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Alien Life Reax


arsenic bugsThe alacrity of the refutations to NASA’s breathless press release have been surpassed only by their vitriol. “Should not have been published“, “scathing attack“, “big idea with big holes“, “arsenic cowards” etc.  But to my googling eyes, there really are two, and only two refutations given to the Science paper,

a) The technique was sloppy, and the arsenic might be just a contaminant, not a constituent of the cell, making the phosphorus levels low, but still consistent with phosphorus-starved normal life.

b) Arsenic bonds are 100x less stable than Phosphorus bonds, so the claims for As replacing P in DNA are theoretically impossible.

Now both comments are valid, as far as they go, but can be refuted with the simple observations. Neither is a disproof of the paper, both are merely implausibility arguments. That is, the authors of the paper knew their results were a bit sloppy. After all, the first author is a post-doc who graduated last year! You can’t exactly expect her to have 20 years experience in laboratory technique under her belt.

So they did what any normal experimentalist would do under those circumstances–looked for verification methods that didn’t rely on spotless laboratory technique.

Read more…

Dr. Sheldon, SETI Ignorance Gets Stronger Excerpt: Steve Benner, an origin of life researcher, “used the analogy of a steel chain with a tinfoil link to illustrate that the arsenate ion said to replace phosphate in the bacterium’s DNA forms bonds that are orders of magnitude less stable.” http://www.creationsafaris.com/crev201012.htm#20101209a bornagain77
Semi OT: New Video upload: Evolution vs. Genetic Entropy - Book Review - video http://www.vimeo.com/17671762 bornagain77
My apologies. Bentley's argument relies on experiments conducted on arsenates as compared to phosphates. The arsenates "react 10^4 to 10^6 times more rapidly than analogous phosphates." Here's the link to the article Bentley cites. So, no, there are no lab produced arsenate DNA's around apparently. Nonetheless, Bentley's main point is that once the putative "arsenic-backboned" DNA is placed in water, it should, contrary to normal DNA, disintegrate rather rapidly. And, in their experiment, it was in a water solution long enough to have done so. I'm willing to wait for scientific validation or invalidation of this claim. In the meantime, I remain highly suspect. PaV
Dr. Sheldon, I am more than willing to accept the results of the paper if they are indeed true, but as for myself, not to question your judgment in the matter, I will not accept them as true until the results are either confirmed or refuted by another lab looking specifically to test the claim of Arsenic based DNA.,,,, It is a radical claim and as such should produce thoroughly unquestionable evidence to back up its claim!,,, Moreover Dr. Sheldon, though I don't know if 'proof of evolution' was actually claimed in the paper, none-the-less the implicit claim taken from the paper by the general public has been for solid proof of evolution even though you, as well as I, know that the adaptation, even if rigorously true, in all likelihood from what we know from foundational principles of science (Second Law and Conservation Of Information) came at a loss of preexisting functional information that was already present in the parent species genome.,,, etc.. etc... bornagain77
Pav & BA, As I said before, the criticism is neither proof nor counter-claim, but merely implausibility arguments. As an experimentalist, implausibility only counts until you have data, after that it is irrelevant. PaV seems to think that someone has put arsenic in DNA and measured its half-life in water. If they have, it would be news to me. On the contrary, Bradley is reporting on some wet chemistry of simple arsenic compounds which may or may not be relevant to the bugs. Interesting, but disproof it isn't. Furthermore, Redfield's critique is on the possibility of contamination. Once again, a serious critique but it would not explain the EXAF data, the MRI data or the gel-electrophoresis data. So it may be true, but once again, irrelevant. And finally, impugning the motives of every paper that is submitted to Science is a way to make your journal irrelevant. We must live in an atmosphere of trust, or we cannot do science. That's why science comes out of a Western culture, and not out of a Muslim, animist or Chinese culture. It's the job of the referees to tell us if the data look clean, not some reader of the journal who sees imaginary motives behind it. In some sense, science and science publications are a material expression of the sermon on the mount, and without Jaki's "Savior of Science" standing behind it, we can't objectively even blow our own nose. Robert Sheldon
semi-related: How do DNA components resist damaging UV exposure? - Dec. 2010 http://www.sciencedaily.com/releases/2010/11/101130103829.htm bornagain77
shoot these guys are doing it too: First carbon-rich exoplanet discovered Excerpt: meaning that for life to exist on these planets, it might have to survive with very little water and oxygen, and plenty of methane, says Madhusudhan. That might not be so far-fetched given last week's announcement by NASA of the discovery on Earth of bacteria that can survive in arsenic, a poison to humans. http://www.physorg.com/news/2010-12-carbon-rich-exoplanet.html bornagain77
Man these guys are trying to milk this arsenic thing for all its worth before it is formally refuted: Evidence for ET is mounting daily, but not prove http://www.physorg.com/news/2010-12-evidence-mounting-daily-proven.html bornagain77
