Some Steps Toward Abiogenesis, Part 2

There is more evidence that it is possible than that it is impossible.



Large portions of the following text were posted in 2006 at this web site discussion:
The text included here, from that discussion, was written by someone who chose the handle “FutureIncoming”. I have acquired that author’s permission to expand upon it, replace bad links, and otherwise revise it as appropriate to create this Knol.

Some Steps Toward Abiogenesis

The following itemized sequence has been re-ordered from the original text by FutureIncoming. If for no other reason, one of them sort-of began with “Iforgot to say” –which is something that can be corrected by the editing done here. The current goal is to present the sequence in a more “smooth” way:all the primary background stuff first, then the secondary stuff that depends on the background, then the stuff that depends on the secondary stuff….

1. The Primordial Soup, wherever it happened to exist (off-Earth if we accept Panspermia), existed in an energy-rich environment. There was volcanicheat, lightning, and ultraviolet sunlight, to name just three things that could affect simple molecules. Another important source was the emanationsfrom radioactive materials, which was much more significant then than nowadays. For example Uranium-235 has a half-life of something like 700 millionyears, so on Earth 4.2 billion years ago was 6 half-lives ago, and the amount of U-235 back then would have been 6 doublings of the current amount (64times the current amount in the world). Potassium-40 has a 1-billion-year half-life (and today’s atmosphere is 1% Argon-40 because of the decay ofK-40), so that early age was 4 half-lives ago, meaning 4 doublings or 16 times the current world supply of K-40 existed back then. Uranium-238 has ahalf-life of 4 billion years, so that long ago it was twice as abundant as today. And so on. It is almost laughable how worried some scientists areabout the effects of radiation upon Life, when Life evolved in that ancient radiation-rich environment. Well, they do have a point, because Life thesedays has adapted to much lower background-radiation levels. Still, the biologists have expressed surprise at how well Life is coping these days in thevicinity of Chernobyl. We should not take that as a rationale to have a nuclear war, of course. But we can have slightly more hope of surviving one….

2. The ancient atmosphere has to be considered “one with the Soup” (the ancient ocean), since it is thought to have contained large amounts of methaneand ammonia (and water vapor and carbon dioxide, of course) — and when a flash of energy (say by lightning) is added to some of those molecules, theycan break apart and recombine in quite a few different ways. Big-enough molecules would have fallen out of the atmosphere and ended up in the Soup, ofcourse.

3. If we are talking about the Earth and the Sun, then we should take note of the fact that astrophysicists, modeling how stars live, say that the Sun’stotal radiance has increased by something like 30% since it first started shining. Levels of ultraviolet light would have been considerably less in theearly days, than today. (Meanwhile, the Earth stayed warm because that primordial methane was a tremendously effective greenhouse gas.)

4. Like lightning, UV can break apart molecules. However, if UV is low-level, then a broken molecule here is not necessarily going to encounter piecesof a broken molecule here. I venture to guess that most of the molecular action in the atmosphere was lightning-caused, because lots of molecules areaffected, and they are in close proximity. Meanwhile, if UV is low-level, newly-built larger molecules can more easily survive while falling toward themain body of the Primordial Soup.

5. It is an interesting point that after a molecule falls into Soup it receives a kind of protection; ultraviolet light is far less effective atbreaking up underwater molecules. So, in the Soup, molecules more complicated than methane and ammonia can accumulate to significant levels (dependingon solubility).

6. Note that the Primordial Soup contained a lot of different compounds that could persist for quite a while — but which today on Earth wouldn’t lastfive minutes. That’s because existing Life eats those compounds. But since Life didn’t orginally exist, those molecules could persist.

7. In an energy-rich environment, water flows uphill. I’ll explain that in a moment, and am deliberately phrasing it that way to show opponents ofabiogenesis one of the key mistakes they make. They use the fact of Entropy (everything runs down, like water going downhill) to claim that it istherefore impossible for such complexity as Life to happen spontaneously. However, they are forgetting the equally valid fact that in an energy-richenvironment, water does flow uphill…by evaporation/rising-as-vapor. Technically, there is no difference between evaporated water and boiled water;energy must be acquired by water molecules to shift from the liquid to the gaseous state — and this easily happens in an energy-rich environment.Likewise, when plenty of energy is available, some of that energy can become trapped into increased molecular complexity. I described a piece of that,involving lightning, in Items 2 and 4.

