Joined: Sep. 2007
|Quote (Louis @ Oct. 16 2008,14:16)|
|Quote (Daniel Smith @ Oct. 16 2008,19:50)|
|Quote (Louis @ Oct. 15 2008,15:36)|
|Rather than get stuck in an endless loop of generalities, let's take one simple chemical issue: the origin of homochirality. Do you think that none of the best chemists have found possible natural pathways for the origin of homochiral biologically significant monomers?|
Stick with this one simple issue, then we can move on to others.
I don't see homochirality as the big issue. It's a small part of the overall problem though. Even if all amino acids were left-handed, that still does not explain the way they are utilized in life. There has to be some form of amino acid synthesis that will work within the mild conditions of the aqueous solution required for life (Miller's synthesis method will not work inside a living cell). There must also be some form of polynucleotide synthesis, some form of polypeptide synthesis, some method of tying these two things together and some form of self-replication. These are far bigger hurdles that chiralty.
Homochirality is not a big issue eh? Wow!
Miller-Urey conditions won't work in a cell? Double wow!
Did it ever occur to you that the origin of homochirality is an enormous problem in abiogenesis? Explaining such a massively distinct use of one (energetically identical) enantiomer over another is a big deal....well it is to real scientists. No one claims that because amino acids are (predominantly) homochiral in living systems that this explains "the way they are used in life". I think you're a bit confused. You can hand wave it away, but it is a real success story.
As for the Miller-Urey conditions not being applicable to the cell, well, erm, how do I put this delicately: OF COURSE THEY'RE NOT! They are proposed conditions for the synthesis of biologically significant molecules from a non biological source. These are things that are meant to happen before cells arise. Oh and whilst I think of it, brush up on the molecules that are available in space why don't you. You might find it interesting.
Take the next issue, polymerisation, do you have any idea how energetically favourable formation of the amide bond is? Especially in aqueous solution, one simple activating agent for the carboxylic acid and booooom! Polymers. Polymerisation isn't a problem, controlled polymerisation is. Bear in mind however that the current biological system of DNA/RNA + proteins is a highly evolved (i.e. "advanced") one. It's by no means certain that it, or anything like it, was the "first system". In fact it's very unlikely. If you have any background in chemistry I suggest you check out the book I recommend on the other thread by Pier Luigi Luisi. It's a cracker!
Why do I suspect that whatever hurdle we mention science has crossed you'll retreat to another one? I don't think you're entering into this discussion in good faith, which is a pity, because it's potentially a very interesting one. Still, like with FTK, I'm willing to help out if you're interested. I'd suggest you start with the basics, you appear a tad confused.
I appreciate the lesson on homochiralty being a bigger problem that I thought. Of course that does nothing to lessen my argument since the "explanation" given was just that it might be possible (theoretically), under the right conditions, to form all one-handed amino acids. From the T.O. article:
|First, L- amino acids will randomly convert to D- amino acids over time, and D- forms will convert to L- forms. This is called "racimization" because eventually you will end up with equal amounts of L- and D- amino acids. The rate that this occurs at varies with the amino acid, and its surroundings. The fastest conversion happens to amino acid molecules all by themselves in hot water. Under cold, dry conditions when the amino acids are attached to one another, or better yet, if they are also attached to a mineral, racimization can be very slow. Very, very slow.|
This means that if there is even a tiny advantage one way or the other, the favored form will become the dominant form.
First, I'm not sure how the second statement follows from the first. I don't see how a "tiny advantage" will cause a "dominant form". I can see it perhaps causing a slight imbalance, but not a dominance - especially since it's only under cold, dry conditions; while attached to a mineral; and under intense selective pressure, that amino acids will supposedly favor one-handedness. What about the mild conditions and aqueous solution necessary for life? According to T.O., they'll naturally revert to a 50/50 mixture (unless regulated).
Then there's this is from the paper
"Homochiral growth through enantiomeric cross-inhibition"
So chiralty developed "when the first RNA molecules formed" and "at a stage when there is already growth and self-replication"? How does this jibe with the cold dry meteorite that formed all these left-handed amino acids in the first place? I guess you'll have to explain to me how this problem has been solved.
|The chirality of molecules in living organisms must have been fixed|
at an early stage in the development of life. All life that we know is
based on RNA and DNA molecules with dextrarotatory sugars. There
is growing evidence that the RNA world (Woese, 1967; Crick, 1968;
Orgel, 1968; see also Wattis & Coveney 1999) must have been preceded
by a simpler pre-RNA world made up of achiral constituents (Bada,
1995, Nelson et al., 2000). An alternative carrier of genetic code are
peptide nucleic acids or PNA (Nielsen, 1993). These can be rather
simple and are currently discussed in connection with the idea to build
artificial life (Rasmussen et al., 2003). Furthermore, although PNA can
still be chiral (Tedeschi et al., 2002), there are also forms of PNA that
are achiral (Pooga et al., 2001), suggesting that chirality may have
developed later when the first RNA molecules formed.
In current proposals to build artificial life, chirality does not seem to
be crucial. The PNA molecules is proposed to act primarily as charge
carrier, i.e. a very primitive functionality compared to the genetic code
in contemporary cells (Rasmussen et al., 2003). At this stage, homochirality
may have been introduced by chance. This is also supported
by the fact that chiral polymers of the same chirality tend to have a
more stable structure (Pogodina et al., 2001) and would therefore be
Since the introduction of chiral molecules is assumed to take place
at a stage when there is already growth and self-replication, it is also
plausible to assume that the existence of chiral molecules has an autocatalytic
effect in producing new chiral molecules of the same chirality
(Kondepudi et al., 1990).(my emphasis)
As for polymerization, the favorability of the amide bond is a plus for your side of the argument, but without some form of organization and some form of regulation, these polymers are essentially useless. That is a very big minus.
As for the Miller-Urey conditions, the fact that most of the chemical reactions within a living cell would occur far too slowly to be of any value unless catalyzed by specific enzymes is a big minus for you. Enzymes, as I'm sure you know, are specific proteins. But, without some form of protein synthesis we can't get any proteins! Yet the chemical reactions involved in protein synthesis require - (you guessed it) enzymes! Kind of a Catch-22 there isn't it? Of course the standard explanation is that early life was much simpler so perhaps no enzymes were required. To that I can argue - if life was that simple, we should be able to re-create such a thing in the lab. I'm predicting they'll never cross that bridge.
Also, it doesn't really matter much that they were able to form amino acids from non-living molecules because, as you said, the building blocks of life are abundantly available throughout the universe. It's the specific organization of these molecules that separates living organisms from their constituent parts. They must show that chemicals are able to self-organize, self-catalyze, self-regulate, and self-replicate, then they'll actually be getting somewhere.
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance." Orville Wright
"The presence or absence of a creative super-intelligence is unequivocally a scientific question." Richard Dawkins