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Coffee House => Coffee House Boards => CH / Science and Technology => Topic started by: Karlos on December 15, 2004, 02:08:48 PM
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For fluffy :-)
Rather than continue hijacking the_leander's threads, I figured it would be rather better to create one...
So, going back to this one, lets take a stock check. Existing evolutionary models explain the diversification and origin of new species of entire organisms relatively well. I have no issue with this at all.
For me, as we have discussed, the problem is the biochemical level. Prebiotic chemistry is a fascinating area that I studied intensely for a while. Foregoing for a moment the argument about how it all started, let's think about it for a moment.
It seems to me that there has been no significant (bio)chemical evolution for a very, very long time. What do I mean by this? Well, there may be small improvements in cell chemistry here and there, but by and large your human internal cellular machinary is not far in advance of any other eukaryotic organism - just look at yeast and you will find the same chemistry going on. Eukaryotes are themselves a step up from prokaryotes that have new biochemical pathways added on top of the prokaryotic set but do not significantly change those they inherited.
If you look at the most primitive forms of viral life you can find (and arguably they are not even really living), you find that they still use the same chemistry. They still use at least RNA to store their compositional make up and they use protein casings etc.
It seems therefore, that the biochemical complexity known today is largely unchanged in every organism known. Were still using the same nucleic acids, proteins, electron transport chains, photosynthetic systems since pa(ramecium) fell of the bus (to paraphrase X-Ray). Of course there are better examples of some metabolic systems, but fundamentally the chemistry has not changed.
This is one reason I don't think that existing evolutionary theory (as it applies to biology) applies to the chemistry that enables the biology to exist.
If we consider that biological evolution is taking place all around us, why do we not observe the same in chemistry? Once you have a self replicating, sustainable chemical system there is no reason to assume it would be completely replaced by a more efficient one, just as bacteria still exist in profusion, despite being biologically usurped by more sophisticated organisms competing for the same resources.
If the existing evolutionary models apply to chemistry, why are there no pre - nucleic acid / protein chemstry based organisms known? Just because the latter may be more efficient, the former system(s) capable of self replication should still exist. Yet none do.
So, the biochemistry we know - that is nucleic acid / protiens / sugars / redox / electron transport / photosynthesis - has been around relatively unchanged since life began, despite the vast changes in the biology it has enabled. In fact, the only variations we see are in how that chemisrty sources the energy it needs in order to drive itself (be it photosynthesis, iron-sulfur, carboyhdrate oxidation etc).
There is no evidence that the chemistry itself was ever any less sophisticated; there are no rival self-replicating chemistries known, no evidence any have ever existed and no evidence that the existing biochemistry has changed significantly or is changing. In short there is no tangible evidence of "chemical evolution".
So the questions remain. Where did the present chemistry come from and how did it establish itself so quickly given that it appears to have moved so little since? After all, it is generally believed the first single celled organisms powered by this chemistry were happily replicating wihin 200 million years of conditions being favourable.
There are many other reasons why I don't believe the existing evolutionary paragdims (as applied to biology) apply to the underlying chemistry, the above are just a few.
In my opinion, there is so much more to discover - sticking to creationalism or darwinism are not going to get us far.
If the_leander is reading this, feel free to hijack - it is only fair :-D
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Karlos wrote:
eukaryotic organism -
Until now I thought that was the name of a Finnish metal band.
It seems therefore, that the biochemical complexity known today is largely unchanged in every organism known. Were still using the same nucleic acids, proteins, electron transport chains, photosynthetic systems since pa(ramecium) fell of the bus (to paraphrase X-Ray). Of course there are better examples of some metabolic systems, but fundamentally the chemistry has not changed.
The upshot is "if it ain't broke then don't fix it". Despite the obvious progression of evolution over however many billion years, basic fundamentals barely change. However far you go back, the realisation that what evolution created was not necessarily "primitive" but a response to an environmental challenge. The Crocodile hasn't changed much in 120 million years, but it's purpose has remained the same, the Ceolocanth has remained the same creature for 200 million years.
The primate family can trace it's direct ancestry back 80 million years, mammals predate Sauropods and many species of plant are fundamentally unchanged since before the great extinction 65 million years ago.
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I know what you are saying, but I think you are missing my point. There is no available evidence to support the notion that the fundamental biochemistry we know of is evolved from anything less primitive - no matter how far back you go, find the same chemistry. There are no cousins, no other evolutionary offshoots, rivals or specialisations that you might expect to find given the way biological evolution appears to have worked.
