Genome of Controversial Arsenic Bacterium Sequenced 56
Med-trump writes "One year ago a media controversy was ignited when Felisa Wolfe-Simon and her colleagues held a press conference to announce the discovery of a bacterium that not only survived high levels of arsenic in its environment but also seemed to use that element in its DNA. Last week, the genome of the bacterium, known as GFAJ-1, which gets its name from the acronym for 'Give Felisa a Job.' (No joke!), was posted in Genbank, the public repository of DNA sequences for all who care to take a look. But it doesn't settle the debate over whether arsenic is used in DNA."
Re:Shouldn't it be fairly simple to determine that (Score:5, Insightful)
They know that this bacteria lives in an environment of Arsenic and may use it in its cell process. So any Spectrometric study will show Arsenic as contamination. Even if you clean up for that, there might be bits of Arsenic stuck in the DNA, but which do not do anything. I believe what they are trying to do is to see if Arsenic is a "functional" part of DNA. ie would the DNA without Arsenic be the same as arsenic without it.
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Indeed. How much of Human DNA is actually useful? How mUch is just aking up space?
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More than you think. Most of that "junk" dna serves additional purposes that we have only started realizing. Sometimes it is just filler, which is great and allows for genetic flexibility. Sometimes it is used in creation of the immune system, even if it is normally inactive.
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Wrong.
Here's a nice talk for you: http://www.youtube.com/watch?feature=player_embedded&v=DRsN7w7iW08 [youtube.com]
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http://www.sciencedaily.com/releases/2011/10/111025122615.htm [sciencedaily.com]
Re:Shouldn't it be fairly simple to determine that (Score:5, Interesting)
Mass spectrometry using ESI ionisation should be able to detect DNA bases with arsenium replacing phosphor in the 5' phosphoester bound to ribose. It should be trivial to distinguish free arsenic from incorporated arsenic.
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Enhance!
Re:Shouldn't it be fairly simple to determine that (Score:5, Informative)
They know that this bacteria lives in an environment of Arsenic and may use it in its cell process. So any Spectrometric study will show Arsenic as contamination.
What matters is whether the arsenic is covalently bound to functional groups like adenosine, which mass spectrometry is able to detect.
Re:Shouldn't it be fairly simple to determine that (Score:4, Insightful)
Two words: Mass Spectrometry [...] It seems sort of ridiculous that there is a debate over it.
OMG, how is it they never thought of this?! /sarcasm
Why is it the stupider someone is, the most certain they are other people are overlooking "the obvious"? I can understand not knowing the details of why a particular idea wouldn't work, but how oblivious to your own ignorance do you have to be to figure that when the experts aren't using a particular idea, it can't be there are reasons it won't work that you aren't aware of, and rather you instead come to the conclusion that the experts understand their own field less well than you do based on what you learned "Back in High School"? The mind boggles...
Re:Shouldn't it be fairly simple to determine that (Score:5, Insightful)
The counterpoint of this is that if *everyone* assumed someone smarter than them was already "on it", then the forward progress of our society would grind to a halt.
Calling someone out on it is counter productive because it discourages asking questions, thus making you simply a troll.
Science is all about asking questions. In fact I learned something because of their question. It is something that had I thought about it I likely could have come up with the answer, but having it elucidated for me was helpful, and that was about not being able to tell (and ways you could possibly tell) whether the arsenic was merely sticking to the DNA strand, or if it was actually in place of the phosphorous.
Remember the greatest discoveries are not usually preceded by "eureka!", but rahter "hmmm... that's funny".
-nB
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It seems like someone is trying to do exactly that:
http://cosmiclog.msnbc.msn.com/_news/2011/12/02/9168255-arsenic-life-debate-still-percolates [msn.com]
Correct me if I'm wrong, but the linked article seems to suggest that the problem has been that no one else has tried to replicate the experiment until now.