8. A crucial chemical concept here is “equilbrium”. Yes, complex molecules can naturally break down into simpler molecules, in accordance with Entropy.And more can be built in an energy-rich environment. A state of equilibrium exists when both things happen at the same rate — and the total quantity ofa particular complex molecule, that will exist in equlibrium, depends on just what its natural breakdown rate is. The more stable the molecule, the moreof it can exist. So molecules like water and ammonia and methane and carbon dioxide are very stable and very common….

9. It is possible that radioactive K-40 was the most influential of the background-radiation group. Most natural inorganic compounds that containpotassium are soluable in water. So any molecule anywhere in the Primordial Soup had a chance of being zapped randomly, as a result of the decay of somenearby dissolved K-40 atom. Depending on the molecule and just how it got zapped, two different significant outcomes are possible. One is for themolecule to be destroyed into smaller pieces. Another is for one small piece, perhaps a single atom, to be snipped off in a way that leaves the rest ofthe molcule “hungry” to attach to something. “Free Radicals”, these kinds of molecules are called. It is truthful to say that a Free Radical is an”energized” molecule, and from the standpoint of it being zapped by radiation, that description is perfectly understandable. Well, if it manages toattach to some other somewhat-complicated molecule, then the total result, of course, is more-complex still.

10. Let’s look at “amino acids” for a bit. An amino acid is a particular type of generic molecule. It has two required subcomponents (an amino or NH2group, and a carboxylic acid or COOH group), plus any of a variety of other subcomponents. All of the 20 best-known amino acids are fairly simpleorganic molecules, ranging from 10 atoms to 27 atoms in composition (including the 7 atoms of the required subcomponents). They also happen to be fairlyeasily created in a Primordial Soup environment. But more than 100 others are known to naturally exist, so that word I used, “generic”, is applicable.Next, any two amino acids (even two of the same type) can chemically react with each other, simply because the reaction involves only the two requiredsubcomponents: COOH + NH2 -> CO-OH + NH-H -> CONH (peptide bond between the two original molecules) + OHH (or H2O, water produced-by/ejected from thereaction). Note that if the amino group of Amino Acid 1 (AA1) reacts with the acid group of AA2, then the Combined Molecule still has a left-over acidgroup (from AA1) and a left-over amino group (from AA2). It is therefore possible for a third and a fourth and a fifth (and so on) amino acid to connectto either end of the Combined Molecule. The result is generically called a “polypeptide chain”.

11. Polypeptide chains are fairly tough molecules; they don’t fall apart for no reason. This means, in the Primordial Soup, they could randomly growquite long. Biochemists generally start using the word “protein” when a polypeptide chain has connected from 50 to 100 amino acids together, and itsweight is about 10,000 times that of a single hydrogen atom. (Nevertheless, there are exceptions; the “aspartame” molecule is made from just two aminoacids and yet sometimes is called “a sweet protein” –it’s used as a low-calorie sweetener.) Complicated proteins can easily weigh more than 1,000,000times a hydrogen atom.

12. An enzyme can be a fairly simple protein (while not being an especially simple molecule), and it works as a catalyst. If it encounters some MoleculeA that it can affect, it will latch onto it for a while. If, while latched onto A, some appropriate Molecule B is encountered in the Soup, then theenzyme can do work of encouraging A and B to combine to make a more-complicated molecule. And the enzyme drifts away to do this same mindlessnon-animated thing over and over and over again. Note that this Scenario only requires some sort of enzyme molecule to be randomly constructed fromsimpler molecules, and of course Molecules A and B are also random. Note also that the work an enzyme does is not a violation of Physical Law. MoleculesA and B must be a pair that can unite, first. This usually means that some energy (not necessarily a lot, but something greater than zero) will bereleased when they combine. A catalyst like an enzyme merely facilitates the reaction.

13. Much of the Chemistry of Life is managed by enzymes. They can steadily cause molecules to combine in ways that release energy, which is why I calledLife “low-speed combustion”.