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Karlos wrote:
I know what you are saying, but I think you are missing my point. There is no available evidence to support the notion that the fundamental biochemistry we know of is evolved from anything less primitive - no matter how far back you go, find the same chemistry. There are no cousins, no other evolutionary offshoots, rivals or specialisations that you might expect to find given the way biological evolution appears to have worked.
What a very interesting statement.
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The amino acid code for the simplest self-replicating molecule than can be thought up is Lee's peptide:
RMKQLEEKVYELLSKVACLEYEVARLKKLVGE
Where each letter corresponds to an amino acid. This is the best that theorists can come up with, and it's pretty simple. It is probably impossible to find simpler self-replicating molecules.
So supposing you had a system that allowed peptides to form and join up, which no naturally existing non-bioligical system today allows (because water and oxygen in excess don't favour peptide bonding - ask Karlos).
There are about 2000000000000000000000000000000000 different ways of forming a polypeptide that are exactly 32 long like the one above. Only one way will make that self-replicator.
Even if the earth was 20 times the size and covered by one huge "warm pond", this would not happen by chance. Clearly, pre-biotic chemistry has a long way to go.
The answer of course is probably that it's not by chance, and that some symmetry inhereted from the quantum fluff that makes up the foundation of the universe favours life. In fact, there's no doubting it: it does, or we wouldn't exist.
This in itself does not disprove the engineering of a higher power. Some would even say it proved it.
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I thought these might be interesting to this thread.
http://www.answersingenesis.org/creation/v19/i4/blood.asp
http://www.talkorigins.org/faqs/dinosaur/blood.html
http://www.naturalselection.0catch.com/Files/fossilrecord.html
They all three basically refer to the discovery of red blood cells within a partially fossilized T-Rex bone. The first seeks to support it, the second seeks to disprove it, and the third is sort of neutral and just talks about it. What is interesting to me though is that none of the three denies that there is unfossilized bone tissue there. This tissue could give us a better understanding of the biochemical makeup of these extinct reptiles, especially if the DNA strands in the nuclei are intact. I wonder if these dinosaurs have been extinct for as long as it has been estimated.
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KennyR wrote:
RMKQLEEKVYELLSKVACLEYEVARLKKLVGE
What does that come out to as a triple word score in scrabble?
Seriously, Kenny is right - prebiotic earth, with its reducing atmosphere, abundence of base materials and energy etc. possibly did favour spontanous peptide formation - soemthing which today only works thanks to the biochemical machinery that performs it - but would still be extremely lucky to even get as far as Lees peptide within the lifespan of the planet today, let alone 3.5 billion years ago. You still have to arrive at RNA as a better source of self replication and cataltytic activity (there are known RNA strands that perform various self-splicing and self-assembly within biochemistry), let alone moving towards the dual protein / nucleic acid system we have today. Yet all this must have been in place within about 200 million years of the raw chemical precursors needed for their assembly.
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While I have a long and complex answer for you Karlos, one phrase that keeps repeating over and over in my mind is: "The Laws of Physics haven't changed in 3.5 billion years!"
By the way, you must be forgetting your crystal chemistry (or maybe you have sucessfully purged from your mind as I spend every waking hour trying to)... but Crystals are a classic example of a self replicating system and totally inorganic too!
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bjjones wrote:
They all three basically refer to the discovery of red blood cells within a partially fossilized T-Rex bone. The first seeks to support it, the second seeks to disprove it, and the third is sort of neutral and just talks about it. What is interesting to me though is that none of the three denies that there is unfossilized bone tissue there. This tissue could give us a better understanding of the biochemical makeup of these extinct reptiles, especially if the DNA strands in the nuclei are intact. I wonder if these dinosaurs have been extinct for as long as it has been estimated.
One problem - red blood cells have no nuclei and no DNA! :-(
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Karlos wrote:
KennyR wrote:
RMKQLEEKVYELLSKVACLEYEVARLKKLVGE
What does that come out to as a triple word score in scrabble?
i thought it was welsh.
:-D
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KennyR wrote:
One problem - red blood cells have no nuclei and no DNA! :-(
I was not referring to the red blood cells, but the bone tissue itself. Bone cells must have a nuclei in order to be self replicating. Of course the red blood cells do not replicate but are produced by the marrow. The existence of the red blood cells is under debate. But if some bone cells are intact...
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cecilia wrote:
Karlos wrote:
KennyR wrote:
RMKQLEEKVYELLSKVACLEYEVARLKKLVGE
What does that come out to as a triple word score in scrabble?
i thought it was welsh.
:-D
Actually it's a small village a short way from Abergavenny.
