Abiogenesis and the evolution of complex life

[Moontanman]

Originally Posted by Pyrotex

The difficulty with these kinds of conversations is where to begin? Your post is an excellent example, so, thank you?

One must be VERY careful of one's starting point.

"Lets say that DNA actually got formed for a sec." Nope, cannot do that. Can't put one molecule of DNA in a testube of pond water, watch what happens, and deduce from THAT how DNA originated. Sure that one DNA will disintegrate in pond water. So what?

DNA did not suddenly originate in a "vaccuum". It co-evolved with all its replication and repair machinery. But this is hard to visualize.

I think DNA got started long before, in the generation of sugars and amino acids as "wastes" of one process, and these wastes were then used as "inputs" or "feedstock" to other processess. A sugar and an amino can link together.

A linked pair, sugar + amino, could link to two other pairs, to form a
TRIPLET. When this triplet encountered a certain large molecule, it triggered the large molecule to spit out a protein. These proteins did things that resulted in even more sugars and aminos, and this loop became a core feature of the local chemistry. The triplet would be the basic building block of RNA some day. The triplet in RNA codes for a specific protein.

Another thing was going on. A linked pair, sugar + amino, could link to yet another linked pair, in a different way: sugar + amino--weak hydrogen bond--amino + sugar.

This meant that a triplet could bond with another triplet, using 3 weak hydrogen bonds. This would be the basic building block of DNA some day: the "codon".

I imagine that in the primordial days, before real LIFE, these free floating triplets and codons served their purposes, perhaps temporarily storing "information", or serving to identify which chemical loops should be favored and which should be suppressed--behaving like a chemical "switch".

And over geologic time, the triplets and their chemical partners and the codons and their chemical support systems all co-evolved. All at the same time. So, when codons began to be linked, forming the first primitive instances of DNA, it had with it the first primitive set of polymerase molecules and enzymes and whatevers.

It is interesting to note that some biologists believe that the time between biological chemical systems and LIFE was very short, perhaps only a few million years. Or less. Or a LOT less.

Yeah! What he said! Pyro, you have a much better grip on this than I do. Great explanation, I wish there were more teachers with your grasp of the facts.

[ronthepon]

I guess that's a possible way it could be.

[Moontanman]

I think this link is an important addition to this thread.

New Way To Think About Earth's First Cells

[InfiniteNow]

Originally Posted by Moontanman

I think this link is an important addition to this thread.

New Way To Think About Earth's First Cells

Nice find, moontanman, and published just this week.

A team of researchers at Harvard University have modeled in the laboratory a primitive cell, or protocell, that is capable of building, copying and containing DNA.

Since there are no physical records of what the first primitive cells on Earth looked like, or how they grew and divided, the research team's protocell project offers a useful way to learn about how Earth's earliest cells may have interacted with their environment approximately 3.5 billion years ago.

[InfiniteNow]

Another good video. Enjoy.

YouTube - 3 -- The Origin of Life made easy

[Pyrotex]

So, abiogenesis is the beginning of Life from non-living chemistry. Literally, "lifeless beginning".

We have discussed that the reproductive cycle of Life could have begun as non-living chemical "loops".

Well, I discovered an article in The Scientist magazine online that directly addressed the problem of abiogenesis. And it, too, suggested that prior to there being DNA, RNA or Life (as we know it), there were basic, primitive, chemical cycles. There were more than one. The waste products of some cycles became the feedstocks of other cycles. The overall affect of these "ecosystems" of chemical loops was:

1. The basic molecules necessary for the loops were not only NOT consumed, but were re-created and even multiplied. One "ecosystem" of chemical loops eventually became TWO sets of loops. Can anyone say, "reproduction", boys and girls?
2. The overall net affect of these loops was that external chemical energy obtained by, for example, combining carbon with oxygen to produce carbon dioxide, was stored as energetic electrons in molecules that could transport this energy through membranes. Can anyone say, "metabolism", girls and boys?

These loops were not alive in any sense of the word, but simply repetitive chemical cycles that took a simple exothermic chemical reaction (C2 + 2O2 = 2CO2) and used it to produce "energy". Most of this energy went to powering the chemical cycles.

