NASA to Hold News Conference on Astrobiology

[Copasetic]

Some interesting review's of the work by microbiologists;

From Rosie Redfield

Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC, Anbar AD, & Oremland RS (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science (New York, N.Y.) PMID: 21127214

Here's a detailed review of the new paper from NASA claiming to have isolated a bacterium that substitutes arsenic for phosphorus on its macromolecules and metabolites. (Wolfe-Simon et al. 2010, A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus.) NASA's shameful analysis of the alleged bacteria in the Mars meteorite made me very suspicious of their microbiology, an attitude that's only strengthened by my reading of this paper. Basically, it doesn't present ANY convincing evidence that arsenic has been incorporated into DNA (or any other biological molecule).

What did the authors actually do? They took sediment from Mono Lake in California, a very salty and alkaline lake containing 88 mg of phosphate and 17 mg of arsenic per liter. They put the sediment into a similarly alkaline and hypersaline defined medium containing 10 mM glucose as a carbon source, 0.8 mM NH4SO4 as a nitrogen and sulfur source, and a full assortment of the vitamins and trace minerals that might be needed for bacterial growth. Although this basic medium had no added phosphate or arsenate, contamination of the ingredients caused it to contain about 3 µM phosphate (PO4) and about 0.3 µM arsenate (AsO4) as. For bacterial growth it was supplemented with arsenate or phosphate at various concentrations.

The interesting results came from sediment originally diluted into medium supplemented with the highest arsenate concentration they initially tried (5 mM) but no phosphate. Over the course of several months they did seven tenfold dilutions; in the sixth one they saw a gradual turbidity increase suggesting that bacteria were growing at a rate of about 0.1 per day. I think this means that the bacteria were doubling about every 10 days (no, every 7 days - corrected by an anonymous commenter).

After one more tenfold dilution they put some of the culture onto an agar plate made with the same medium; at least one colony grew, which they then inoculated into the same defined medium with 5 mM arsenate. They gradually increased the arsenate to 40 mM (Mono Lake water contains 200 mM arsenate). Descendants of these cells eventually grew in 40 mM arsenate, with about one doubling every two days. They grew faster if the arsenate was replaced by1.5 mM phosphate but grew only about threefold if neither supplement was provided (Fig. 1 A and B, below). The authors misleadingly claim that the cells didn't grow at all with no supplements.

In Fig. 1 (below), the correspondence between OD600 (Fig. 1 A) and cfu (Fig. 1 is not good. Although the lines in the two graphs have similar proportions, OD600 is plotted on a linear scale and cfu/ml on a log scale (is this a shabby trick to increase their superficial similarity?). OD600 in arsenate medium was almost as high as that in phosphate medium, but the number of cfu was at least tenfold lower. And the OD in arsenate continued to increase for many days after the cfu has leveled off. I suspect most of the continuing growth was just compensating for cell death. It would be interesting to test whether the cells were scavenging phosphate from their dead siblings.

The authors never calculated whether the amount of growth they saw in the arsenate-only medium (2-3 x 10^7 cfu/ml) could be supported by the phosphate in this medium (or maybe they did but they didn't like the result). For simplicity I'll start by assume that a phosphorus-starved cell uses half of its phosphorus for DNA and the rest for RNA and other molecule, and that the genome is 5x10^6 bp. Each cell then needs 1x10^7 atoms of phosphorus for DNA, and 2x10^7 for everything. The medium is 3.1 µM phosphate, which is 3.1x10^-6 moles per liter. Mutiply by Avogadro's number (6.02x10^23 atoms per mole) and we have 1.9x10^18 atoms of phosphorus per liter, or 1.9x10^15 per ml. Divide by the phosphorus requirement of each cell (2x10^7) and we get 9.5 x 10^7 cells per ml. This value is just comfortably larger than the observed final density, suggesting that, although these bacteria grow poorly in the absence of arsenate, in its presence their growth is limited by phosphate. (Note: This calculation originally dropped a decimal point. I've changed it a bit and corrected the error.)

Link

[Copasetic]

Redfield blogged a scathing attack on Saturday. Over the weekend, a few other scientists took to the Internet as well. Was this merely a case of a few isolated cranks? To find out, I reached out to a dozen experts on Monday. Almost unanimously, they think the NASA scientists have failed to make their case. "It would be really cool if such a bug existed," said San Diego State University's Forest Rohwer, a microbiologist who looks for new species of bacteria and viruses in coral reefs. But, he added, "none of the arguments are very convincing on their own." That was about as positive as the critics could get. "This paper should not have been published," said Shelley Copley of the University of Colorado.