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bloodline wrote:
By the way, you must be forgetting your crystal chemistry (or maybe you have sucessfully purged from your mind as I spend every waking hour trying to)... but Crystals are a classic example of a self replicating system and totally inorganic too!
No, I didnt forget at all. But I don't regard crystal self assembly as comparable to biochemical where different systems are involved in a complex symbiotic process - eg proteins replicate DNA and transcribe it, but the DNA stores the information required to assemble the proteins.
Symmetry (dictated by ionic/covalent concerns) and close packing hardly compare to the above.
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Karlos wrote:
bloodline wrote:
By the way, you must be forgetting your crystal chemistry (or maybe you have sucessfully purged from your mind as I spend every waking hour trying to)... but Crystals are a classic example of a self replicating system and totally inorganic too!
No, I didnt forget at all. But I don't regard crystal self assembly as comparable to biochemical where different systems are involved in a complex symbiotic process - eg proteins replicate DNA and transcribe it, but the DNA stores the information required to assemble the proteins.
Symmetry (dictated by ionic/covalent concerns) and close packing hardly compare to the above.
I personally see no difference, simply the scale of the problem, nothing more nothing less.
I also don't see why life didn't "hitch a ride" on a Crystaline scafholding before the complex RNA/DNA structures developed.
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bloodline wrote:
I also don't see why life didn't "hitch a ride" on a Crystaline scafholding before the complex RNA/DNA structures developed.
For one, there are no vestigial remmenants of this. Whilst it is true that many complex clays can interact with biological systems and in some cases are used, it seems to be the case that biology has found a use for the clays *since* reaching it's present level of complexity and not during its origin.
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@ Karlos
>> there has been no significant (bio)chemical evolution for a very, very long time.
Hum,
It seems to me that to have evolution in chemistry, then the carbon-based life forms have to have variation.
However, since there are only a set amount to amino acids then that narrows down diversification.
(The `best` are always used and survive)
I believe that the modern approach to evolution, envisages a contoured `landscape` that dictate the paths of evolution. The landscape being formed by random values such as the type of star we orbit, the gravity and composition of the earth, temperature and chemistry, etc…
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blobrana wrote:
@ Karlos
>> there has been no significant (bio)chemical evolution for a very, very long time.
Hum,
It seems to me that to have evolution in chemistry, then the carbon-based life forms have to have variation.
However, since there are only a set amount to amino acids then that narrows down diversification.
(The `best` are always used and survive)
I believe that the modern approach to evolution, envisages a contoured `landscape` that dictate the paths of evolution. The landscape being formed by random values such as the type of star we orbit, the gravity and composition of the earth, temperature and chemistry, etc…
Exactly my point... Physics is still the same as it always was.
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@Blob & bloodline
None of these arguments explain how the existing biochemistry came to be and especially in the timescale. This is the thing I don't think people realise. You to have evolved the near-present level of biochemical level of sophistication required to support the most primitive iron-sulphur bacteria *within* 200 million years of the conditions being suitable enough to allow the chemical agents required to exist. This implies that whatever "chemical evolution" occured in pre-biotic times must have been super accelerated, even if you allow for clays etc playing an active role in the initial stages of self replication.
If we simulate as best we can the environment the evidence suggests prevailed at this time we can observe the formation of guanine like heterocycles, primitive amino acids (and even oligiopeptides) and various other life related chemicals. Which is great, but these are the most elemental building blocks. We do not observe anything like Lee's peptide for example. Even if we did, the step up from that to RNA is as great as the formation of Lees in the first place, not to mention any symbiosis between the two.
If you perform any meaningful calculation on the likleyhood of these events, even making generous concessions to the probability of intermediate stages encompassing the change of function you end up with rediculous odds.
Kenny may well be right that the universe tilts odds into the favour of life via some as of yet unknown means because left to chance alone it is as good as impossible.
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Karlos wrote:
For fluffy :-)
In my opinion, there is so much more to discover - sticking to creationalism or darwinism are not going to get us far.
This is far too much to try to address while I'm supposed to be working ...
But why are you hung up on creationism and darwinism.
Darwinism is only really concerned with what happens after you have a living cell, creationism is only really interested in building an unquestioning army for "god".
And the principle of amplification and filtering which is the underlying mechanism behind darwinism is self evident and trivially demonstrable to the point that it's very silly to question it.
Applicability to non reproducing things? Nill. They lack the amplification. IFF it reproduces with variability it will be subject to evolution. That does not mean that it will change over time just as the tone from an oscillator will not (hopefully) change over time unless the filter is adjusted. In a constant environment, evolutionary forces work to conserve rather than diversify.