14. In Item 12 it was mentioned how an enzyme works. However, what an enzyme is able to do is actually somewhat more versatile than what was describedthere. It is more accurate to think of Molecule A and Molecule B as possessing Tab A and Slot B. Perhaps they would naturally encounter each other andunite without the help of an enzyme, but an enzyme still qualifies as a “facilitator” of that reaction. Anyway, the thing being pointed out here is thatTab A and Slot B might exist on more different kinds of molecules than Molecule A and Molecule B. So if Molecule Q has a Tab A and our enzyme latchesonto it, that enzyme won’t care if it encounters Molecule B or Molecule K; if it has an accessible Slot B, then the enzyme can facilitate the joining ofthe two molecules. The first randomly-formed enzyme, therefore, is not going to do only one thing in the midst of the Primordial Soup. It is going tohelp a lot of different more-complex molecules come into existence.

15. What if one of the those more-complex molecules that our first enzyme happens to help make is another and different enzyme? This one might connectTab C with Slot D. Or it might connect Tab A with Slot D. Or it might even be one of those enzymes that can unplug Tab A from Slot B, if first it getsenergized somehow. And that shouldn’t be uncommon in an energy-rich environment. The net result, if we step back and take a longish view, is that therewill exist a kind of “competition” between enzymes for Tabs and Slots. And Competition is a driving force for Evolution, even at the molecular level.

16. One of the things that polypeptide chains and proteins do is ‘fold up”. Chains of molecular bonds are naturally kinked, and when lots of bondsexist, involving different molecules like amino acids, you can have lots of kinks aiming every-which-way in 3 dimensions, and following such a chain iskind of like taking a “drunkard’s walk” –a classic mathematical problem:’s_Walk Each kink represents a partialfold in the chain, and a long chain can can accumulate (or cancel out) those partial folds. Next, the subsections of amino acids that can differ fromeach other also can have various amounts of attraction for each other, which almost always add-to or contort or otherwise-affect the folds. A commonresult is that a well-folded chain tends to crumple into a ball (although plenty of exceptions exist to that simplistic statement). And a ball-shapedprotein is one in which a significant fraction of the length of the chain has become covered up within its center. This is important because it“counters” one of the main arguments against Abiogensis. Let’s consider a 70-unit chain randomly built from the 25 most common amino acids. Since anyamino acid can occupy any place in the chain, a two-unit chain could exist 25×25=625 different ways, a three-unit chain could exist 25x25x25=15,625different ways, and a 70-unit chain has 25-to-the-70th-power possibilities (a 7 followed by 97 zeros). There aren’t enough atoms in the Universe forNature to have expressed all those possibilities at once (“in parallel”), and not enough Age of the Universe for all those possibilities to be tried insequence (“in series”), and even an optimal series/parallel approach might (or might not) only have just recently found it — so if one particular70-unit protein appears to us to be an enzyme required for a particular task, how did Nature find that enzyme billions of years ago, to say nothing ofalso finding thousands of other equally-special molecules?

17. Part of the answer relates to the “active site” on the outer surface of our folded protein (which in an enzyme would be the part that encourages TabA to go into Slot B). It doesn’t matter much what the complete composition of the protein is, so long as when folded it exhibits the relevant activesite, a consequence of adjacent amino acid subcomponents. And how many ways are there to do that, eh? Remember that the pharmaceutical industry has puta lot of effort into finding alternatives to existing proteins, with equivalent active sites, and almost all of that work has been done blindly, notknowing all the rules by which proteins naturally fold up. And awkward side effects are typical, as you know (due to other active sites on that samealternative molecule). You can expect that as soon as those rules are thoroughly understood, then using computers we will be able to crank outalternative protein designs, with desired active sites, by the billion. Perhaps some will even be found that have no side-effects, but that is not soimportant here, because….

18. The other part of the answer is “evolution” — and not particularly evolution of the protein molecule, but evolution of the dynamic system thathappened to incorporate a particular protein molecule that happened to have an effective active site! An analogy involving electronics: This is an important point that I will try to explain more clearly. In the Primordial Soup,the first enzyme to come along to do something that later got incorporated into Life could indeed have had awkward side-effects. Well, Life has hadbillions of years to accommodate and even make use of those side-effects. But replace that protein with some new and different constructed drug, andeven if it does the main thing as that Original Enzyme, it can be expected to have different side-effects for which there haven’t been billions of yearsof accommodation. Thus the answer to the anti-abiogenesis problem in Item 16 is simply that the first random protein to come along that could work in acertain way is the one that nowadays seems to be a perfect fit in a complicated dynamic system, simply because the system grew around that molecule –and around the first-encountered of many other proteins that also worked in certain ways. (The details of that, of course, mostly remain to be workedout.)