None of the scientists I spoke to ruled out the possibility that such weird bacteria might exist. Indeed, some of them were co-authors of a 2007 report for the National Academies of Sciences on alien life that called for research into, among other things, arsenic-based biology. But almost to a person, they felt that the NASA team had failed to take some basic precautions to avoid misleading results.

When the NASA scientists took the DNA out of the bacteria, for example, they ought to have taken extra steps to wash away any other kinds of molecules. Without these precautions, arsenic could have simply glommed to the DNA, like gum on a shoe. "It is pretty trivial to do a much better job," said Rohwer.

In fact, says Harvard microbiologist Alex Bradley, the NASA scientists unknowingly demonstrated the flaws in their own experiment. They immersed the DNA in water as they analyzed it, he points out. Arsenic compounds fall apart quickly in water, so if it really was in the microbe's genes, it should have broken into fragments, Bradley wrote Sunday in a guest post on the blog We, Beasties. But the DNA remained in large chunks—presumably because it was made of durable phosphate. Bradley got his Ph.D. under MIT professor Roger Summons, a professor at MIT who co-authored the 2007 weird-life report. Summons backs his former student's critique.

Link

Edited December 7, 2010 by Copasetic

[d e v i c e]

You don't need to go to university for 50yrs to know the universe is crawling with life. Probably an infinite variety too throughout eternity. It's just common sense. So Heeey, good on the scientists for attemting to break through their own dogmas on this one.

[badeskov]

You don't need to go to university for 50yrs to know the universe is crawling with life. Probably an infinite variety too throughout eternity. It's just common sense. So Heeey, good on the scientists for attemting to break through their own dogmas on this one.

Really?

Can you point me to anybody that really knows? I know of plenty of people that think they know, but the difference is both distinct and important. But I know nobody that knows.

Cheers,

Badeskov

[d e v i c e]

That's because ppl who know are rare.Whitley Streiber, the guy who wrote Communion, he knows. Anyway,through weighing up the mountain of evidence, the pro's and the con's, by trusting your own observations of life and having a bit of an understanding about the vast possibilities and immensity of this universe, even if you've never met an alien, youd have to admit they exist. And if they exist, it only stands to reason that some of them already know we're here.

[booNyzarC]

That's because ppl who know are rare.Whitley Streiber, the guy who wrote Communion, he knows. Anyway,through weighing up the mountain of evidence, the pro's and the con's, by trusting your own observations of life and having a bit of an understanding about the vast possibilities and immensity of this universe, even if you've never met an alien, youd have to admit they exist. And if they exist, it only stands to reason that some of them already know we're here.

Whitley Strieber knows? Are you so sure? Tell me then, friend, why in the world would he have written this?

from "The Communion Letter"

Whitley Strieber's cover letter from the Spring Issue, 1991; Volume 3, No. 1.

Dear Reader:

I would like to thank you for your patronage of the Communion Letter. Your subscription ends with this issue, and we are not taking new subscriptions or renewals. A list of available back issues is printed on the reverse of this letter for those who may be interested in collecting.

I had always intended to run the newsletter about two years, and that amount of time has now passed. During this period the Communion Letter has gained a large circulation and, I believe, published some remarkable articles.

But all good things must come to an end. I am not a UFO researcher and do not wish to endure the continued media attack that is associated with being involved in this field. In addition, the so-called "UFO-ologists" are probably the cruellest, nastiest and craziest people I have ever encountered. Their interpretation of the visitor experience is rubbish from beginning to end. The "abduction reports" that they generate are not real. They are artifacts of hypnosis and cultural conditioning.

What we are experiencing is a perceptual anomaly that is sufficiently ambiguous and intense that it demands explanation. It is something that human beings have been experiencing for a long time. It is the cause of religion, of mythology, of folklore. Presently it is the cause of the "alien abduction" belief.

What is *really* behind our experiences? We are. This is a human thing. However, I would also say that it indicates that we--and our world--are vastly different, and far more strange, than we have ever dreamed, or dared imagine.

