Time factor in self assembly calculations?

Dear Singularity,
Ever sonicated (lysis through vibration) a culture of bacteria? How long will it take -- according to your scenario -- before a living bacterium will arise from this organic soup? Notably, all required biolecules are present in this soup.
Best wishes,
Peter

You say,
"I was just pondering the process of nuclear transplant as used in animal cloning"To clone an animal you need viable DNA in a nucleus and bring it into a viable cell. Viable DNA is not simply the plain DNA molecule, it also involves the histons and the histon-code, and the coactivater code of transcription present in the acceptor cell. The recent discovery/inference of these eukaryotic DNA associated codes of transcription prohibits the cloning of the extinct (?) thylacine (and other extinct animals. It is nothing but a waste of money!). Maybe ponder these mechanisms also.And:
"Doesnt the implantation of a nucleus into an egg represent the recreation of living matter from non living matter?"No.Best wishes
Peter

dear Shane,You say:"I don't think anyone is seriously proposing that something as complex as a modern bacterium would have formed spontaneously."Problem is that nobody is proposing anything that can hold.
What do you propose?And:
"synthetic genomes"Copies of existing genomes? To what benefit?BW
Peter

Dear John,
There are dozens of answers to a question.
It is just a matter of choise.
You are free to choose.
Best Wishes
Peter

Dear Shane,You state:
"startling naivety of theoretical calculations about the probability"It seems that you are a Dawkins disciple. Read "The watchmakers blindness" (chapter 6 (?) Spetner's book Not by Chance). It will pay off to read opposite opinions.Best Wishes,
Peter

You say (among other things) that:"Surely this is a very simple example of destroying and recreating life sensu stricto?"According to your definitions it would be the recreation of life.But according to your definitions the following is also recreation of life: Imagine a population of dividing cells. Add a cell cycle inhibitor. Now, the cells are non-living/dead.
Next, wash away the cell cycle inhibitor. The cells start dividing again. According to your definitions the cells are alive again.Q: Did you recreate life by adding and washing the cell cycle inhibitor?Best wishes
Peter

Dear Shane,You state:
"It certainly makes more scientific sense than any historical creation story you care to cite".I care to cite? Where?Peter

Excellent!

Dear Shane,You write:
"unobservable and unreproducible, otherwise it falls within the bounds of science. Can God can only exist by not existing?????"I think that you cannot interchange the words "observe" and "exist". Some things may not be observed but may be existing. For instance, consider organisms that aren't able to observe light. Does it say anything about the existence of light? No. It is just a matter of having the right receptors, or to tune in the right receptors.And:
"gaia hypothesis"
It is pretty much a hypothesis and very timely.have a nice day
Peter

dear Shane,You write:
"Do you perhaps think that the origin of life and the universe as a whole is irrelevant to modern existance"Yes. Science tries hard to explain things that have never been observed. In my opinion that is gratuitous. It should not be the realm of science.And:
"primitive isolated tribe in Malaysia discovered in the late 20th century which had no such mythology"If I recall properly, the alleged isolated Malaysian stone age tribe without origin-mythology was a hoax.Best wishes
Peter

dear Shane,You write:
"....but I think more work in to the recently discovered nanobes from deep sediments might be more crucial."So I checked the claims about nanobes. If you have a look in biological scientific literature "nanobes" do not get a single hit (try NCBI homepage search program). This clearly demonstrates that they are not considered to be organisms. Furthermore I've read the article by Phillipa Uwins et al (American Minarologist, volume 83, p1541-1550.)
The authors claim a lot.
1) nanobes grow = unwarranted conclusion. Probably it is nothing but crystalisation/polymerisation,
2) nanobes have a heterotrophic metabolism = unwarranted conclusion. polymerisation requires monomers from their environment,
3) nanobes resemble actinomycetes and fungi = so what, there are piles of rock on Mars that resemble a face,
4) nanobes are composed of C, O, and N and that is consistent with living matter = unwarrented conclusion. The atmosphere is also composed of C, O and N.
5) nanobes appear to be membrane bound structures, a cytoplasma and nuclear area = unwarranted conclusion. All they show is that nanobes are morhological distinct microvessels.
6) nanobes have amorphic wall structres = sowhat. Stones have amorphic wall structures.
7) nanobes contain DNA as indicated by DAPI, Acridine orange and Feulgen staining = unwarranted conclusion. The nanobes may stain aspecificly. They did not include negative controls. They did not isolate DNA (very simple procedure).My conclusion: this article is a hoax. If it really had been something it would have been published in Nature, Science or other leading scientific journal. Don't believe the hype!best wishes,
Peter

