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So it is impossible to measure anything and it is impossible for anybody to replicate anybody else's experiments?
How did we get physical constants and equations that describe physics?
Nope....
Not where you keep trying to take the logic. Ever heard of Brownian motion... or the Heisenberg Uncertainty principle? There are certain random processes that are not subjectable to precise predictability.
Anyways the few permutations that would allow for a steady state. Would still not be 'identical'.
So it is impossible to measure anything and it is impossible for anybody to replicate anybody else's experiments?
How did we get physical constants and equations that describe physics?
So each molecule has a chance of being at the end of the wire and becoming an ion?
Ok, spidey fans follow the methods of obfuscation here.
By your own admission present day organisms are more complex than past organisms.
Based on the observed fact that organisms become more complicated over time, would a prions 4 billion years ago be more or less complex than observed ones today?
So here is actually a more relevant tidbit as, to my understanding, prions aren't entirely self-replicating.Even some of the simpler (self catalyzing) ribozymes mentioned earlier by sabar are at least 350 polypeptides long.
How long is the simplest self-catalyzing ribozyme?
Don't digress... that's not what you're looking for... you've been keying this whole repe ive conversation in order to justify the basis for using speculative parameters in a simple statistical model? One that implies that the odds for the formation of complex biological molecules is independent of kinetic limitations. That's the gist of it no?
When confronted about the fact that the existence of multiple factors precludes the use of simple mathematical models, you then go on to say that 'randomness' becomes the basis for your calculations.
When confronted about the fact that 'randomness' cannot be predicted without first having to assume constants for factors that are actually changing... you then question the validity of physical constants; these, of course being derived from data and multiple equations that eliminate as many of the degrees of freedom as possible... this elimination in turn allowed by incorporating as many functions as possible (none of which include any of the typcial 'random' functions).
The key point in all this being that by trying to use a simplified model your calculated odds are much higher than would be calculated if all the kinetic limitations were factored in. How would you? One would have to know exactly which path led to the formation of proteins... otherwise it would all be pure speculation. One thing is for certain though... the odds get smaller; not greater by factoring in the limitations. Wanting thus, to factor in a corrolary of Drake's equation into the mix is also highly speculative in nature since you would have no 'earthly' clue for deriving the amount of earth-like-life-sustaining planets/moons in our universe. Claiming then that multiple universes solved the problem was also far fetched considering that the emergence of this one was highly improbable to begin with.
I promise to give you an answer if you would at least read the fallacy of your logic first.
Based on the behavior of prions today... it is unlikely that they developed before DNA/RNA... which makes the question moot and thus the answer becomes .... irrelevant.
About 95 base pairs (using all 4 bases) but with the additional incorporation of 4 functional groups not found in any of the amino acids (some small, some complex):
SO4 SULFATE ION
O4 S 2-
P1P 3-{[OXIDO(OXO)PHOSPHINO]OXY}PROPAN-1-OLATE
C3 H6 O4 P -
NCO COBALT HEXAMMINE ION
H18 N6 Co 3+
A2M 2'-METHYL-ADENOSINE-5'-MONOPHOSPHATE
C11 H16 N5 O7 P
So although the 4 others functional groups are located at specific junctions of the chain we would have to assume that their incorporation could have developed anywhere.
What this all means is that you would end up having to use the following number:
1/(8^95) = 1.6 x 10^-86 <--- a number which only gets smaller once kinetic limitations are factored in.
Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39
Top view
Yeah it's pretty complex... for being the simplest one we have found so far.
It's pretty, right.I promise to give you an answer if you would at least read the fallacy of your logic first.
Based on the behavior of prions today... it is unlikely that they developed before DNA/RNA...
Proofs of that.
which makes the question moot and thus the answer becomes .... irrelevant.
Yes.