A good chemistry is not likely to change unless it can change radically all at once to produce a better system and the chances of that are vanishingly small.
As to there being no evidence of any other biotic chemistry in the past, we don't have much evidence of much in the past and the absence of evidence is not the evidence of absence.
Yes, there are many questions but that does not mean that answers cannot be found. Mathematics has run into many roadblocks over time but we didn't throw it out at the first sign of trouble.
Evolution is a principle, a frame-work more than an answer per-se. It does not give specific answers to any question but it does show a path. Why are there ducks? Evolution doesn't specifically answer that question but it gives us a framework in which to examine the question.
As to how it all started, that is a different question. Of course it is. So what? It certainly isn't answerable by calculating permutations as that sort of thing is devoid of context. What are the odds or 100 spinning magnets in a row all lining up end to end north to south and vice versa? Mathematically speaking you're not likely to see it in your lifetime. The fact that this outcome tends to happen a lot should tell you that there is something missing from your mathematics but it shouldn't make you assume that there is an invisible guy nearby lining up all your magnets because that is a more "intelligent" configuration.
Yes, it means that we do not know everything about the universe, but it doesn't mean that we should just chuck out the basic principles which have helped us know what we do know of the universe.
Like I keep saying, just because we cannot apply darwinism to prebiotic chemistry does not mean that we have to throw it out all together. This is the creationists arguement, and you are not one, and therefore you should not be making an arguement which can so easily be mistaken by creationists as support for their position and then used by them, however erronously, to tear down your own position.
The fact that biology is complex does not argue against evolution, nor does it support ID. Period. (translation to English - Full Stop). Most of what the IDers bring up doesn't support ID either. Listening to them as a source of questions is a waste of time since they do not ask them honestly. They ask them with a specific agenda and that is to open the door to the "Creator" and make "Him" necessary. You can think of better questions yourself.
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FluffyMcDeath wrote:
Like I keep saying, just because we cannot apply darwinism to prebiotic chemistry does not mean that we have to throw it out all together.
And nowhere do I say we should. It's a matter of appropriate method. One does not use quantum mechanics to help explain everyday physics. We know that classical physics is essentially an approximation for h=0 and that works fine for us. Likewise we don't use classical physics to explain the microscopic world since it falls on its bum.
It's just that people do apply the existing evolution model to the problem at hand, glossing over the inadequacies and questioning the motive of anybody who disagrees, which is as dogmatic as any old school 'creationalist' and I believe is putting off people from seriously looking into it.
This is the creationists arguement, and you are not one, and therefore you should not be making an arguement which can so easily be mistaken by creationists as support for their position and then used by them, however erronously, to tear down your own position.
I'm just calling it as I see it. I do try to keep an open mind; I mean, if it were proven beyond reasonable doubt that there is some ID going on I like to think I'd be able to accept it.
They ask them with a specific agenda and that is to open the door to the "Creator" and make "Him" necessary. You can think of better questions yourself.
Well, that's just it. The people questioning it originally didn't have any such agenda. It has been taken up by those that do since, but it is now the case you cannot raise the qestion without being so accused.
Of course the other thing is, even if the questions are asked with an agenda behind them it doesn't make the (properly considered) answers any less important. After all there is no guarentee which 'side' the answer will support anyway.
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Karlos wrote:
It's just that people do apply the existing evolution model to the problem at hand, glossing over the inadequacies and questioning the motive of anybody who disagrees[...]
But what model is that? Evolution happened, evolution is happening, it can be seen to be happening, so anyone who says they have some information that brings evolution into doubt should be viewed with as much suspicion as the guy who finds a helium baloon and says it disproves gravity.
I'm just calling it as I see it. I do try to keep an open mind; I mean, if it were proven beyond reasonable doubt that there is some ID going on I like to think I'd be able to accept it.
And if someone can prove fairies beyond a reasonable doubt I think I'd be able to accept it. There's a difference between an open mind and gullibility.
They ask them with a specific agenda and that is to open the door to the "Creator" and make "Him" necessary. You can think of better questions yourself.
Well, that's just it. The people questioning it originally didn't have any such agenda.
The people who question how it may all have started have an agenda to figure out how it all started. The first person to claim ID had a different agenda and claims deceptively not to have such an agenda. It is a ruse.
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Hum,
I don’t think that Darwinism is really applicable to the pre biotic stages of life.
It probably is another mechanism that stacks up the odds for having more and more complexity to chains of amino acids leading up to something like RNA.
What ever that mechanism is we know that it was probably quite a rapid process due to the signs of life, which shows up relatively soon after the molten earth had cooled down.