Dear Shane,You write:
"I think it is reasonable to highlight the limitations in our current understanding of the details of evolution (not surprising given the fact we have only had reasonable genetic tools for the last 10 years) but to dismiss it without offering a more plausable (and testable) alternative that fits all the evidence gathered so far does nothing to further our understanding of the origin of biological diversity."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.
So, in conclusion: Darwin was wrong, and so are all evolution biologists. It will take ages before they will admit this, since there is no naturalistic alternative. Evolution theory is the best naturalistic explanation they have. Frankly, I am not interested in the best naturalistic explanation as it is not in accord with our observations. I am interested in truth. I don't mind whether the truth should include a Creator.In addition, there are scientific alternatives. They do not include the origin of life and the origin of genes (because of the principle of genetic uncertainty), but they can be tested by the predictions they do.
Best Wishes
Peter[This message has been edited by peter borger, 07-29-2002]

dear Shane,You say in reply:
1) "What is the magic ingredient if not life of some kind?"
A carefull scrutiny will reveal that this proces has nothing in common with life. Probably it is a selfpropagating reaction.2) "organic contamination from human fingerprints in the petri dishes suggests that nanobes have some need for organic substrates..."..to attach to.And:
"..nanobes were originally observed in the sandstone samples"Sandstone containing N and C?3) "I think it is not an unwarranted observation.."
You are free to think whatever you like.And:
"It is a necessary part of the argument- looks like life-> behaves like life-> is chemically consistent with life---> might be life"I do not follow your logic. Firstly, "it looks like life" is an utterly subjective observation. Maybe someone else doesn't think it looks like life. Maybe it resembles some filamentous micro-organisms, but so do carpet fibers. As mentioned before, even if you find molecules that have a similar consistency as biomolecules it doesn't say anything. It is a fallacy similar to: blood and seawater have similar levels of ions, so our ancestor was an aquatic ape (this has actually been proposed by some evolutionist). These fallacies are called non-sequiturs, meaning that the conclusions drawn are not followed from the evidence presented.4) "The composition of the atmosphere is C:N of about 1:70:29 from memory. The nanobes C:N is about 60:10:30 (from figure 9 in the original article). This is about the same as it observed for living organisms. More importantly there is insufficient metal or counterion present to suggest the formations are mineral in nature."One doesn't need ions to polymerise.5) "In one image there is a suggestion of a darker area toward the centre of the cavity which they suggest as a possible nuclear area, but could just as easily be a sectioning artifact given the difficulties they report in preparing the TEM samples. The conclusion that they observed membrane bound structures is fairly hard to dispute though. Again this is a small but essential piece of the whole argument."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.6) "This is a big misunderstanding. Stones have distinct crystalline structure on a microscopic scale. Other examples of microscopic bodies which were mistaken for organisms based on morphology alone have crystalline microstructure. They are rightly eliminating the possibility these structures are mineral in nature."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.7) "DAPI displays a specific flouresence when it binds to AT rich DNA sequences and is the best indication DNA presented in the paper but is admittedly qualitative. They did not isolate DNA for two reasons. Firstly they are a microscopy group rather than a microbiology/genetics group."This is no argument. 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).And:
"Secondly isolation of DNA is not always a "very simple procedure", especially when working with tissues which have never been successfully extracted before."This is also no argument. If DNA is involved it can be extracted. The authors claim that they are able to see the nanobes-colonies by eye, thus indicating that heaps of DNA can be isolated. (By the way how do you think these nanobes synthesise their DNA?)"The nanobes display unusual cell wall properties, grow slowly and represent a very small sample as individual colonies- all of which would impede DNA isolation."You are mislead by the author's jargon: cell growth, cell walls, membranes, DNA etc.And:
"Even if the DNA tests are false positives the organisms may not contain DNA but could still be considered living. Their size is not inconsistent with a different mode of reproduction. Too much is unknown at this stage."That would be something and I expect to read it in Nature or Science, not in the American Mineralogist.7) "DAPI displays a specific flouresence when it binds to AT rich DNA sequences and is the best indication DNA presented in the paper but is admittedly qualitative."And may also bind aspecifically to C-N-0 compounds. As long as the authors do not include appropriate controls I am not able to interpret their results.You say:
"My conclusion is the same as theirs: it could be a new form of life but more research is needed."Your conclusion is unwarranted.Question: Why hasn't a follow up of this study been published on DNA isolation? There was ample time since 1998.
Answer: Because there is no DNA involved.best wishes
Peter

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

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]