I did not know 'arsenic-backboned' DNA has already been tried. Did they synthesize it artificially or did they use an organism? What about histones and other DNA binding proteins? tragic mishap
First of all, As is a poison that one can get habituated to. How many remember that fact. Wasn't that in "The Name of the Rose"? Second, it appears that Dr. Sheldon wants to put his weight behind these experimental results. I think he's wrong to do that. I think Alex Bradley is a much more experienced experimentalist, and I believe his observations are devastating. To begin with, it seems to me that one has simply to consider the following to completely dismiss the results of Wolfe-Simon: But here's the relevant question: Is 3 micromolar phosphate a lot? Or a little? One point of comparison is the Sargasso Sea, where plenty of microbes survive and make normal DNA. Here, the phosphate concentrations are less than 10 nanomolar - or 300 times less phosphate than the "phosphate-free" media in the GFAJ-1 experiment. At such low phosphate concentrations, some bacteria compensate by removing phosphorus from their lipids - but not from their DNA. Where is the "selective pressure" to switch to As when other bacterial species can survive on 300 times less P and yet not change their DNA structure On the other thread about this article, I conjectured exactly what Bradley tells us (a conjecture based on certain facts taken from Bradley's blog item) happens: that is, in low Phosphate environments, one switches out the P present in lipids with the available As; thus freeing the P to be used as the bacterium needs. Also, Bradley is quite clear that part of the experimental procedure required that this 'arsenic-backboned' DNA was stripped out of the cell, freed from any cell contaminants, and then left in only water for over an hour at a time as tests were done on the solution. But chemists know from already peformed experiments that 'arsenic-backboned' DNA falls apart in water solution after but ten minutes time. I think this experiment is hocus pocus. PaV
BA it would really not be that radical of a change. It sounds more radical than it is to people unfamiliar with chemistry because most people only know "arsenic" as a poison. As has the same chemistry as P because it has the same number of valence electrons. In fact (somebody correct me if I'm wrong), arsenic poisoning happens because body chemistry mistakes arsenic for phosphorous and utilizes it in exactly the manner being claimed for these bugs. The problem after that is the stability of the arsenic. If the bug is able to stabilize arsenic compounds somehow, this would give it a selective advantage in the arsenic growth medium they used. In fact, if the bug is starting to get better at utilizing As in its normal biochemical processes, that would require its proteins, normally highly specified for P, to lose their specificity to accomodate As. That's something ID says is not only possible, but probably the only way evolution can do anything. One ID prediction is already known to be true about these bugs: They grow slower in arsenic than in a normal medium, making it highly likely that if the adapted bugs were put back in a normal growth medium, they would most likely revert to normal. The second ID prediction would be that the adaptations required for growth in the arsenic medium (whether or not it actually incorporates As in its DNA) are the result of loss-of-function mutations and the destruction of pre-existing information. tragic mishap
I will be glad when a more formal refutation is conducted. The whole thing smells very fishy to me, especially given the tightly integrated complexity of the cell we know of now that far surpasses, in integrated complexity, any machine man has ever built. To me proposing such a radical change to such a core component of the cell, as the DNA backbone is, is somewhat similar to suggesting that a different diameter drive-shaft could be inserted into a car without also making major changes to the transmission interface and the rear wheel axle interface. It simply is not possible from an evolutionary framework and is only possible from an Genetic Entropy framework with a fairly significant drop in functional information from the parent strain,,, In fact given the extreme level of integrated complexity we are dealing with, it should be expected to be a far worse problem that the 'simple' drive train example I cited. bornagain77
Note to Joseph (#4): Yes, I'm aware that it was published in Science. I'm saying that if there had been no press conference, there would have been a more muted response, mostly as letters to Science. When it is played up in a press conference in order to get more attention, then we shouldn't be surprised that it got a lot more attention. Neil Rickert
Neil, The paper was in the peer-reviewed journal Science but apparently didn't get the press NASA thought it deserved. Joseph
from physorg: Critics raise doubts on NASA's arsenic bacteria 12/9/10 http://www.physorg.com/news/2010-12-critics-nasa-arsenic-bacteria.html bornagain77
Scientists poke holes in NASA’s arsenic-eating microbe discovery http://news.yahoo.com/s/yblog_thelookout/20101208/sc_yblog_thelookout/scientists-poking-holes-in-nasas-arsenic-eating-microbe-discovery bornagain77
The reaction is, in part, a reaction to science by press release and news conference. Neil Rickert

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