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FluffyMcDeath wrote:
As to there being no evidence of any other biotic chemistry in the past, we don't have much evidence of much in the past and the absence of evidence is not the evidence of absence.
Yes, there are many questions but that does not mean that answers cannot be found. Mathematics has run into many roadblocks over time but we didn't throw it out at the first sign of trouble.
Another very interesting statement. :-)
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bjjones37 wrote:
FluffyMcDeath wrote:
As to there being no evidence of any other biotic chemistry in the past, we don't have much evidence of much in the past and the absence of evidence is not the evidence of absence.
Another very interesting statement. :-)
And there might be fairies too. I think you're running a bit far with this. That's a straw you are grasping at and your faint hope is showing.
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@Blob
I think there are multiple stages in wich you can apply Darwinism on
@fluffy, at least he's happy with it, and he isn't bothering others with it :-)
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FluffyMcDeath wrote:
Karlos wrote:
It's just that people do apply the existing evolution model to the problem at hand, glossing over the inadequacies and questioning the motive of anybody who disagrees[...]
But what model is that? Evolution happened, evolution is happening, it can be seen to be happening, so anyone who says they have some information that brings evolution into doubt should be viewed with as much suspicion as the guy who finds a helium baloon and says it disproves gravity.
Yes, biological evolution that is, and I agree. However, as you said yourself earlier, it has no applicability to non-living systems.
As for the gullability remark, I hope that wasn't directed at me :-)
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I hope no one minds my entering into this little debate. My first two years in college were as a Chemistry major. I had two years of Chemistry, two years of Calculus, and a year of Engineering classes. Just so you will understand why I am fascinated with what Karlos has to say. I must say I am inclined to agree with him, perhaps because he does debate from the standpoint of math and chemistry. I have followed the debate raptly. It only falls down for me when it devolves into some kind of theological discussion. My stance is that God can neither be proved nor disproved with science. He did that deliberately. I view science as a description of what God did. So the facts are of value to me no matter what viewpoint you present them from. If the purpose of the debate is to disprove the existence of God, then I will step out of it right now, it is a waste of my time. But if the purpose is to explore nature for a pure love of science and research, I would love to be involved and learn. There are some very educated people here who have much of value to say.
I would like to ask some questions and I would even promise not to debate the response, just perhaps clarify my position or ask for clarification.
Respectfully,
BJ
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@Bjjones
It is really a conundrum as far as I am concerned. The speed with which life "as we know it" took hold is staggering when one views it from the prebiotic position.
I wouldn't hope for an answer to the problem any time soon, however. Presently were are on the uphill curve - the more we find out about it, the more questions we end up with.
Still, I sure as anything hope I live to see the answer - it's driven me nuts for the best part of 11 years :-)
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@Karlos
Sometimes, from a scientific point of view, asking the right questions can be just as important as having the right answers. The question gives the answer context and makes it meaningful. So finding all of those questions can be a good thing. :-)
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Quite; it's just that I am not entirely patient :-D
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Heres a link to evolutionary landscapePDF (http://www.tbi.univie.ac.at/~pks/PUBL/03-pks-004.pdf):
Or here (http://www.edpsciences.org/articles/epjb/abs/2003/03/b02522/b02522.html)
That may be key to asking the correct questions.
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KennyR wrote:
The amino acid code for the simplest self-replicating molecule than can be thought up is Lee's peptide:
RMKQLEEKVYELLSKVACLEYEVARLKKLVGE
Where each letter corresponds to an amino acid. This is the best that theorists can come up with, and it's pretty simple. It is probably impossible to find simpler self-replicating molecules.
So supposing you had a system that allowed peptides to form and join up, which no naturally existing non-bioligical system today allows (because water and oxygen in excess don't favour peptide bonding - ask Karlos).
There are about 2000000000000000000000000000000000 different ways of forming a polypeptide that are exactly 32 long like the one above. Only one way will make that self-replicator.
Even if the earth was 20 times the size and covered by one huge "warm pond", this would not happen by chance. Clearly, pre-biotic chemistry has a long way to go.
The answer of course is probably that it's not by chance, and that some symmetry inhereted from the quantum fluff that makes up the foundation of the universe favours life. In fact, there's no doubting it: it does, or we wouldn't exist.
This in itself does not disprove the engineering of a higher power. Some would even say it proved it.
It took me a while to come up with a meaningful reply to this argument. The underlying assumption is that self-replicating molecules started out as single entities, which consisted of aminoacids which had to stuck together 'just so'. Which of course leads to very worn reasoning that it couldn't have arisen by chance. You demonstrated that easily enough.