19. Note that the preceding is not a denial that molecular modifications take place. They do. In an energy rich environment, especially with randomradiation zaps, it is a certainty that a molecule that does a certain task well is going to occasionally get randomly assembled differently from usual.A living system will either accommodate it or eject it or dismantle it and construct another, or perish. In the Primordial Soup, however, before therewere any living systems, it is a moot point, partly because there was no Life-based manufacturing line for particular molecules, that could becomefouled up. An Original Enzyme that did some particular thing was not going to be frequently replaced by a similar-acting but different protein.

20. Stable molecules will tend to persist, as mentioned in Item 11, but less-stable molecules can randomly obtain a degree of protection if they manageto loosely link to the more stable ones. That is, a disruption might come in from any direction, but if the nearby more-stable molecule blocks thedisruption, then the “shadowed” less-stable molecule persists a little longer.

21. A loose grouping of molecules constitutes a crude degree of organization, and an energy-rich environment will naturally promote more-stableorganizations over the less stable.

22. The more stable an organization is, the more complex it is capable of becoming.

23. Thanks to the principles of feedback, it becomes possible for simple chemistry, energy, and Time to combine in ways that drive molecularorganization toward enormously complex dynamic stability — which is Life, of course.

24. The well-known designators “DNA” and “RNA” have in common the letters “NA”, which stands for “nucleic acid”. Here is a link to some basicinformation about them: Technically, the phrase “nucleic acid” normally applies to thosehuge huge molecules, but in theory it could also apply to very abbreviated versions of those molecules. Per the definition of a protein in Item 11,nucleic acids cannot really be called proteins. They are not directly built up from amino acids like polypeptide chains. Instead, they are built in asimilar way from a different kind of specific/generic organic molecule, called a “nucleotide”. That is, just as two amino acids can combine to form thefirst part of a polypeptide/protein chain, so can two nucleotides combine to form the first part of a nucleic acid chain. And, just as there are manykinds of amino acids, yet Life tends to mostly use a modest number of them, so can there be a variety of nucleotides — and Life tends to use a smallsubset of them (five or so).

25. Relevant as preparation for the next Item, and as an extension of Items 12 and 14, remember that the two portions of a “monomer” molecule, which canlink to form a “polymer” molecule, can be physically rather different. In proteins the peptide bond forms between an amino portion and a carboxylic acidportion; in nucleic acids a phosphate portion combines with a sugar portion. In either case, if an enzyme exists to encourage a reaction that builds amolecular chain, that enzyme/protein can have an “active site” that holds onto one of the two portions, and lets the other portion dangle. That otherportion could be extensively connected as part of a chain, of course; the enzyme only needs to hold onto the part that it can actually manipulate. So,when a new monomer comes along that the enzyme can influence, to join the end of the chain that it is holding, the result of the reaction is a newmolecular structure that no longer fits in the active site of the enzyme. In most cases the enzyme is then free to float away, someday to encounteranother end of a molecular chain, to attach yet another loose monomer from the Primordial Soup.

