Other than the dinosaur tracks, MarcUK and Hassan i Sabbah are up to their old tricks of not reading my posts and then posting ignorantly. For those that want to make their own conclusions about the dinosaur tracks, go to this link
. Also, let me get this straight: talkorigins believes that the very human-looking tracks are the result of selective water erosion of dinosaur tracks. Wow. No wonder you guys believe macroevolution can occur.
Originally posted by hardeeharhar
1) We have detected the (presumably IR) spectral signatures of both nucleotides and amino acids in distant nebulae. They arise spontaneously in space.
I've seen the research that observed nitrogen heterocyclics in space, as well as some of the simpler amino acids. Those are not, however, nucleotides. The are only the bases (and there are a lot more nitrogen heterocyclics than those used in DNA/RNA, as you know). Additionally, they are hardly in the concentrations needed for what you're talking about...but we'll get to that.
High concentrations aren't necessary unless you want this to be done on a laboratory time scale -- and I am trying very hard to argue that we have bucket loads of time so that really isn't an issue.
That's my point though, you don't have bucket loads of time. Unless you are trying to say that the oceans were one big pool of amino acids and nucleotides all at 100mM (which is laughable in the extreme), you're not going to get anything close to even a measureable turnover from even the most optimized enzyme/inorganic catalyst.
Additionally, there are lots of chemical reactions completely separate from life that can break down your pre-biotic materials. Oxidation immediately springs to mind (some people have postulated O2 didn't exist much early in time), free radical degradation, heat, and a million other organic reactions.
2) Autocatalyzing reactions are only necessary after the first basic components have been created -- in my example, the activated nucleotides.
First of all, I don't know any natural mechanism (other than the ones used by life...obviously) to take a sugar, add a base, and then add three phosphates. So you're all ready in trouble, and you still have the problem with autocatalyzing reactions not having even a fleeting concentration of their substrates to work on.
But autocatalyzing reactions are necessarily the ones that would have a reduced kinetic barrier in a system with no other catalysis, that is the products of the reactions that are autocatalyzed would build up much more rapidly than those that aren't autocatalyzed.
Well, as you know, catalysts do not change the equilibrium position. So what you're saying is: A perfectly (or near perfectly) optimized crystal (we haven't even got to proteins yet, I'm assuming) happens upon a decent concentration of amino acids and polymerizes them (randomly, of course) into a protein. This happens a whole lot of times, until eventually a functioning protein is made. Now we have a single (functioning) protein. Great, so you just made alcohol dehydrogenase. Now what?
3) I have again never argued that all the components for life needed to be in the first reaction vessels, if you will. I think we can both agree that there are selection pressures on reactions which are catalyzed well, that don't build up side products that damage the catalyst or kill the substrates, and even so far as catalytic reactions whose products protect the reaction conditions.
No, I don't agree, and here's why: Other than your last example (which, as you would have to agree, is very rare), making a single substrate from a single enzyme does not help the enzyme to be any more fit. Only when the enzyme is observed in a larger context, and where it's products can help the organism for which it works, does the enzyme make life better for itself. For those out there who don't understand what I've said so far, I'm going to make an analogy:
Say you have a shoemaker. He can make 50 shoes a day. He, however, only needs a single pair of shoes once a year. It does not benefit him to make 50 shoes a day, let alone one, unless there is a market for him.
I know Dr. Behe has been much maligned for his "irreducible complexity", but that's a great example of what's going on here.
Also, what happens if your protein is inactivated by a free radical? Then what? You have to start all over again.
4) Lipid bilayers are quite obviously one of the most recently evolved traits of cellular life -- think of the major thing that really separates physiologically the three forms of cellular life (prokaryotes, archea, and eukaryotes). It is their membranes, how many, how diverse, and what linkages are formed between the phosphorylated glycerol and the alkyl chain.
Actually, lipid bilayers are observed in every life form, so I would say that they're probably one of the oldest tenets of life, but I suppose you could make a statement for a protein envelope (a la viruses).