However, I draw the line at 'something inherited from the quantum fluff that makes up the foundation of the universe' for an explanation. We are dealing with chemistry, not with the space-time continuum (or if you prefer, quantum foam.) Okay, if you insist, then I admit that chemistry is an exceedingly low-energy manifestation of it. However, I simply refuse to introduce high-energy physics into the equation on the grounds that the energy available on the ancient Earth was simply not sufficient. (The temperature was below the melting point of rock; radiation levels were a lot higher, but still not high enough. Gravitation was probably equal.) There is not a single shred of evidence to indicate that under these circumstances the Schrödinger equation must be amended with G, as you do (in very complex ways) in quantumgravity theory.
Which leaves us with the question what happened then. We don't know yet. One also has to take into account that by current standards, the ancient Earth was a decidedly hostile place: hot, radioactive, bombarded with radiation from an emerging sun, and a reducing, poisonous atmosphere. I get the impression that non-equilibrium chemistry with autocatalytical limit-cycles is very popular these days. Clays laden with metal ions (which are famous for their catalytical properties) are likely to have played a role.
And then I will admit that there might be some truth in Karlos' original statement that clinging to the biological concept of Darwinian evolution might not yield an answer, although---supposing for a moment that life did arise from a limit-cycle---it raises interesting questions on what life and evolution are, exactly. Yet I don't think people in this scientific field are studying it in terms of evolution: they are studying it from a chemical viewpoint. (At least, I would.)
However, just as I draw the line at inheritance from quantum fluff as an explanation, I draw the line at anything hinting at intelligent design too. I've argued before that I consider that to be intellectual capitulation. We've only just begun to develop the tools needed to tackle this very complex problem, I say, give it another century or so. Or two.
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If I may take an opposing viewpoint, just for the sake of discussion and understanding. Consider the effect of entropy on a chemical reaction. It is obvious that there is an inverse relationship between energy and entropy. But this relationship has causal implications. Within a closed system, the kinetic energy of the present substances affects more than simply the rate of reaction. It is a known phenomenon that when two substances react, there are more than one or two products to the reaction. Take for instance H2 and O2. 2H2 + O2 yield 2H2O in theory. In actuality, there will be H2O, H2O2, H2, O2, and possibly a variety of other by products to include O- and H+. This is a result of the causal effect of the kinetic energy inducing the higher entropic state. So one of the consequences of this increased state of disorder, at least from the standpoint of Chemistry, is actually the production of some more complex compounds. Granted these are produced in very minute quantities. But they are produced nontheless.
It has been some 20 years since I took chemistry so if there is some flaw in my reasoning, please point it out.
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Cymric wrote:
However, I draw the line at 'something inherited from the quantum fluff that makes up the foundation of the universe' for an explanation. We are dealing with chemistry, not with the space-time continuum (or if you prefer, quantum foam.) Okay, if you insist, then I admit that chemistry is an exceedingly low-energy manifestation of it.
It's more than that. It's structures in the quantum world that actually define chemistry. They ARE chemistry! Matter and its chemical interactions are just an expression of this quantum world. Change any tiny part of the underlying structure and perhaps neutrons wouldn't be stable, or electrons would have 100000 times the mass.
Just as quantum physics "just happened" to be perfect for physics, which allowed chemistry, which allowed biology. The formation of life, through whatever means, was as predetermined as the formation of quarks, protons, and atoms.
And every chemical reaction too, involves quantum physics directly. When molecules react, they don't do it like lego or clockwork. At the instant of a reaction, they exist in a quantum superstate, where simultaneously all of the possible products of the reaction exist, until something causes the quantum state to break down. Usually the most probable product of the reaction finishes up.
Chemists should already be familiar with quantum superstates via the benzene molecule. I was taught in high school that benzene constantly swaps its pi and sigma bonds. However it was also known for years that this does not fit what we observe of its properties. Chemists found out later that all the possible configurations of the kekule ring structure exist at once. It's the same properties of conjugated bonds that allow some polymers to conduct electricty. Neither of these phenomena are chemical, both are quantum.
In the same way, it's possible that all 2000000000000000000000000000000000 polypeptides existed at once, and some underlying symmetry made it more likely for our self-replicator to form. Well, it's not so far-fetched; it was the same kind of "bias" in the quantum world that allowed matter to gain the upper hand over antimatter.
