Time factor in self assembly calculations?

Hi PeterYou said:>With our reasonable genetic and molecular biological tools it has
>become clear that evolution theory cannot account for:
>1) the origin of life,
>2) the origin of genes,
>3) (the origin of) biodiversity.Strictly speaking the theory of evolution does not have to account for the origin of life or genes (or do you mean "novel" genes here?). I think Darwin himself still left room for god to start the whole process off but these questions are more relevant to abiogenesis (are we in the wrong forum for this discussion?). Evolution concerns the changes of organisms across generations in response to their environment.Genetics does support a common origin to life on earth. The highly conserved set of amino acids and base pairs used by all organisms are a great example given that unnatural amino acids and basepairs have been shown to do the job just as well or even better in some cases.Within the very limited time frame of human studies we have observed populations of organisms in the laboratory and field undergo detectable genetic changes in response to selective pressures. We have not yet observed a new species form from selective pressure which is so novel that no-one could dispute its recognition however. Here is the abstract of a nice viral example though where the previous evolution of a bacteriophage was predicted from genetic similarities and then reproduced in vivo!Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3,Pajunen MI, Elizondo MR, Skurnik M, Kieleczawa J, Molineux IJ,JOURNAL OF MOLECULAR BIOLOGY 319 (5): 1115-1132 JUN 21 2002We report the complete genome sequence (38,208 bp) of bacteriophage T3 and provide a bioinformatic comparative analysis with other completely
sequenced members of the T7 group of phages. This comparison suggests that T3 has evolved from a recombinant between a T7-like coliphage and a yersiniophage. To assess this, recombination between T7 and the Yersinia enterocolitica serotype O:3 phage phiYeO3-12 was accomplished in vivo;coliphage progeny from this cross were selected that had many biological properties of T3. This represents the first experimentally observed recombination between lytic phages whose normal hosts are different bacterial genera.
_______The original assumptions of ToE *are* being revealed as simplistic, but the emerging picture is that evolution is part of the "design" of genomes and is a much more efficient process than first imagined. We have observed numerous mechanisms by which larger scale genetic modifications are made other than by base pair mutation alone, namely transformation, transposition and polyploidy. We are getting glimpses into the operational complexity of the genome by studying the intricacies of gene regulation. Access to whole genomes is demonstrating that modern evolution is more about genetic rearrangement than functional innovation. Life already has enough existing tricks up its sleeve to meet any challenge thrown at it. All of the basic biochemistry of life seems to have been sorted out well before multicellularity arose.And you don't address my main point that molecular biology techniques that allow rapid genome sequencing and the study of gene interaction are recent discoveries- it takes a lot of time to accumulate the necessary data. Why is it reasonable to expect the current data to be irrefutable given that 99% of the current genetic information in the world is still waiting to be sequenced and those genomes already available are decades away from being well interpreted? I personally can't wait for the chimpanzee genome to be completed- that ought to rock the boat a bit Are you seriously proposing that we already understand the significance of the majority of the thousands of genes in a human or nematode? Last time I checked there were even still plenty of bacterial genes with unknown functions.Lastly I want to express my belief that the position of life being so complex that an outside influence was necessary is a cop out. It merely excuses us as a species from doing all the painstaking scientific data collection and as individuals from trying to comprehend it all. Irreducable complexity is in the mind of the (irrepressably simple?) beholder and our personal inadequacies cannot be construed as evidence of external influence.