About 95 base pairs (using all 4 bases) but with the additional incorporation of 4 functional groups not found in any of the amino acids (some small, some complex):
SO4 SULFATE ION O4 S 2-
P1P 3-{[OXIDO(OXO)PHOSPHINO]OXY}PROPAN-1-OLATE C3 H6 O4 P -
NCO COBALT HEXAMMINE ION H18 N6 Co 3+
A2M 2'-METHYL-ADENOSINE-5'-MONOPHOSPHATE C11 H16 N5 O7 P
So although the 4 others functional groups are located at specific junctions of the chain we would have to assume that their incorporation could have developed anywhere.
Proofs of that.
What this all means is that you would end up having to use the following number:
1/(8^95) = 1.6 x 10^-86 <--- a number which only gets smaller once kinetic limitations are factored in.
Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39
Top view
Yeah it's pretty complex... for being the simplest one we have found.
And dead boring simple.
It was a matter of actually doing the experiments, rather chatting about them.
No proof... just based on observation that the only way prions can replicate is by borrowing several large and complex proteins that exist only because DNA/RNA exists. Hence if DNA/RNA did not exist first... those proteins would have needed independent formation mechanisms of their own (and outside of the DNA/RNA pathway the probability would actually decrease because odds calculated using 20 amino acids as the basis would be lower than odds calculated using 4 base pairs as the basis).Proof of that
For the AA/bp relationship, one has to calculate a triplet for each AA, so formally 64. Actually less, considering the degeneracy of the code.
>20, anyway.
Because certain simplifying assumptions come in handy.
Er... in the middle. Yeah.
Are you agreeing or disagreeing?? It's hard to decipher your overall stance with some of the incomplete sentence fragments you sparsed around in my quote...
I didn't bother assuming that the protein was a reverse-transcribed in its formation... otherwise you would flat-out need DNA/RNA.
The logic then follows that if relevant proteins were made without the use of DNA/RNA... then that would mean that their formation was dependent on the union of amino acids by some other process... if the proteins grew simply by the addition of AA with each other then one would be forced to use the number 20.
Of course from observations today we know that polypeptide bonds are created with the use of enzymes. Without them the growing protein would encounter more and more resistance the larger it grew (in solution of course). In eithercase, that's why the odds if one included kinetic limitations would have to fall further.
As far as rules being different 4 billion years ago; radiation was higher (less ozone in the atmosphere), earths magnetic field was slightly stronger, atmospheric pressure was lower, and temperatures depending on the era were all over the place. So yeah they were different. But again, these factors aren't even being incorporated... how would we be able to anyhow? It's moot.
Last edited by Phenomanul; 09-13-2006 at 06:21 PM.
.
Last edited by Phenomanul; 09-13-2006 at 06:18 PM. Reason: double post.
You want some syrup with that waffle?
You know exactly where this is going, but don't want to admit it.
You might notice that I never really said prions were *the* thing, but rather a good example of some simple organisms.
I *did* say, however, that the culprit was probably simpler in terms of the number of sequences needed.
The self-replicating ribozymes fit the bill.
So if tomorrow we find a self-replicating ribozyme that only has 25 base pairs a lot of those zeros disappear, don't they?Yeah it's pretty complex... for being the simplest one we have found
so far.
Last edited by RandomGuy; 09-13-2006 at 10:53 PM. Reason: edited for clarity
What?
You intimated something about an ion at the end of a chain. I corrected you, since the ion is formed somewhere in the middle, and said "yeah," as in, "other than that detail, you get the gist. Continue."
And while I'm interested in seeing where your point is going, I haven't figured it out yet.
Yes... and people in your camp would irrelevantly shout with glee.... what type of question is that?
That is the overall pursuit of science no? To learn as much about our natural world as possible.
Did you even see the structure? Some of the kinetic limitations I've been constantly bringing up arise from the complexity of the three-dimensional structure that is being created. The functionality of the molecule depends on the exact three-dimensional stability of the molecule, and on the fact that some parts of the proteins are rigid, and other parts shift and 'move' while interacting with other biological molecules. They are highly specialized.
Last edited by Phenomanul; 09-14-2006 at 11:30 AM.
Yes, and measure it.
