Rosie Redfield: No convincing evidence that As has been incorporated into DNA | Hacker News Reader

Rosie Redfield: No convincing evidence that As has been incorporated into DNA

rrresearch.blogspot.com

59 pointsbbgm23 comments

The comments are great too. In particular I like what chemDroid had to say:

    Hi. I have posted on many places, they should not be
    doing standard DNA preps and the experiment we need 
    to see is to see a caesium chloride density gradient
    ultracentrifugation (not a gel)... If indeed the DNA 
    has arsenic, it should be getting denser and we would 
    see that as a band shift. Ethidium bromide's mode of
    action would not be affected by arsenic substition.

Gels are used to measure the length of a DNA fragment. Here's how they work: Ethidium bromide (EtBr) is an intercalating agent -- think of the DNA as a ladder, it slides between the rungs and gets stuck there. EtBr is also luminescent under UV. Agarose (purified seaweed extract) is used to make a gel doped with EtBr. A DNA sample is placed in a well on one end of the gel and an electric current is applied to the gel. The sample gets dragged through the gel, the longer it is, the more slowly it progresses.

As chemDroid wrote, there is no reason to believe that arsenic would have any impact on this process.

You can extend the density gradient experiemnt and get the DNA out in super pure form and then run mass spec on it to show that arsenic has indeed been incorporated.

With a claim this important, we cannot do enough to try to disprove it. Only after we try everything we know and get consistently convincing evidence that arsenic is indeed incorporated into the DNA can we start believing it.

I'm quite surprised at the amount of work done at NASA to push this paper as something extraordinary without so much as a critical eye. The claim made in the paper is extraordinary and that alone should be reason for caution, not for bringing out the big drums.

The bigger problem is that if it turns out the result is bogus this will be a net negative, both for NASA and for the scientific community, the public at large will not see this as proof that 'the system works' but as proof that they were being duped.

The public will be correct in their presumption that at least this part of the system didn't work.

It has gotten to the point with NASA that when they make a life-based announcement, the Bayesian-style rational response is to ignore them entirely. It isn't too big a step from here to think that this research ought to be simply shut down, so that it can get out of the funding stream and then at least there's a chance the funding will go somewhere useful.

They did the same thing with the "life from Mars" thing a few years ago. It's a way of attracting attention in order to raise money.

Judging by how that worked out for them they ought to have known better. You can only cry wolf so many times before you are labeled the village idiot, too bad for you if the wolf eventually shows up and nobody believes you due to 'past performance'.

I'm a big NASA supporter, but this whole episode has made me think they deserve a little less funding.

From the way they handled the whole thing from the start with the "aliens, but living here" spin to finding out the results aren't all that solid, it seems they need to clean some house.

I don't know, it won't make a change to the way the place is administered to reduce the budget, it's mostly going to affect the amount of money scientist can use to advance their research. Making the quality slowly decline more.

Restructuring NASA is a hard problem maybe even impossible. But I do think it's still producing good enough stuff that removing it would be a mistake. I'm a believer in public research. It has produce some incredible benefits to society in the 20th century and hopefully will continue in the 21st.

You gotta love the peer review process working in public. Now (thanks to the internet) readers correct mistakes so that by the time the paper reaches the journals, it's already been vetted quite a bit. Before that, the public pre-publication vetting process would have been a lot slower (e.g. to be done in conferences) if done at all.

It would be nice if it happened before the press conference too.

And miss all the publicity? Imagine a story of line of "hey we thought it was doing this, but turns out not, so oh well". Not as enticing as "arsenic based life form" is it?

Rosie Redfield is another eurasian government hack scientist operating through colonial Canada. She claims to play the atheist card, but is a known eurasian cheerleader, all those gods be told. Her work is pseudoscience and can never be trusted or taken seriously. Her principle position in America is to take American biology for the holey sleigh ride through eurasian political hierarchy. Fortunately, she has no substantial chance of succeeding.

Extract the DNA. Do X-ray scattering and crystallographic studies, which would clear this issue up nicely.

What would you expect to see in crystallography? A different pitch and radius on the helix?

If that is the case, then assuming there is arsenic in the DNA: how did they manage to PCR it? I would expect it to wreck havoc with the polymerase.

The first experiment would be to determine if Arsenic is present. A quite direct experiment would be to take advantage of the anomalous scattering of As vs. P by using a tunable X-ray source (synchrotron). By using a wavelength of just over 1 Angstrom As will be quite distinct from P.

I would expect the radius and pitch not be drastically influenced. However, three dimensional structural prediction is quite difficult and it feels a bit uncomfortable speculating.

If the number of arsenic atoms incorporated are as few as the molarity calculations indicate (i.e. ~1 per 5kb), I doubt that x-ray experiments would be definitive. And they're hard to do.

At any rate, you'd have to extract and crystallize a fragment of DNA that was particularly enriched for As, which would necessitate most of the other controls that people are suggesting anyway. You'd probably have a pretty good confirmation/refutation of the paper's claims by the time you were set up to shoot x-rays at a crystal.

Why would arsenic wreak havoc on the polymerase?

My apologies if my comment implies that As creates an issue with the polymerase. I would guess that it doesn't since amplifying the sequence was successful.

My fault -- I implied it.

    I would guess that it doesn't since amplifying the sequence was successful.

Or the sequence doesn't contain (enough) arsenate.

I'm guessing that this just refers to the altered As-DNA structure causing major problems with binding of the enzyme to the DNA.

Crystallographic studies? What is wrong with simply doing the gradient suggested by two commenters in the blog entry? If that turns up negative, you can immediately get an answer and scrap the whole paper. (Which in itself leads to quite some speculations...)

Anyway, if the calculations and assertions made in the blog (and the commenters) turn out to be correct, this will be a big black eye for Science (the journal...) for publishing this.

There are quite a few biophysical techniques that could be done such as AUC, spectroscopy, scattering and crystallography. The facilities and equipment would play a role in which to pursue. The experiment I am suggesting is not very complicated, but of course depends on people's backgrounds.

You don't want X-ray scattering crystallography, you want elemental spectroscopy.

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