26. One of the more interesting protein enzymes is called “polymerase”. It acts to encourage nucleotides to combine together. More, it acts to make acopy of an existing nucleic acid chain. Please note that in a Lifeless environment, there is no hurry involved, in encouraging molecules to do things.We can easily imagine some randomly-formed nucleic acid chain, not a very long chain, floating in the Primordial Soup, and we can perhaps imagine somerandomly-formed polymerase-type molecule encountering it, eventually. So the polymerase protein/enzyme latches onto the nucleic acid chain, and doesnothing more until some particular nucleotide happens along. The active site of the polymerase is deformed according to the place on the nucleic acidchain where it is attached, so only a certain type of nucleotide will be attracted to the polymerase. Once that particular molecule happens by, it isheld by the active site, but its mere presence also distorts the polymerase. This distortion shifts the place where the polymerase has latched onto thenucleic acid chain. (In the simplest imaginable type of polymerase, we could picture a ring-shaped molecule, or a fat doughnut, that “rolls” along thenucleic acid chain.) That next nucleotide in the chain then distorts the polymerase in a way that enables a second active site to attract anotherparticular nucleotide from the Primordial Soup. Eventually that nucleotide happens by, and the polymerase can connect it with the first one, and let thefirst one loose as described in Item 25. Also, another shifting/rolling of the position of the polymerase along the nucleic acid chain occurs, whichallows that first (and now freed-up) active site to become the site that is influenced by that third nucleotide in the nucleic acid chain, readied toattract a new/third particular nucleotide/monomer from the Primordial Soup. Eventually, of course, the polymerase enzyme rolls off the end of the firstnucleic acid chain, having created a new chain, not necessarily an exact duplicate (the simpler the enzyme, the more corrupt the copy is likely to be),and the enzyme is free to randomly encounter another nucleic acid chain and repeat.

27. In the preceding Item, I have tried to stress simplistic forms of certain complex phenomena associated with Life. I do not see such complexity beingdescribed as cannot happen at random in a rich Primordial Soup, given enough Time. Also, it is a fact that nucleic acid chains are considerably morefragile than polypeptide chains. Very long nucleic acid chains will be rare in the Primordial Soup. And in an energy-rich environment, they might beexpected to decay nearly as fast as random polymerase enzymes happen to copy them. There is a great opportunity here, for nucleic acid chains torandomly become associated with some sort of protection, as mentioned in Item 20.

28. One other type of enzyme can be expected to form in the Primordial Soup. This one would be similar to polymerase, but instead of using itsattachment-points along a nucleic acid chain to construct a new nucleic acid chain, this would construct a polypeptide chain from loose amino acids inthe Soup. Life incorporates such enzymes as the tool for “reading” RNA information, using it to construct proteins. But in the simplest/earliest form,nothing so fancy as meaningful information would exist in any nucleic acid chain. There would simply be the “transcriptase” mechanism, a random enzymehaving certain properties. Nevertheless, when this mechanism becomes associated with the vast variety of nucleic acid chains that would be forming anddecaying in the Primordial Soup, we can suspect an equally vast variety of polypeptide chains starting to be formed, as well. A chain that mightpure-randomly include only the commonest amino acids in the Soup is not the kind of chain that we would normally expect from this mechanism. It willhold onto a partly-constructed polypeptide chain and only allow a particular amino acid to join the chain. So, proteins that might rarely be formed,directly in the Soup, might far more easily be formed as a random result of this nucleic-acid-reading mechanism. Well, what if some of thesenewly-common proteins turn out to be “protectors” for nucleic acid chains, eh?

29. In partial answer to the question at the end of Item 28, one way that a nucleic acid chain can obtain a small amount of protection from randomdisruption is for it to find a “mate”. Remember that a DNA molecule is made up of two separate chains, that happen to mesh together. The two chains arenot linked by ordinary chemical bonds; they are only linked by “hydrogen bonds”, a low-level electrostatic attraction between otherwise-independentmolecules. It’s my guess that shortly after the earliest polymerase enzyme came along to start making lots of bad copies of short nucleic acid chains,significant numbers of those chains “found” each other and linked to form short DNA segments. These double-helix structures expose their “backbones” tothe world, their strongest features. They also became unavailable to polymerase, for making more copies. The greater degree of common-ness that theyobtained by pairing up to become more stable and more complex, is now offset by a slowed rate of production, as “bare” nucleic acid chains became rarerin the Primordial Soup. (And RNA chains, even if two of them cannot form a double helix, they can find mates with unmatched DNA chains.)

