4 ms·

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

59 points by bbgm 16y ago

pierrefar 16y ago
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.
- waterlesscloud 16y ago
  It would be nice if it happened before the press conference too.
  - pierrefar 16y ago
    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?
bhickey 16y ago
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.
- pierrefar 16y ago
  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.
kayhi 16y ago
Extract the DNA. Do X-ray scattering and crystallographic studies, which would clear this issue up nicely.
- bhickey 16y ago
  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.
  - kayhi 16y ago
    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.
    - timr 16y ago
      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.
  - shadowpwner 16y ago
    Why would arsenic wreak havoc on the polymerase?
    - sandipc 16y ago
      I'm guessing that this just refers to the altered As-DNA structure causing major problems with binding of the enzyme to the DNA.
jacquesm 16y ago
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.
- Estragon 16y ago
  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.
  - jacquesm 16y ago
    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'.
    - waterlesscloud 16y ago
      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.
      - nkassis 16y ago
        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.
MrScience 16y ago
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.

59 points by bbgm 16y ago

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.

waterlesscloud 16y ago
It would be nice if it happened before the press conference too.
- pierrefar 16y ago
  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?

bhickey 16y ago

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.

pierrefar 16y ago
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.

kayhi 16y ago

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

bhickey 16y ago
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.
- kayhi 16y ago
  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.
  - timr 16y ago
    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.
- shadowpwner 16y ago
  Why would arsenic wreak havoc on the polymerase?
  - sandipc 16y ago
    I'm guessing that this just refers to the altered As-DNA structure causing major problems with binding of the enzyme to the DNA.

jacquesm 16y ago

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.

Estragon 16y ago
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.
- jacquesm 16y ago
  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'.
  - waterlesscloud 16y ago
    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.
    - nkassis 16y ago
      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.

MrScience 16y ago

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.