One such chemical cycle, and one of the most important to Life As We Know It, is the Citric Acid Cycle, also known as the Krebs Cycle. It is not hard to image this cycle "evolving" from far longer, less efficient, predecessor cycles, until it finally achieved the 11-step perfection that powers all oxygen-breathing life on Earth today. That's right. Eleven steps. It converts one glucose molecule into 6 carbon-dioxides, creating 2 molecules of ATP in the process, which carry off the energetic electrons.

Here is a fascinating and simple animation of the Kreb's Cycle.

Here is what Wikipedia has to say about the Krebs Cycle. Check out the gorgeous color diagram of the cycle and follow it around. Awesome.

Here is the magazine article, 'Before Darwin' that started it all.

There are many other chemical cycles, basic primitive, elemental cycles, necessary for Life, cycles that, in my opinion, pre-date cellular Life. The Citric Acid Cycle is the core process within Mitochondria, which supply the energy for nearly all Eukaryotic cells on the planet.

I believe the cycle came first. Then the gradual encapsulation of the cycle(s) within membranes, then the development of a memory system (DNA.RNA) to aid in reproduction. Then the merger of prokaryotic cells to form cooperative, self-contained cells.

[Moontanman]

Originally Posted by Pyrotex

So, abiogenesis is the beginning of Life from non-living chemistry. Literally, "lifeless beginning".

We have discussed that the reproductive cycle of Life could have begun as non-living chemical "loops".

Well, I discovered an article in The Scientist magazine online that directly addressed the problem of abiogenesis. And it, too, suggested that prior to there being DNA, RNA or Life (as we know it), there were basic, primitive, chemical cycles. There were more than one. The waste products of some cycles became the feedstocks of other cycles. The overall affect of these "ecosystems" of chemical loops was:

1. The basic molecules necessary for the loops were not only NOT consumed, but were re-created and even multiplied. One "ecosystem" of chemical loops eventually became TWO sets of loops. Can anyone say, "reproduction", boys and girls?
2. The overall net affect of these loops was that external chemical energy obtained by, for example, combining carbon with oxygen to produce carbon dioxide, was stored as energetic electrons in molecules that could transport this energy through membranes. Can anyone say, "metabolism", girls and boys?

These loops were not alive in any sense of the word, but simply repetitive chemical cycles that took a simple exothermic chemical reaction (C2 + 2O2 = 2CO2) and used it to produce "energy". Most of this energy went to powering the chemical cycles.

One such chemical cycle, and one of the most important to Life As We Know It, is the Citric Acid Cycle, also known as the Krebs Cycle. It is not hard to image this cycle "evolving" from far longer, less efficient, predecessor cycles, until it finally achieved the 11-step perfection that powers all oxygen-breathing life on Earth today. That's right. Eleven steps. It converts one glucose molecule into 6 carbon-dioxides, creating 2 molecules of ATP in the process, which carry off the energetic electrons.

Here is a fascinating and simple animation of the Kreb's Cycle.

Here is what Wikipedia has to say about the Krebs Cycle. Check out the gorgeous color diagram of the cycle and follow it around. Awesome.

Here is the magazine article, 'Before Darwin' that started it all.

There are many other chemical cycles, basic primitive, elemental cycles, necessary for Life, cycles that, in my opinion, pre-date cellular Life. The Citric Acid Cycle is the core process within Mitochondria, which supply the energy for nearly all Eukaryotic cells on the planet.

I believe the cycle came first. Then the gradual encapsulation of the cycle(s) within membranes, then the development of a memory system (DNA.RNA) to aid in reproduction. Then the merger of prokaryotic cells to form cooperative, self-contained cells.

Yes, these chemical cycles do indeed suggest the beginning of life. many random self replicating proteans encased in bubbles of hydrophobic hydrocarbon molecules, absorbing more necessary molecules until they divide and start swelling with replicating protean molecules again. RNA was also part of this thin soup and RNA could have penetrated these cells and copied themselves by using the proteans contained in these bubbles (cells) when the cells burst the RNA that was most efficient at reproducing from the proteans in these cells produced more RNA penetrated more cells and so on. the beginning of evolution. from there is was just a matter of time before you had cells that replicated with out bursting and absorbed proteans from the surrounding water to make more cells full of proteans and RNA, the RNA world was born!

[Thunderbird]

Originally Posted by Pyrotex

I believe the cycle came first. Then the gradual encapsulation of the cycle(s) within membranes, then the development of a memory system (DNA.RNA) to aid in reproduction. Then the merger of prokaryotic cells to form cooperative, self-contained cells.

