.

Saying that God "breathed life into some mud" represents a biological interference, if it is given that God exists and is of the Judeo-Christian model. Man is made in God's image, man is alive, therefore God is alive. God is a living creature, abiogenesis requires an absence of living creatures, therefore God may have no hand in abiogenesis.

I understand what you mean, and my argument with it is more semantic than practical, but I was making the case for an atheistic rise of biology. As stated, it did not have to be likely, only possible, and it only had to happen once.
_________________

[McCulloch]

Saying that God "breathed life into some mud" represents a biological interference, if it is given that God exists and is of the Judeo-Christian model. Man is made in God's image, man is alive, therefore God is alive. God is a living creature, abiogenesis requires an absence of living creatures, therefore God may have no hand in abiogenesis.

Contrary to the claims of many theologians, God is not alive in the biological sense. Let me re-phrase.

Abiogenesis it not a theory. It is a fact. Once there was no biological life. Later there was biological life. Biological life must have therefore come from non-life. How it happened is still undetermined. Perhaps DNA was formed by some process from other existing chemicals or perhaps almighty God or some other supernatural entity breathed life into some mud. NB: the life is in the blood.

[olivergringold]

Thank you for the clarification. It is possible, given the existence of an all-powerful God, that said God would set into motion life on Earth. If such a God were to do this, however, it raises a whole host of questions about said deity's nature and intentions. That, I think, would best be discussed elsewhere. I was merely laying out the possibility that an atheistic genesis wouldn't have to rely entirely on chance alone.

[otseng]

I posit, then, that it is plausible, if not outright likely, that because many of the chemicals involved were already predisposed to creating chemical bonds, the probability of abiogenesis occurring on an Old Earth extends well beyond that of pure chance.

I fail to see how it offers to explain much of how the first cell arose. Even if chemicals were predisposed to create chemical bonds, it's still very far from being able to explain the origin of the first cell.

(Also, can I suggest for you to scale down your signature image?)

[olivergringold]

You're forgetting, though, that the reason cells have many of the components that they do is to protect themselves or to permit themselves to function in light of the existence of competing or cooperating cells. A First Lifeform would not need this...it would only need its self-replicating DNA. RNA instructions copied from DNA create proteins, and from there everything else becomes possible. If a self-replicating, varying model were subjected to time, competition with said replications and natural selection caused by competition (sentient or not) for energy sources would weed out those DNA models not fit for continued reproduction.

Slightly off-topic, it's worth noting that the components of the cell are hardly ideal...an intelligent designer easily could have created something far more efficient. Instead it, like all forms of life, high and low, is constructed much like a Rube Goldberg machine, stacking function atop function until the necessary end is reached by mind-blowingly inefficient means. But I digress...as for the signature image, consider it done.

[QED]

You're forgetting, though, that the reason cells have many of the components that they do is to protect themselves or to permit themselves to function in light of the existence of competing or cooperating cells. A First Lifeform would not need this...it would only need its self-replicating DNA. RNA instructions copied from DNA create proteins, and from there everything else becomes possible. If a self-replicating, varying model were subjected to time, competition with said replications and natural selection caused by competition (sentient or not) for energy sources would weed out those DNA models not fit for continued reproduction.

What an excellent point. The evolution of any entity is always operating within a framework of all other evolving things -- but the first complex chemistry's wouldn't be facing the same difficult challenges that they would face today. This reminds me of a troubling thought I once had about why there's only really "one system of life". It's like the reason that we only really have "one PC operating system" (OK, not exactly, but you should get my drift. Here in the UK it's looking like there will only be one supermarket chain if market-forces were left to themselves).

Another pet gripe of mine is the argument over when evolution by natural selection kicks-in. I think it's always there "running in the background" and is the "hand" that's assembling the molecules into patterns from the word go. Of all these patterns, some are more persistent and we're on our way.

[olivergringold]

While based on the same principles, few people would call eukaryotes and prokaryotes of the same model. So there's your Mac VS PC analogy in spades...they may not have the same kernel, but they all have to be processed in binary.