Also, it is quite evident that lipid bilayers are quite a bit more complex than your average grease slick. They must contain transporters, structual proteins, etc.
But what is clear is that there was a lot of glycerol and phosphate in the initial cesspool of life. As far as these lipid bilayers being generated by catalyst -- well they are now, and there is no functional reason to believe that there creation couldn't be catalyzed by nucleotide based catalytic mechanisms (although, given the timing of the creation of the membranes in the branches of life the machinery for peptide synthesis may well have existed.
Oh, I see, you are talking about the RNA world. Ok, that makes things a bit simpler. Well, other than the fact that little more than self-excising RNAs have been observed operating in a catalytic function, you can make the leap (as some have done) that they were the first enzymes. As well as lipid bilayers being synthesized, you are being somewhat disingenuous when you say that they are generated by a single catalyst. If I remember correctly, there's more like 12 or so.
Also, as we both know, lipids and their related precursor molecules will form bilayers spontaneously.
Yes, but usually not structually useful ones, and they definitely still need ways to transport materials across the membrane.
All it takes is a pressure to develop a membrane around the ever more complicating "machinery" -- and we know why we need membranes, it creates the possibility of generating energy from potential gradients across the membrane as well as providing a means to separate the growing list of reactions preformed by our biomolecules from undesirable side products (the second probably came as a reason before the first).
Agreed, but if you get a lipid bilayer too soon, you're screwed. You need to have all
of your ducks in a row before you enclose your machinery, otherwise you've done the cellular equivalent of suffocating yourself. How a pre-cell managed to corral everything it needed from randomly floating active enzymes (of which the probability of creating is slim enough), into a enclosed space is truely an exercise of the imagination.
Also, if there was as much glycerol as i think there was in the cesspool, these bilayers wouldn't be as selective as ours are today -- and there is no reason to think that they would need to be.
For even this very simple step you are forced to constrain the supposed inital environment in a very unlikely setup.
5) It is an insurmountable problem to think of this as having arisen from peptides and somehow -- mysteriously -- got back translated to RNA or DNA.
I'm glad we agree about that. Although, it would be really cool to find a mechanism capable of doing that (I can't think of why a cell would ever need to). Talk about nobels for everybody (I'll share it with you!).
However, I will not say that it is impossible -- a system that accidently creates the biomolecules that are keeping it around has a better chance of surviving than those that don't -- hence back translation by being able to produce more catalysts.
But that's different that the reverse-reverse transcriptase that we were talking about earlier. This is much more plausible, at least from a probability POV, but still, you're making the jump from a single catalytic RNA construct to a functioning "system". Making one enzyme is a big enough jump. Making more than one in the same vicinity and time and having them come together is...impossible.
And a note to the non-math people out there. It's possible
that Elvis is still alive. Heck, it'd be possible
for him to be living a hundred years from now, if only he reached some eastern shaman during his post-faked death (and subsequent coverup) that taught him the keys for long life.
However, is it plausible? Hardly.
Also, a note to MarcUK and Hassan, if they post my elvis thing out of context to "prove" I'm a moron, you really are pathetic.
I do actually subscribe to the simpler RNA world hypothesis since we have a great deal of evidence that these things can be catalytic -- it also reduces the complexity of the initial steps, involving less inorganic compounds and more stuff we know works.
Yeah, if I was a naturalist, I'd probably go with the RNA world thing myself, however, making the jump from a self-excising polynucleic acid to a repeatable enzymatic construct is a rather large one.
And if I were nature, I wouldn't mess with things that work. However, as a person who does de novo protein design, I must say, at this point we are reinventing the wheel with each iteration. There are rules we garnered from nature/geometry, but really each design isn't related to the previous designs as much as we find in nature. Perhaps we are going about this stupidly, but the ability to make leaps from one protein design to another is a trait of human intelligence...