Re:Shouldn't it be fairly simple to determine that (Score:4, Informative)
If only they had thought of that~
"Redfield has sent purified DNA samples to collaborators at Princeton University for mass spectrometry analysis — to see whether any arsenic was really taken up into the molecular structure. "We just got the DNA from Rosie Redfield," one of those collaborators, Leonid Kruglyak, told me this week. A graduate student in Kruglyak's lab, Marshall Louis Reaves, is currently working out the protocols for analyzing the DNA."
Of course it isn't a joke (Score:5, Informative)
We geneticists come up with some of the most goofy names for genes.
Smaug is a fun one.
So is "MADD", which stands for "Mothers Against Dumpy Drosophela"
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Don't forgot Sonic Hedgehog (SHH), an important protein used in development.
Re:Of course it isn't a joke (Score:5, Interesting)
Don't forgot Sonic Hedgehog (SHH), an important protein used in development.
Which ends up being an unfunny problem for doctors, that have to explain to a mom that her baby's congenital malformation is caused by a "Sonic Hedgehog Mutation": http://www.nature.com/nature/journal/v439/n7074/full/439266d.html [nature.com]
Re:Of course it isn't a joke (Score:4, Insightful)
Of they could not be stupid and say "caused by an SHH Mutation".
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Don't forgot Sonic Hedgehog (SHH), an important protein used in development.
Which ends up being an unfunny problem for doctors, that have to explain to a mom that her baby's congenital malformation is caused by a "Sonic Hedgehog Mutation": http://www.nature.com/nature/journal/v439/n7074/full/439266d.html [nature.com]
I think Shakespeare may have had a particular point about the meaning of names... hmm.
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I also like the "I'm Not Dead Yet" (INDY) gene that they had found in fruit flies.
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I almost hate to say this, and certainly hesitate before typing this, but "Darwin Award, anyone?"
Remove (from your gene pool) the ones with spelling and/or writing problems (or thinking problems, to not realise this might be a problem in the future), and eventually the number of people with such problems will decrease. If we wer
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Re:Of course it isn't a joke (Score:5, Informative)
examples (along with the translation if necessary)
Spätzle (a swabian kind of noodle), wingless, toll (either great or crazy), Gurke (cucumber), tube, Pelle (husk/peel), Krüppel (cripple) etc....
Basically they tried to destroy/deactivate/mutate random genes necessary for the development of the fly, without knowing what they'd hit. Then they looked for larvae or flies that looked weird or behaved funky and named them with whatever they associated with it. Finally they took the animal and tried to find the gene they deactivated. If successful, they'd give that original name to the gene, no matter how stupid the name was and no matter how important the gene is. Hilarity ensued.
Re:Of course it isn't a joke (Score:4, Informative)
I googled Mothers Against Dumpy Drosphela and this site came up.
http://jpetrie.myweb.uga.edu/genes.html [uga.edu]
You people are strange. I like you.
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When he says that the table does not align on Firefox, well, he's not kidding. Not even ordering seems to be preserved!
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Well, she got the job. (Score:4, Interesting)
Wolfe-Simon is now at working (sic) at Lawrence Berkeley National Laboratory (LBNL) with John Tainer.
Good for her.
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Please don't hold it against LBL - most of the people I've spoken to here think the paper was bullshit. I'm not sure what Tainer was thinking; his lab normally does crystallography and small-angle X-ray scattering (SAXS), which rarely stray into controversial territory. We do have the necessary equipment to verify her claims, however, if that's possible. I'm just not looking forward to the in
Re:Well, she got the job. (Score:5, Informative)
The paper was fine. Her handling of some of the samples may not have been what one would want.
The sensationalism is the problem. Her conclusion, while unexpected and quite possible wrong, are fine based on the experiment.
This will be worked out like science is worked out. People will try to recreate it, and the DNA will be put under a Mass Spec.
All of which is in the article.
Shit. I just realized you posted AC. So, you are crap. Normally I don't bother with AC, but since I wrote it, I'll post it.
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Please don't hold it against LBL - most of the people I've spoken to here think the paper was bullshit. I'm not sure what Tainer was thinking; his lab normally does crystallography and small-angle X-ray scattering (SAXS), which rarely stray into controversial territory. We do have the necessary equipment to verify her claims, however, if that's possible. I'm just not looking forward to the inevitable public reaction if she holds another hand-waving press conference; the DOE doesn't need that kind of publicity.