With that I leave you.

You do realize that before his books about abduction experiences he was a fiction writer, right? A struggling fiction writer at that. What does a talented writer in need of a financial boost do anyway? Well, he keeps writing. The last fiction novel not doing so well? Maybe we need a new spin on things?

And honestly, this "mountain of evidence" that you are talking about crumbles away into an inconsequential hill when it is put under the eye of scrutiny. If it was so conclusive, as you appear to assume and believe, there wouldn't be much of a debate would there? Maybe you should take a step back and re-evaluate why you are so convinced?

Up to you, of course. I certainly don't want to stomp on anyone's religion, but if you'd rather have certitude than hopeful belief, you might be wise to actually study the cases that have you convinced before quoting them as scripture.

[d e v i c e]

Thnx booNyzarC for trying to illuminate me, but who better to describe ones own xperience in detail and with clarity than a writer himself? Dr Carl Sagan wrote fiction but I don't hear anyone discrediting his observations. W.Streibers motives for writing about this were to raise real awareness in th hope that th scientific comunity may take it seriously, and thereby provide answers to those who are going thru th same thing. True, th mountain of evidence does crumble away - to reveal a core reality that should not be ignored so easily. To cut a long story short, W.Streiber is a very courageous man to attemt such an undertaking. I beleive in what he's doing and I can tell he is an honest man. I'll leave it there booNyzarC, been nice chattng wth u.

[booNyzarC]

Thnx booNyzarC for trying to illuminate me, but who better to describe ones own xperience in detail and with clarity than a writer himself? Dr Carl Sagan wrote fiction but I don't hear anyone discrediting his observations. W.Streibers motives for writing about this were to raise real awareness in th hope that th scientific comunity may take it seriously, and thereby provide answers to those who are going thru th same thing. True, th mountain of evidence does crumble away - to reveal a core reality that should not be ignored so easily. To cut a long story short, W.Streiber is a very courageous man to attemt such an undertaking. I beleive in what he's doing and I can tell he is an honest man. I'll leave it there booNyzarC, been nice chattng wth u.

Loosely quoted:

Carl Sagan was an astronomer, astrophysicist, cosmologist, author and highly successful science popularizer and science communicator in the space and natural sciences. During his lifetime, he published more than 600 scientific papers and popular articles and was author, co-author, or editor of more than 20 books. In his works, he advocated skeptical inquiry and the scientific method. He pioneered exobiology and promoted the Search for Extra-Terrestrial Intelligence (SETI). My link

How exactly can you compare the greatness of Carl Sagan with the likes of Whitley Strieber? Speaking of which, spell your Messiah's name correctly and you might gain a little more credibility. The word "the" has an "e" at the end too, in case you didn't realize.

But alright, believe in whatever you'd like. It matters very little to me overall, even if I feel disappointed whenever I see someone cling to a path that I personally find not only completely fallacious but also potentially detrimental...

I'll leave it there electro13. Good luck to you.

[Hazzard]

Willful Ignorance -- A bad faith decision to avoid becoming informed about something so as to avoid having to make undesirable decisions that such information might prompt.

[Space Commander Travis]

Personally, i'd say it seems quite a fair assumption, that the universe may indeed be teeming with life, but it can only be an assumption until - and I think this is what we ought to do - we concentrate on seriously studying other planets- not just Mars (which, although it's relatively easy to get to, is probably not (now, although it may have been once) conducive to life). And Venus as well, and even Jupiter if we're likely to be able to get there in a reasonable length of time. Places that we've always considered the idea of life of some sort would be absolutely ludicruous; and that's not even to mention all those moons of Saturn, Jupiter etc - i think the posibilities there, in the light of what we're still finding out on this our Earth, really are limitless. And approach it with no preconceptions of what is and isn't possible. I really do think that this above all is the field of scientific endeavour we ought to be concentrating on - perhaps the Large halon collider may come up with something that could siginificantly contribute to development of space travel, but we ought to be concentrating on research for practical ends rather than searching for vast abstract concepts like the God Particle and Dark Matter.

[lost_shaman]

Wolfe-Simon et. al., have posted a "response to questions" regarding their recent paper.

Response to Questions Concerning the Science Article,

“A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

-As of December 16, 2010-

http://ironlisa.com/gfaj/GFAJquestions_Response_16Dec2010.pdf