What predetermined life? We could go for the anthropomorphic theory and decide that this was by total chance that, among an infinite number of infinitely varying universes, ours was special and allowed the creation of self-replicator - simply because if it hadn't, we wouldn't be here to see it. Or we could go running to God. Either way is just as useless at the moment, but there is no doubting that our universe was destined to develop life the moment it was created. We just have to find out how it did it, and what "its method" was. Why is better left to philosophy.
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KennyR wrote:
Chemists should already be familiar with quantum superstates via the benzene molecule. I was taught in high school that benzene constantly swaps its pi and sigma bonds. However it was also known for years that this does not fit what we observe of its properties. Chemists found out later that all the possible configurations of the kekule ring structure exist at once. It's the same properties of conjugated bonds that allow some polymers to conduct electricty. Neither of these phenomena are chemical, both are quantum.
Oh how I regret missing out on quantum chemistry. This opens up a whole new line of thought.
We just have to find out how it did it, and what "its method" was.
So very true.
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KennyR wrote:
In the same way, it's possible that all 2000000000000000000000000000000000 polypeptides existed at once, and some underlying symmetry made it more likely for our self-replicator to form. Well, it's not so far-fetched; it was the same kind of "bias" in the quantum world that allowed matter to gain the upper hand over antimatter.
What predetermined life? We could go for the anthropomorphic theory and decide that this was by total chance that, among an infinite number of infinitely varying universes, ours was special and allowed the creation of self-replicator - simply because if it hadn't, we wouldn't be here to see it. Or we could go running to God. Either way is just as useless at the moment, but there is no doubting that our universe was destined to develop life the moment it was created. We just have to find out how it did it, and what "its method" was. Why is better left to philosophy.
It's now way past my bedtime, so my thought processes are beginning to falter and wander off in random directions. If I suddenly write nonsense, you know what's causing it.
After a good deal of thinking and searching and remembering the weird chiral preference of the living nature, hypothesised to be caused by the chiral preference of the weak nuclear force, I am grudgingly forced to admit there is more to quantum chemistry than just electrons and quantum alone. And once you get to the weak nuclear force, you're touching upon hypothesised CP-violation (or CPT conservation, whatever you prefer), and you end up with very, very fundamental physics in something which is quite, for lack of a better word, normal. (With that I mean that students of today are not really surprised any longer about the quantum mechanical description of many chemical processes.)
However, the influence is seriously small, and I am quite hard-pressed to admit its influence on the scale you seem to be proposing. Chalk that up to my engineering, rather than scientific, background. I can dig chiral preference, I can dig the benzene molecule, I can dig the transition state of a molecule undergoing a reaction. I cannot dig without extremely good reason (read: Nobel prize-winning experimental evidence, which is what it would be anyway) transition states specifically favouring what we would now call replicating molecules. I just cannot see (which is definitely a non-authoratitive opinion, given my knowledge of the subject) what sort of fundamental physics would favour self-replication. Nature favouring matter over anti-matter is 'understandable' by comparison. In other words, you seem to be mixing various instantiations of the quantum thingie, and I'm not sure whether that is correct or even allowed.
In addition, I'm not sure you can say that this particular universe was 'destined' to produce life thanks to its particular setting of basic parameters. More correct would be to say 'life as we know it', and even more correct that this universe simply did. To be destined for something implies a broader knowledge of alternatives, and we don't know of any. We don't---heck, we wouldn't even---know if you can have a universe with a chemistry as ours, but no life from its 'beginning' to its 'end', whatever those may be. That implies knowledge of the solution to the problem we are trying to solve: how did inanimate matter become alive?
Me go sleep now. Brain shutdown imminentz.. zzz..
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Cymric wrote:
It's now way past my bedtime, so my thought processes are beginning to falter and wander off in random directions. If I suddenly write nonsense, you know what's causing it.
Ah, that's what's been causing my recent coding gripes :-D Must remember to sleep.
It's a fascinating problem. When I discovered prebiotic chemistry was available in as an option in my master's year I jumped on it. I generally like to keep abreast of developments in the field, despite giving up on chemistry as a career option. Life is just so fascinating at the microscopic level - it irks me slightly to think I probably won't live to see it completely unravelled although I don't rule out the possibility.
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bjjones37 wrote:
Oh how I regret missing out on quantum chemistry. This opens up a whole new line of thought.
Yep, quantum mechanics has revolutionised understanding in may areas of chemistry from spectroscopy (probably the first area affected) right through to reaction and structure prediction. Really liked quantum mechanics. So simple in basic concept and yet so complex at the same time.
I have to confess that I was unable to keep a straight face in one lecture (in a series on frontier orbital theory, a QM application used in explaining reaction pathways) when the completely sombre lecturer announced: "And here we see the end result of the backside attack of the HOMO on the LUMO".