- a Berkeley Lab scientist
I would be tempted to hold YOUR comment against LBNL, except you might not actually be a scientist there and just a troll (I hope so), and even if you are, your attitude might actually not be representative.
She published a paper, and put her data out there. She drew a conclusion from the data that others don't agree with, but she explained her reasoning with supporting data. Working in "controversial territory" is nothing to be ashamed of. She may be right, she may be wrong, let actual data settle the qu
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My concern is that it appears that she seems to have been ostracized and punished by members of the scientific community for publishing her paper. Science and peer review aren't supposed to inject personal feelings into research. It's not supposed to be a case of liking or disliking her data but, whether or not it's accurate.
Re:Well, she got the job. (Score:4, Insightful)
The criticism of Dr. Wolfe-Simon has largely focused on the publicity surrounding the paper. The paper itself has problems but in and of themselves these would not reflect too badly on Dr. Wolfe-Simon, because the conclusions as stated in the paper are not too extreme and are supported by the evidence in the paper, such as it is.
However, she and her lab orchestrated a rather extreme degree of publicity for the paper, even though it was likely unwarranted based on the quality of the results, with much of it focusing on what a great scientist she was and how groundbreaking these findings were. Considering that the findings are widely disputed and possibly false, which is sort of the opposite of good and groundbreaking science, this rubbed a lot of people the wrong way.
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Same AC here.
I should elaborate: Sometimes a result that is disputed and possibly false ends up becoming good and groundbreaking science. However, this will only be the case after it has been confirmed independently and the disputed issues addressed. Publicizing it immediately, before that process occurs, as though this uncertain and doubtful piece of science is the gospel truth, is irresponsible.
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The BIG problem was getting the PR people involved. They started hyping it as if it were the discovery of the century. A paper with 'weird' results is fine - even if it turns out wrong. A paper with a dozen PR flacks hyping an entirely new paradigm in molecular biology not so much.
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Moronic headlines strike again. (Score:2)
You see those letters code for very specific chemicals Adenine, Cytosine, Guanine and Thymine, none of which have Arsenic.
When you change the nucleotides, you get something BESIDES ATCG. A prime example of this is RNA, a similar chemical that has no Thymine. Instead it uses Uracil wh
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If you use the word "adenine" to refer to the entire combination of adenine bound to the phosphorous-containing backbone, it makes absolutely no sense to claim that it's "something BESIDES" adenine just because a phosphorous atom in the backbone (not really even part of the adenine itself) has been replaced with arsenic. It's still adenine bound to a scaffold; the scaffold is different, but the adenine isn't.
So OP's point was completely invalid. No matter how pedantic you care to be, it makes just as much s
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This is simply not true (otherwise known as bull cookie)
The authors claim that some of the posphor in the ACTG bases may have been substituted by arsenic. All currently available genome sequencers "read" bases by either PCR based (Sanger, Illumina, Roche, Pac-bio or Ion-torrent) or ligation based (Solid) techniques. These techniques do not discriminate on the phosphor group.
In addition even if the arsenic in the DNA would interfere with the sequence, genome sequencing is not single molecule sequencing; So i
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Let me ask you a simple question:
Someone gives you a written Portuguese book.
You have a Spanish translation program.
Would you then run it through the Spanish translation program and claim you have 'translated it"?
NO OF COURSE NOT, ONLY A MORON WOULD DO THIS.
I totally agree that if you use PCR (which I have experience in - minimal, but recent), or a ligation based system (of which I have read), on an arsenic bas
Well I might have no clue but .. (Score:2)
Well, I might have no clue how you sequence a gene or genome today, but I would guess the procedure would involve using traditional rna in a non-arsenic environment to multiply the dna before analysing it.
This process would of course not preserve the arsenic.
To get better tools, you would have to look at how the adapted lifeform reads and processes its dna, and how the cells factories actually translate the messenger rna, as this might be different.
See
http://en.wikipedia.org/wiki/Genetic_Code#Variations_to_ [wikipedia.org]