And now to attempt to continue what I started toward the end of Msg #147, and continued in #150, hopefully without sticking my foot down my throat.
15. It turns out that I got ahead of myself by mentioning enzymes too soon. So 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 NH2 group, 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 simple organic molecules, ranging from 10 atoms to 27 atoms in composition (including the 7 atoms of the required subcomponents). They also happen to be fairly easily 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 required subcomponents: COOH + NH2 -> CO-OH + NH-H -> CONH (peptide bond between the two original molecules) + OHH (or H2O, water produced-by/ejected from the reaction). 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 acid group (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 connect to either end of the Combined Molecule. The result is generically called a "polypeptide chain".
16. Polypeptide chains are fairly tough molecules; they don't fall apart for no reason. This means, in the Primordial Soup, they could randomly grow quite long. Biochemists generally start using the word "protein" when a polypeptide chain has connected from 50 to 100 amino acids together, and its weight is about 10,000 times that of a single hydrogen atom. (Nevertheless, there are exceptions; the "aspartame" molecule is made from just two amino acids and yet sometimes is called "a sweet protein" --it's used as a low-calorie sweetener.) I goofed earlier when I wrote in Item 7 that an enzyme can be a fairly simple molecule; actually an enzyme is often a fairly simple
protein. Complicated proteins can easily weigh more than 1,000,000 times a hydrogen atom.
17. One of the things that polypeptide chains and proteins do is 'fold up". Chains of molecular bonds are naturally kinked, and when lots of bonds exist, involving different molecules like amino acids, you can have lots of kinks aiming every-which-way in 3 dimensions, and following such a chain is kind of like taking a "drunkard's walk" (a classic mathematical problem; look it up). Each kink represents a partial fold 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 from each other also can have various amounts of attraction for each other, which almost always add-to or contort or otherwise-affect the folds. A common result is that a well-folded chain tends to crumple into a ball (although plenty of exceptions exist to that simplistic statement). And a ball-shaped protein 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 any AA can occupy any place in the chain, a two-unit chain could exist 25x25=625 different ways, a three-unit chain could exist 25x25x25=15,625 different 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 for Nature to have expressed all those possibilities at once ("in parallel"), and not enough Age of the Universe for all those possibilities to be tried in sequence ("in series"), and even an optimal series/parallel approach might (or might not) only have just recently found it -- so if one particular 70-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 of also finding thousands of other equally-special molecules?
18. 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 Tab A 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 active site, a consequence of adjacent amino acid subcomponents. And how many ways are there to do
that, eh? Remember that the pharmaceutical industry has put a lot of effort into finding alternatives to existing proteins, with equivalent active sites, and almost all of that work has been done blindly, not knowing 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 same alternative molecule). You can expect that as soon as those rules are thoroughly understood, then using computers we will be able to crank out alternative protein designs, with desired active sites, by the billion. Perhaps some will even be found that have no side-effects, but that is not so important here, because....
19. The other part of the answer is "evolution" -- and
not particularly evolution of the protein molecule, but evolution of the
dynamic system that happened to incorporate a particular protein molecule that happened to have an effective active site! 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 had billions of years to accommodate and even make use of those side-effects. But replace that protein with some new and different constructed drug, and even 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 years of accommodation. Thus the answer to the anti-abiogenesis problem in Item 17 is simply that the first random protein to come along that
could work in a certain 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 worked out.)
20. Note that the preceding is not a denial that molecular modifications take place. They do. In an energy rich environment, especially with random radiation 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 there were any living systems, it is a moot point, partly because there was no Life-based manufacturing line for particular molecules, that could become fouled up. An Original Enzyme that did some particular thing was not going to be frequently replaced by a similar-acting but different protein.
To be continued.
Edited by FutureIncoming, : fixed typo
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