Everything else is left to philosophy and religion.
And then, of course, anybody can say just about anything.
Here we have the crux of the argument.
Your "infinitessmally small probability" is a lot more probable than you like to put forth.
The "car parts in a vat" analogy is put forth a lot, as is the "jet plane/tornado" thing. Let's break that analogy here.
In the beginning of evolutionary theory, people who wanted to disprove it, would say "you have animal A that you allege evolved into animal C, but you can't find animal B, the link between the two, so HA! you must be wrong about the whole theory".
Then some enterprising archeologist finds animal B, and then the same argument shifts to "you have animal A that you allege evolved into animal B, but you can't find animal A.1, the link between the two, so HA! you must be wrong about the whole theory!"
Now since this tack doesn't really cut it any more intellectually, we see a very similar line of point/counterpoint here.
"It's impossible for a single cell to spontaneously appear because the gene coding is so complex, and even so, there wasn't enough time for earth to make such a thing"
Then, surprise, we can reasonably assume our earth isn't the only place in the universe with the capacity to support life. Not only that there is a good chance that the universe has LOTS of places similar to our own.
Then "impossible" becomes "really really improbable", then the "really really improbable" assumption hinges on spontaneously developing a complex cell. Then suddenly some enterprising bio-chemist finds a self-replicating molecue that doesn't require a cell, and then the "really really improbable" assumption suddenly becomes "really improbable".
By your own admission, if someone finds a really simple self-replicating molecule, that "really improbable" assumption will come to "improbable" or (gasp) "probable".
You are right about pursuit of science, in that it is to learn as much as possible about the natural world as possible.
Everything we have learned so far points to that simple self-replicating molecule, even though we haven't found it exactly yet (to my knowledge).
So, let me ask you this:
Would it deminish your faith any less to learn the method that God used was simple random probablilty, as opposed to active particpation?
Assume I am right about everything here. The universe has a LOT of earth-like planets, and that spontaneous generation of life is commonplace.
Would you believe in God any less?
Last edited by RandomGuy; 09-19-2006 at 08:08 AM. Reason: readability
Oh, is that where you are going? OK, I see now.
Yeah, I have a problem when Christians turn this argument into an either/or thing. As in, "Either my dogma is correct or science is correct. It can't be both." So then of course, they've already decided their dogma is correct, so they simply will disregard readily identifiable facts.
In doing so, they raise the stakes unreasonably. If they accept mainstream science, their entire faith system becomes shattered. Their entire iden y becomes shattered.
And to what lengths do you think people will go to prevent that from happening?
That goes a long way to explaining the rampant anti-intellectualism in American evangelicalism.
Few ever consider, "Hey, maybe my faith is correct but my dogma is flawed." Perhaps this has something to do with a reaction against liberal theology's emasculation of Christianity. Nevertheless, the Bible states quite clearly that there is such a thing as "natural revelation," and that it informs man about the nature of God. Why can it not inform one's reading of Scripture?
Besides all that, though, one can have a philosophical debate about the degree to which science is going to be able to explain some of these complex and precise phenomena in the universe. Just because it wouldn't disprove the existence of God does not mean it is so.
For one, I believe you have oversimplified the problem into irrelevance once again.
More like by "my interpretation of Phenomanul's comment...." -- I didn't suggest what you just wrote, I said people in your camp would irrelevantly shout with glee... The number I gave you was still extremely 'improbable' -- and even then, I still haven't factored in any of the kinetic limitations that would oppose a stepwise growth to form said molecule. And even if I could factor these in, as this is not an easy task, they would exponentially hinder the molecule's creation altogether.