30. Eventually a new enzyme (a polypeptide protein) will happen along. It may already have existed in the Primordial Soup by this time, but didn’thappen to do much. Remember that an enzyme is only effective when the task it is able to do, exists to be done! This particular enzyme is an “unzipper”,that gets into one end of a double helix and splits it partly apart. The section of exposed innards are now accessible by a polymerase enzyme. However,most of those random polymerase enzymes will not be the right shape to work right, to copy one strand of this structure. That’s because the unzipper isin the way. Only a more complicated form of polymerase will work here, to “push” the unzipper along, as it makes its copy of a strand of the doublehelix. We can imagine the Primordial Soup having a great many bottlenecked partly-split double helices floating about, with unzippers and polymeraseenzymes connected but nonfunctional, due to being in each other’s way. We also can recognize that the opened-up double-helix is more vulnerable todisruption. And there is a fair amount of molecular complexity in that vicinity, that can be torn apart and reformed differently, when some disruptioncomes along, like a K-40 radiation zap! (Two nucleic acid strands, one unzipper enzyme/protein, and up to two primitive polymerase proteins, one hookedto each nucleic acid chain.) How long will it take for an unzipper-pushing polymerase molecule to be randomly formed, in a Soup full of bottleneckedpotential?

31. The preceding Question, in a way, points at how “molecular evolution” can happen in a lifeless environment. The “Natural Selection” here is thetying-down and eventual destruction of ineffective molecules, while the effective ones gradually accumulated in the Primordial Soup. And why, you mightask, would a molecule loose in the Soup not be as subject to a random radiation zap as a tied-down molecule? The answer is, it would be as subject, inthe Soup, to a random radiation zap. However, a tied-down molecule is by definition part of a big heavy complex molecule, and gravity is going to tendto pull it to the bottom of the Primordial Soup. And in the Early Days of a World, most of the rocks at the bottom of the Soup are igneous rocks likegranite and basalt, relatively rich in other radiation-emitting substances, like uranium, thorium, and radioactive “daughter” nuclides. So, greateropportunities exist for tied-down and sunken molecules to get zapped, and to re-enter the Soup as smaller and even differently-formed pieces.

32. With the arrival of an unzipper-pushing polymerase enzyme, most of the components for a “distributed” and slow kind of Life-form now exists. Somemodestly long DNA helices can start to exist, due to the stability and protection they obtain from having that shape. An unzipper randomly/eventuallycomes along and starts unzipping it. A polymerase randomly/eventually comes along and gradually makes a copy of one of the two chains (as appropriatenucleotides are encountered), pushing the unzipper all the way through the double helix. A transcriptase randomly/eventually comes along and graduallymakes a protein from the new-made nucleic acid chain (as appropriate amino acids are encountered). Eventually, at random, this protein is going to beone of those three enzymes. If it is an unzipper, then a greater proportion of DNA strands in the Primordial Soup will become “ready” for copying bypolymerase. If it is a polymerase, then a greater proportion of “readied” DNA strands will have both strands copied, not just one. (If the copies arerelatively good copies, then the two strands can link to make a whole new DNA molecule –isn’t a copied DNA molecule the most basic result of Life InAction?) And if the randomly produced enzyme is a transcriptase, then an almost-literal explosion of transcriptase enzymes will start to float away fromthat place in the Primordial Soup, making more random proteins from random DNA strands, as they go. Eventually, at random, all three types of enzymeswill be getting preferentially produced throughout the Primordial Soup; their existence “feeds back” into their production, per Item 23, along with thethree modest DNA molecules, now classifiable as “genes”, associated with those enzymes.

That ends the (edited) itemized sequence by FutureIncoming.

Finally, a relevant famous quotation: “It ain’t what you don’t know that gets you into trouble. It’s what you do know that ain’t so.” is generally unwise to believe things that haven’t actually tested for validity. This Knol has described some things that are eminently possible andbelievable, with respect to a large-enough Primordial Soup. Recall that its title is “Some Steps Toward Abiogenesis” —it never claimed to be about allthe steps. So, the descriptions end where they do because more data is needed, with which to describe additional Steps, data which can only obtained byconducting experiments.

The main mystery remaining seems to be, “How did the replicating and evolving nucleotide chains become associated with thecollection of lipids that became the basis of that thing known as the “cell wall”? Perhaps a study of the shells of virus particles, as well as theshells of bacterial spores –especially when bacterial spores start to become active in a friendly environment– may offer some clues to the solution ofthat mystery….

And perhaps it is skipping a step to focus on that problem. Inside a cell, after all, is something known as a “cytoskeleton”, which helps to organizeits parts. Perhaps a crude cytoskeleton came first, allowing more-rapid replications of the molecules that became associated with (enmeshed by?) it, andthe outer cell wall came later….

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