Hi PeterI find it interesting that you can tell the difference between life and a "self propagating reaction". This response only strengthens my original point that nanobes *might* be a key to understanding abiogenesis. Or perhaps they will turn out to be very small but otherwise unremarkable bacteria or some form of organic artifact. I originally mentioned them in passing only, and also to highlight how incomplete our awareness if of life on earth even on a species and family basis (let alone genetically). The less controversial discovery of normal sized lithotrophic bacteria in similar environments (http://www.sciteclibrary.com/eng/catalog/pages/2832.html) has opened the question about what regions of the earths crust are habitable and their possible involvement in abiogenesis.The sandstones contain some N and C- but mostly Si and O. The formation of the nanobes represents a concentration and organisation of certain elements usually associated with life in a manner which is remeniscent of life except for its size.I would say that something looking like life is a comparative rather than subjective observation. To make the comparison objective you could paramaterise the morphological variables of life if necessary and see the relative proportions of nanobes are within the range of those observed for known life forms (even though their absolute proportions are novel).Carpet fibres have a very different microscopic structure to microbes and nanobes. A biochemical makeup consistent with life is only a piece of corroborative evidence. You must keep in mind the techniques they used- SEM and TEM and Xray diffraction and elemental analysis- are all standard microscopic techniques typical of a microscopy group. The ape/seawater example is a non sequitur, but I nor the researchers never claimed that they had conclusive proof of life, only a suggestion. Their expertise and their limited evidence fits with them publishing in a geological journal also. They only showed the absence of contradictory evidence using the techniques they were most proficient with.>One doesn't need ions to polymerise.But one does need counterions to form inorganic deposits. By this I meant halogens or chalcogens consistent with a metallic or silica based inorganic structure. Inorganic deposits would be crystalline and not polymeric- there is a distinct difference. The researchers showed that the structures were neither crystalline nor inorganic.>You cannot present the nanobes as having a nucleus based on this
>observation. They do not show any membrane bound structures. It is
>wishful thinking.A nucleus is very different from a "possible nuclear area" as stated in the original paper. The researchers were only pointing out an area of higher electron density in the centre of a cross section of a nanobe filament. That the filament itself is membrane bound is convincingly shown. The exact composition of the membrane is unknown but has to be consistent with the elemental analysis of the structures.>What is the big deal being not of mineral nature. They've already
>shown that the nanodes are non-mineral of nature. So it may be not
>stones, but it certainly has nothing in common with life.A self replicating, apparently cellular and non-mineral process has "nothing in common with life"? Puh-lease!>They could have asked anybody in their institute to provide conclusive >evidence of the nature of the DNA. If they send the nanobe to me I
>will extract the DNA (if present).I agree that the lack of published progress in this area in the last few years is puzzling but it is not evidence of the whole thing being a fraud. Claims of nanobes being ubiquitous from other groups though are also emerging. Even verified very small bacteria have only fallen within the range of experimental techniques within the last few decades. Perhaps their silence is political- they are waiting to accumulate enough conclusive data to produce a major report in Science of Nature and claim the area as their own. They wouldnt be the first group to sit on data until the time was right to release it.The existance and biological status of nanobes doesnt rely on them containing any DNA- in fact they would be more interesting if they lacked it. And you should know as a scientist that negative results are never conclusive proof that you started with nothing, only that you may have used the wrong technique so far. The nanobes appear to have especially resistant cell walls- how would you suggest they rupture them without destroying and DNA (or worse RNA) that might be present given that their exact composition is unknown? Can DNA be extracted efficiently from the most resistant bacterial spores?On DAPI and DNA I think you misunderstand how specific the interaction is. The dye binds selectively to the minor groove of DNA with considerable sequence selectivity. On binding the flouresence spectrum of DAPI changes considerably in a well characterised manner. Binding to anything other than DNA would change its flouresence spectrum in a different way (see Biomol GmbH - Life Science Shop). And I will again reemphasise that even if the DAPI result is a false positive that doesn't negate all the other observations of life like behaviour and qualities- it only makes them more intriuging and more relevant to my original reference to nanobes.Shane

This is where I criticize, D'Arcy Thompson's visualization (from Fish research??) that SJ Gould apparently accepted back to Buffon scholarhip but I back out without the pin head of a response for this is a good question to which I hope to find the time to return and continue with.