It was very childish of me, I know :-)
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fascinating stuff, I like the way Darwins theory is more firmly boardered to things once they get going, how it is described as a framework for understanding rather then the end in itself (after reading Darwin's work, it was blatantly obvious to me - a layman that he simply didn't have a clue wtf was going on with regards the mechanics of it.. iirc he suggested that blood of all things could be the stuff responsible, which to me was just ironic, since I believe that the red blood cell is the only cell in the body that doesn't come with its own dna).
I understand it in as much as the principles go, but my lack of higher education shows up blatantly when trying to dig into the detail of it all. I just wish that I could explain it in a way that even hardend fundies like my folks in law that even they couldn't dismiss it.
offtopic, the folks in law have recently gotten back from a trip that lasted a week, so its been bliss... I just wonder when this topic will rear its ugily head again.
@fluffy and Karlos:
Don't worry about the thread, it was good to include what you did because it put context to what caused the necessity for the thread.
I just wish that I had the education you guys did. I guess I will always be more of a mechanically minded person then one for theory :-)
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@KennyR
And every chemical reaction too, involves quantum physics directly. When molecules react, they don't do it like lego or clockwork. At the instant of a reaction, they exist in a quantum superstate, where simultaneously all of the possible products of the reaction exist, until something causes the quantum state to break down. Usually the most probable product of the reaction finishes up.
True. And that product is statistically most likely to be a virtually intractable oily brown crap that requires about 3 purification stages when it comes to any non-trivial organic synthesis, if my experience is anything to go by ;-)
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@karlos
Hahahaha! yeah, organic chemistry was never my fortè either :-D
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bloodline wrote:
@karlos
Hahahaha! yeah, organic chemistry was never my fortè either :-D
Yes, but it was mine :lol: The stuff I was doing at the time however, was entirely novel and was based on my bosses earlier research into (chirally) directed metallation by rotationally restricted amides. Great stuff, except removing the amide (in it's entirety) is next to bloody impossible without destroying whatever else you have in your substrate.
My task was to investigate using removable sulfone / sulfonamide derived systems instead of the above amides, since cleaving these off later is not particulalry difficult.
The first step was to prepare them and investigate their low temperature properties (to see if the sulfur based replacement for the amide sterically locks out and stops rotating). This alone took a few months :-/
Due to the size differences and bond angle issues, getting such a rotationally inhibited sulfonamide was not entirely straightforward. Having to wait weeks at a time for a set of low temperature NMR (getting the spectra for the same sample from say -80C to room temp in 5C increments) didn't exactly help.
Unfortunately, just as I was starting to get somewhere, those neer-do-well Japanese industrial chemists jumped in and published work they'd been secretivley working on, rendering all my work useless. Absolutely nobody awards a PhD for second place.
By then I was pretty disillusioned to say the least...
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Impressive,
Second place is still worth writing about though...(in CV)
Anyway, i noticed this:
"Two years ago, another team showed that polio viruses could assemble themselves from off-the-shelf chemical components mixed in a test-tube.
And several chemists are exploring the kinds of chemical reactions that may have preceded life."
from here... (http://news.bbc.co.uk/1/low/sci/tech/4104483.stm)
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@blob
The theory was very impressive as was the existing work. I did enjoy it at the outset. A year of no results and then getting scooped just as I started to get some was a factor in my deciding to leave the subject (although not the only/biggest one).
About the prebiotics again:
The off the shelf components in question were themselves the product of biochemical synthesis (although some may be artificial of course). Even if they were not and were all present in abundence on prebiotic earth, getting your original polio virus structure in the first instance would be rather more miss than hit. It's an order of magnitude more complex than Lee's peptide. The test tube conditions themselves are likely not quite the conditions on prebiotic earth.
Still, self assembly is one of the critical factors in living systems so they are definately looking in the right place.
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Karlos wrote:
I have to confess that I was unable to keep a straight face in one lecture (in a series on frontier orbital theory, a QM application used in explaining reaction pathways) when the completely sombre lecturer announced: "And here we see the end result of the backside attack of the HOMO on the LUMO".
It was very childish of me, I know :-)
You missed out on the wonderful world of chemical engineering then, where we had to learn about the backside attack of the HOMO and the outcome of the penetration theory.
Of heat, inertia and matter, you sickos. It's respectable science, not some g33k l33t pr0n course!
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Not to mention the spectroscopic aspects of virbrational excitation and stimulated emission.
Finbarr Saunders would have had a field day in those lectures :-D