Back to the point though, finding a smaller self-replicating ribozyme is irrelevant considering the fact that all the ones we have found interact with proteins and DNA in order to subsist (much like everything else - imagine that). Ribozymes placed out of this environment would sit there and do nothing - not replicate. So like your prion example before, I believe ribozymes are actually a product of an RNA splicing event gone awry, a living example that the genetic language tends to break down, not get more structured. A 'genetic bas ' if you will. Consider this: ribozymes don't do anything other than copy themselves in a DNA based biological environment. And so what many poeple like yourself would love to overlook is the fact that they require DNA based proteins to stabilize their own replicative process because they aren't stable enough to propagate them on their own. That ribozymes can self-catalyze a replicative cycle when one feeds them an unnatural amount of amino acids is a bad conclusion drawn from garbage science.
Basically, you would have to prove that these molecules existed before DNA/RNA. So given that a ribozyme existed (in reality far from given), you would have to provide mechanisms that would allow for these molecules to subsist on their own -- a highly difficult task. You would have to provide sufficient mechansims to create the necessary amino acids, adenosine phosphate back-bone molecules, organic sugars and the other random functional groups that are necessary for the ribozyme's replication. You would have to provide protective mechanisms that would keep the molecule from being attacked by any ions or small molecules in solution -- meaning, the molecule would have to survive long enough to even replicate.
Earlier I placed emphasis on the fact amino acids are required in substantial amounts in order for DNA/RNA to use them as building blocks. The specialized proteins that fabricate each of the 20 amino acids would then have to exist to drive the localized order in any given location higher than what was dictated by brownian flux and thermodynamic balance. The agglomeration of amino acids is crucial. The sun model or lightning model cannot account for this molecule specific concentration shift, so don't even bring it up.
The logical conclusion then is that genetically relevant RNA or DNA strands would have to be the first organic molecules in a DNA/RNA run world. Every other molecule stems from it, subsists from it, takes order and directions from it -- the catch? Well, it would have to be long enough to carry genetically relevant code. Long enough to produce viable proteins; proteins necessary for the stability of the DNA/RNA strands themselves, proteins essential to the replicative functions of the molecule.
So why would your example be irrelevant? Because you are wishing to explain life's complexity by trying to derive the smallest possible source. In doing so you're inadvertantly attempting to eliminate the inherent interactions that are required for biological function. All for what? Because smaller molecules have higher odds of formation? And that is supposed to prove that life started as a mixture of simple chemicals? Far more is needed to even make that claim.
Earlier you gave a counter argument to my 'form a functional vehicle inside a whirling vat" analogy... You suggested that all that was needed to justify your line of thinking was the formation of the car's breaking system. Though that too would be unlikely, the premise is erred; A breaking system would serve no purpose without a car much like a any other organic molecule would serve no purpose without the full and complete functionality of the genetic code.
I don't agree with your conclusion... but nothing would diminish my faith. Why? First of all, my faith is not placed on Science. Second of all, I fully understand that Science will not explain everything (the purpose of life, consciousness, sentience of past-present-future etc...). I understand that there is more to this life than the understanding of our natural world. Wishing to diminish GOD's power then, by reducing His Creator role with one suggesting that He was the 'perpetrator of an accident' really serves no purpose. Most importantly, whether you choose to believe me or not, I know that GOD does actively participate in our lives today. And if He has forever been the same, logically, He has always participated.
I can't answer that question because it is based on assumptions that don't describe what I do know. It reminds me of a quote by Princeton's Freeman Dyson, a highly respected physicist, who once wrote about the uniqueness of life on earth, "It's as if the universe knew we were coming." Life everywhere else is not as commonplace as you wish it to be.
Feel free to disagree with my conclusion, but do ask yourself how the universe knew to give you the intelligence to make that decision.
Last edited by Phenomanul; 09-20-2006 at 08:58 AM.
Phenomanul, I think I get where RG is going.
He is trying to caution against the "God of the Gaps" fallacy.
He is trying to make sure people don't put themselves in a theological trap where they have to believe that up is down and balck is white in order to maintain their faith.
As long as you are not doing that, then you two are just having a nice philosophical discussion about how you think God created the universe.
You got it exactly.
That is essentially what I see the whole thing as being. I see a few things in science and common sense that he is ignoring, and actively so, in order to preserve what he conceives of as his faith.
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