dear Shane,In response to:
"what regions of the earths crust are habitable"Any microbiologist can tell you that a positive themodynamically redox-reaction for biosynthesis is all one needs to know to predict where life is possible.And:
"I would say that something looking like life is a comparative rather than subjective observation."Who does the comparison?And:
"Their expertise and their limited evidence fits with them publishing in a geological journal also. They only showed the absence of contradictory evidence using the techniques they were most proficient with."So, it is some abiotic aberration?And:
"The researchers showed that the structures were neither crystalline nor inorganic."But you say in the same paragraph (first sentence) that: "But one does need counterions to form inorganic deposits." I don't get this. Could you please be more clear.Furthermore:
Any hollow object has a "possible nuclear area".
(By the way, I suspect that nanobes is short for nanotubes, so actually there are no cells involved. This is also clear from the figures in the article)And you say:
"A self replicating, apparently cellular and non-mineral process has "nothing in common with life"? Puh-lease!"Self-replicating? It is clear to me that the process the authors describe is a polymerization. I wouldn't call the elongation of a polymere self-replication. As I mentioned before, you are mislead by the authors' jargon.And:
"I agree that the lack of published progress in this area in the last few years is puzzling but it is not evidence of the whole thing being a fraud."I don't say the whole thing is a fraud. It may be some kind of bizarre reaction. I like to have the data confirmed by some other groups before jumping to conlusions. That would make it more scientific.You claim:
"Perhaps their silence is political- they are waiting to accumulate enough conclusive data to produce a major report in Science of Nature and claim the area as their own. They wouldnt be the first group to sit on data until the time was right to release it."As a matter of fact they have already published their major findings, so I do not consider this an argument.You say:
"The existance and biological status of nanobes doesnt rely on them containing any DNA- in fact they would be more interesting if they lacked it. And you should know as a scientist that negative results are never conclusive proof that you started with nothing, only that you may have used the wrong technique so far."Negative results is something completely different. What the authors omitted is to do appropriate negative controls. It means that you have to show that the dey stains specifically, and that you can exclude the possibility of cross reaction with some other substance."The nanobes appear to have especially resistant cell walls- how would you suggest they rupture them without destroying and DNA (or worse RNA) that might be present given that their exact composition is unknown? Can DNA be extracted efficiently from the most resistant bacterial spores?"Are you trying to tell me that rupturing a mebrane will destroy the DNA/RNA? If the nanobes really contained DNA and/or RNA than it can easily be extracted. It is a routinejob in any biomolecular lab, that takes only a couple of hours. DNA can be extracted from fossilized bones, so why not from bio-organic spores (or from nanobes for that matter).Finally you say:
"And I will again reemphasise that even if the DAPI result is a false positive that doesn't negate all the other observations of life like behaviour and qualities- it only makes them more intriuging and more relevant to my original reference to nanobes"What "all other observations of life like behaviour"?
The only intruiging part of the story is the alleged positive DNA staining.best wishes,
peter

Hi PeterThanks for the vigorous debate on this topic.On objectivity/subjectivity a computer program could be made to do a quantitative comparison of microscopic images, with examples of known living organisms and minerals as controls. Or maybe you could show microbiologists random images of nanobes and other bacteria and minerals and get them to distinguish living from non living based on the image alone?On my statement "one needs counterions to form inorganic deposits"- the group were eliminating the possibility of a carbonate mineral by pointing out that there was insufficient oxygen or metal in the sample (eg if it was CaCO3- Ca is the metal, O is the counterion). The abundance of carbon in the nanobes cannot be attributed to an inorganic carbonate due to the lack of metals and counter ions. Oxygen is seen in the elemental analysis but there is insufficient for it to be a carbonate (which needs three times as much oxygen as carbon).On the possible publishing tactics of the group- discovery relies on prior publication so a preliminary but incomplete paper in a lower circulation journal is not an uncommon way to stake a first claim.A negative DNA stain control would be the flourescence spectrum of the dye alone in this case- they were using the change in flouresence on addition of the sample as a way of inferring the presence of DNA. Given that DAPI has already been shown to undergoe this change only when DNA is present (and presumably not when just plain quartz or polystyrene is added) then it serves as reasonable evidence. The possibility of an unknown molecule causing the same effect is very unlikely. Interestingly given the difficulty in handling the specimens possible contamination by real bacteria cannot be ruled out at this stage. The isolation of DNA from fossils is a very fiddly technique and relies on the mineral matrix being soluble. Disruption of an organic matrix is more likely to cause disruption of organic molecules like DNA and I am quite sure that dormant bacterial spores are difficult to isolate DNA from. Any micro people wish to comment?But all of this is immaterial to the basic argument- nanobes would actually be more interesting if they were a carbon based polymerisation reaction which spontaneously produced hollow carbon based structures. Even if they are not alive, don't contain DNA, RNA, proteins or any biomolecules their spontaneous formation, structure and elemental composition alone make them possible participants in abiogenesis. Can't you see that arguing they are not just plain but tiny bacteria is favouring abiogenesis?Shane

dear Shane,All I say is that the present scientific data are not in accord with the NDT. So in fact we do not need to know more. The more we know the more it will show that NDT is incorrect. That's all, but it's enough.
Best Wishes
Peter[This message has been edited by peter borger, 07-31-2002]

Hi PeterYou just said:>All I say is that the present scientific data are not in accord with
>the NDT. So in fact we do not need to know more. The more we know the >more it will show that NDT is incorrect. That's all, but it's enough.I nearly fell off my chair when I read this Are you claiming to have mysterious psychic powers? On what base could anyone make an assertion that any data gathered in the future will or will not support a theory?All I am saying is that we know only a small part of the story of how genes work together to control organisms. The bigger question of how genes change during evolution is even further from be exhaustively addressed. Even if I was to accept that there is currently no conclusive evidence for evolution (or ID for that matter) I would *never* assert that there never will be. To do so would be closed minded and far from scientific. And even if any details of any particular evolutionary theory are disproven that doesnt sink evolution in toto- it only calls for a revision of the specifics. ID should only be invoked where direct evidence of ID is found. At the moment ID isnt the simplest explanation of the facts, only the most convenient.Shane