Indeed, you're right, but we are still left with a few organizational gaps.

Autocatalysis
Catalysts are chemical substances that modify reaction rates without themselves being changed in the process. Their kinetics are characterized by threshold and amplification phenomena. Enzymes are the major class of biological catalysts.

The molecules of an autocatalytic system speed up the very reactions by which they are formed. Autocatalytic loops are like feedback loops in that the presence of a substance stimulates production of the same element and that the kinetic equations describing them are non-linear . (Eg. the rate of variation of the concentration of X is proportional to the square of its concentration)

Cross-Catalysis is a similar loop involving several elements. The first element triggers the production of the second, which in turn produces the first. A hypercycle is a system of autocatalytic reactions arranged in a circle so each reaction's product catalyzes production of its clockwise neighbor.

The gene was described by H.J. Muller in 1926 as possessing the property of "specific autocatalysis," meaning self-replication. "Still more remarkable," he wrote, the gene can mutate without losing its specific autocatalytic power.

Stuart Kauffman studied auto-catalytic sets as a possible explanation of the origin of life, for they tend to grow as long as the materials for their synthesis are available. For Kaufman, at its heart, a living organism is a system of chemicals that has the capacity to catalyze its own reproduction. (See At Home in the Universe, p. 49) Different auto-catalytic sets might compete for the same raw materials and life could indeed have bootstraped itself into existence through this process rather than have waited for some ridiculously improbable random events. But is the occurence of auto-catalysis a simply fortuitous event? Kauffman studied systems to find out when auto-catalysis might occur and found that this tended to happen "at the edge of chaos" This state corresponded to the " phase transition" behaviour studied by Chris Langton and the students of Artificial life. For Langton, Life is eternally trying to keep its balance on the edge of chaos, always in danger of falling off into too much order on the one side, and too much chaos on the other.

For Kauffman, life, instead of being improbable, is an expected, emergent, collective property of complex systems of polymer catalysts when a system acheives catalytic closure. "As the complexity of a collection of polymer catalysts increases, a critical complexity threshold is reached. Beyond this threshold, the probability that a subsystem of polymers exists in which formation of each member is catalyzed by other members of the subsystem becomes very high" (p.289)

(See Prigogine Order Out of Chaos, pp. 133-135, Waldrop Complexity pp 124 - 125

[Pyrotex]

Originally Posted by Thunderbird

Indeed, you're right, but we are still left with a few organizational gaps.

If I read you right, you are proposing that the quotes from Prigogene help to "fill in" the afore-mentioned gaps.

If that is so, then I fully agree and concur.

The Wikipedia reference I gave on Krebs Cycle said a lot about how the various chemicals produced by one part of the cycle inhibited, enabled or self-catalyzed other parts of the cycle.

And did you know that enzymes and many proteins have an on-off switch? Yup. They have an "active site" which performs the molecule's "primary task", and a secondary site which prevents the protein from doing that task, unless there is an enabling molecule (such as an amino acid, or an ATP molecule) temporarily attached at that secondary site.

Fascinating.

[Thunderbird]

Originally Posted by Pyrotex

If I read you right, you are proposing that the quotes from Prigogene help to "fill in" the afore-mentioned gaps.

If that is so, then I fully agree and concur.

The Wikipedia reference I gave on Krebs Cycle said a lot about how the various chemicals produced by one part of the cycle inhibited, enabled or self-catalyzed other parts of the cycle.

And did you know that enzymes and many proteins have an on-off switch? Yup. They have an "active site" which performs the molecule's "primary task", and a secondary site which prevents the protein from doing that task, unless there is an enabling molecule (such as an amino acid, or an ATP molecule) temporarily attached at that secondary site.

Fascinating.

On the chemical cellular level I believe the above references we have given would suffice as the best evidence we have for how life emerged from non life. fascinating indeed. I still think there are quantum coherent molecular structures involved that form around incoming information outside these loops, sunlight-chlorophyll for example, and also geometric principles involved, The chemical factory needs to have an architecture. Environmental cycles would play the first simple rhythms of adaptation. This would signal the start of the evolutionary process.

To me these types of evolutionary constraints are also fascinating aspects of life. The forms. After all consider I am a sculptor. I take gemstones and form them into animals. Form and function develop hand in hand. The form is not addressed in evolution theory as much as I would like.