I looked at protein design a bit as a possible thesis, but I don't think (and you would agree) that we've really got too terribly far yet. (my main area of interest is NMR technique design for biomolecules) As for your example, if you already made one succesful oh, say, kinase, you would use that same domain over and over. (which is what we see in nature). Unless you like masochism, you wouldn't make a different protein for each organism that made the same thing.
Well, there is growing evidence that that is all God needed to have done -- after you have a single celled organism containing all of the mechanisms for the diversification of life, natural history and random chance tells the rest of the story.
I would agree with you quite a bit. Dawkins (or is it Gould?) began to espouse the panspermia theory quite a bit. As I posted before, if someone could somehow convince me that the single cell came about by chance (which is getting more and more remote the further I get in my field), the step from single-celled to multi-cellular would be paltry by comparison.
If I were God, I would stop there, because I am a scientist and not an engineer. If I was an engineer, I wouldn't want things to change from my initial set up. So is your God a scientist or an engineer?
He's more than just that. Based upon what I observe every day in my life and work, he appears to me to be scientist, engineer, and artist.
The bible wasn't written when these people were "alive." From everything we can tell, people living before the spread of agriculture probably did live longer because their particular nutrient requirements were better suited to hunting and foraging.
Even good diet and exercise can't save you from amassing genetic defects though. Look at Mr. Armstrong. Less than 50 years ago he would have been a dead man.
We have all the genetic evidence in the world to suggest that unless something is seriously off the decrease in telomere length of any and all humans provides a reasonable maximum life span. I believe that this is significantly shorter than many of the people's ages in the old testament.
I agree. However, the very long lifespans started to decline dramatically after the flood, and very quickly stabilized on what we would consider a "normal" lifetime (a bit shorter, actually, because of the obvious medical concerns). Protective water canopy?
Actually you don't need an endless supply, you need a degredation reaction that is much slower than the polymerization reaction. You do need enough to get to the point that the system can make them itself -- acetate, ammonia, CO2, glycerol, water and phosphate.
Yes, but based upon my earlier statements, where are you going to find a nice little isolated place with a high concentration of the pre-biotic materials, all free from the ravages of environmental chemistry? Getting a system capable of generating all of these molecules themselves, even in conditions like you state, is not likely at all. (and that's an understatement)
There exist several syntheses to making nucleotides, pick one, it can occur in nature. Again, if we take the view that proteins are where life started, we get nowhere fast (and again, I am not saying however that this couldn't be the case).
All methods of making nucleotides occur in already-living objects. Of course, it's possible I missed something. If you have a mechanism where life (or the critical enzymes from life) isn't/aren't needed for this, I'd like to hear about it.
Actually that isn't true. In truly sterile conditions (which let me tell you, young earth was), biomolecules (excepting largely complex proteins which don't unfold reversibly) are perfectly stable at almost all temperatures an aqueous solution can have.
Acutally, most enzymes become denatured even when you go a little bit above 37C. And also, it's not just the sterility of the solution at question. I doubt you could say that the original "prebiotic" soup was made of distilled, deionized water with just the critical amino acids/nucleotides. (and your crystal, of course)
Most instability is due to irreversible unfolding of protein, and/or nucleases or proteases which now (due to the profundity of life) coat the planet.
See above, also many metal-containing proteins can have the metals titrated out of them via mass action. (Had a real pain of a protein I had to work with that had that problem).
No. There exist kinetic barriers to reactions in nature. A thermodynamic barrier is one in which the product is so high in energy compared to the starting materials that equilibrium lies far to the starting materials. Meaning the reaction would be nearly impossible unless the product was being consumed. Kinetic barriers are overcome by time. Thermodynamic barriers are overcome by chemistry.
I was referring to the activation energy as a thermodynamic barrier. These are overcome by either enzymes, or heat (which cells can't utilize too well).
Hardeehar, I appreciate our discourse. I'm glad your're actually reading my material, and responding to it in kind. I hope that we can continue this fairly civil discussion, and that *ahem* certain others can take a hint and do as well. Thanks.