Dear Shane,You say:
"I nearly fell off my chair when I read this"(Didn't break anything, I hope.)
What I said in my previous mail is that all so called evidence for evolution can be falsified at least once. That makes it a bad theory. In physics it would not be accepted.
Peter

quote:

---

Apart from their startling naivety of theoretical calculations about the probability of for instance the correct sequence of amino acids coming together to form a protein these calculations seem to lack any consideration of time scales involved.
Sure the chances of a single successful event seem astronomical, but how do the odds look when you factor in that there may be billions of molecules reacting over billions of years?

​

Do any mathematicians fancy looking over the figures? A more realistic model might be an imaginary self replicating length of RNA- say eight base pairs (four "unnatural" ones) and a unique 200 residue sequence.

---

Lets just start off with a small protein (100 amino acids). Probability in the right order is 1/20^100. Probability right chirality is 1/2^100. Probability = 1/1^160. Given 10^81 atoms in the universe, and 15 billion years for the age of the universe, and say that each atom undergoes a trillion reactions each producing a different molecule each second, probability becomes 1/1^160 * 1^81 * 1^12 * 365 * 24 * 60 * 60. It still becomes 1/10^59.As you can probably notice, this gives very generous assumptions as well. Most probability arguments for one of 100 amino acids is 1^500, using all the time and atoms in the universe.

quote:

---

Originally posted by blitz77:
Lets just start off with a small protein (100 amino acids). Probability in the right order is 1/20^100. Probability right chirality is 1/2^100. Probability = 1/1^160. Given 10^81 atoms in the universe, and 15 billion years for the age of the universe, and say that each atom undergoes a trillion reactions each producing a different molecule each second, probability becomes 1/1^160 * 1^81 * 1^12 * 365 * 24 * 60 * 60. It still becomes 1/10^59.

---

You are also assuming pure chance, and such isn't the case. These reaction take place within a larger system. That system will skew the results. The chemical, gravitational, radioactive environment has to be taken into account or the probability calculations are worthless. This has been pointed out to you, by Percipient I think, in another thread just a day or two ago.------------------
http://www.hells-handmaiden.com

I also wonder how adequate it is to base the calculations on a single sequence, given that most known catalytic sequences can be modified extensively without destroying their activity.Also if you simplify the system by reducing the number of amino acids (no one is suggesting you need all of them to make a functional protein), or use eight nucleobases as first suggested the initial probability of a specific 100 residue sequence is reduced to 1/8^100, which when multiplied through your very generous mass and time estimates (1^81 * 1^12 *365 * 24 * 60 * 60) gives a "probability" (or estimate of the number of times it should occur in the time frame) of around 1^10- which leaves room for more realistic estimates of mass and time. This shows how sensitive the calculation is to the original assumptions about the complexity of the system. Reducing the complexity further to four sequence elements (ala modern RNA) changes the "probability" to 2^40.

And RNA requires 6 bases to specify an amino acid... so for a 100 amino acid protein produced requires 600 bases? Suggesting 4^600? = 10^360...And you should know how complicated RNA replicates... and suggesting only 8 amino acids used severely limits how the resultant protein can behave... Then there's the probability requirement for the density of the amino acids in a given region for them to react... then there's the amount of matter in planets compared to suns/dark matter... then the amount of them that can actually form amino acids (how many of them are carbon atoms as compared to hydrogen?) And there are 23 currently known amino acids, not 20, then there's the limiting amount of time on earth for it to happen (a hundred million years instead of the billions). And of course, most of the molecules produced by reactions are not unique... H20, CO2, etc (99.99% or more of all reactions at that time?). Then there's the number of atoms that would need to participate to produce a 100-amino acid sized protein, reducing the number that can be made in the universe at the same time.[This message has been edited by blitz77, 08-07-2002]

quote:

---

Originally posted by blitz77:
then there's the limiting amount of time on earth for it to happen (a hundred million years instead of the billions)

---

huh? You lost me here. Why do we have only a hundred million years?[/B][/QUOTE]------------------
http://www.hells-handmaiden.com

Time since surface water became available and the first supposed bacteria. Unless you are supposing it didn't happen in water?

[QUOTE][B]so for a 100 amino acid protein produced requires 600 bases? Suggesting 4^600? = 10^360...[/QUOTE][/B]Your calculation is invalid because it assumes that only one protein is possible. You also pulled the length of the protein out of the air. You also failed to omit repeated sequences.