tag:blogger.com,1999:blog-32079676.post3153874612233366281..comments2024-02-13T21:22:02.522-08:00Comments on RRResearch: Comments on Dr. Wolfe-Simon's ResponseRosie Redfieldhttp://www.blogger.com/profile/06807912674127645263noreply@blogger.comBlogger55125tag:blogger.com,1999:blog-32079676.post-86057825169294193872011-11-23T01:49:38.813-08:002011-11-23T01:49:38.813-08:00The error estimates in S2 seem to say that these d...The error estimates in S2 seem to say that these differences are all real. But then why the large variation between things that should be the same? Where do these error estimates come from? I think I see where they come from for the blank, and the answer is disconcerting.Dental tourism Indiahttp://dentalimplantclinicindia.comnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-39462701781417764862011-08-26T00:45:21.872-07:002011-08-26T00:45:21.872-07:00Poor selection of peers for the review? Your rebut...Poor selection of peers for the review? Your rebuttals have received so much attention, and perhaps deservedly so, but I have to question the widespread insinuations of wrongdoing, if only because they are so vehement. I understand that this study makes claims that if substantiated would fundamentally change our understanding of life, which gives it unusual weight.<br /><br />Regards,<br /><a href="http://cliffmarchant.posterous.com/dr-cliff-merchant-internal-medicine-physician-2396" rel="nofollow">Cliff Merchant MD</a>rosinagrossohttps://www.blogger.com/profile/03310761113177009408noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-36285320915875882642011-04-27T03:35:59.318-07:002011-04-27T03:35:59.318-07:00I understand that this study makes claims that if ...I understand that this study makes claims that if substantiated would fundamentally change our understanding of life, which gives it unusual weight. I also understand that there are methodological factors at issue which can only be fairly evaluated by peers.Sharma Web Servicehttps://www.blogger.com/profile/09406486177216564580noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-88881083980124419002011-01-02T14:22:11.931-08:002011-01-02T14:22:11.931-08:00I know a lot has been said about this, but I notic...I know a lot has been said about this, but I noticed something that may make the arguments about washing the DNA moot. Please bear with me; I predict that it will be worth it in the end.<br /><br />The critical data for the claim of As-DNA is in Table S2 (the numbers in Fig. 2A come from there). This table, as many have noted, raises all sorts of red flags. Why does the As-grown DNA band have less than half the P of the blank? Why does the P-grown RNA have three times less As than the blank? Given these facts, why should we make anything of the less than two-fold excess of As in the supposed As-DNA compared to the blank?<br /><br />The error estimates in S2 seem to say that these differences are all real. But then why the large variation between things that should be the same? Where do these error estimates come from? I think I see where they come from for the blank, and the answer is disconcerting.<br /><br />The P and As numbers for the blank on the left side of Table S2 appear to come from the results reported at the bottom of the "Blanks" section of Table S1. The units given are different, but the numbers make sense. For P, we see values of 795, 1066, and 599 for three replicates. The average of these numbers is 820, which appears in S2.<br /><br />Where does the +/-143 in S2 come from? I think they got this by adding the errors in S1 (80, 107, 60) and dividing by sqrt(3). This is an odd computation in several ways. Critically, it takes no account of how different the measured values were. Given that S2 was supposed to contain twice the standard error, 143 is too low by almost a factor of two.<br /><br />Now here's where it gets interesting. What about the 15 +/-3 value for As in the blank (S2)? In S1 they report values of 42.5, <2, and <2 for As. It seems that they took something like (42.5+2+2)/3 to get the 15. And then they came up with +/-3 by...I don't know. Just divided the +/-9 (for 42.5) by three? In any case, this grossly underrepresents the uncertainty.<br /><br />It doesn't take a sophisticated statistical analysis to see the point. If my interpretation is correct, <i>one of their three replicate measurements of the blank had greater than 50% more As than the supposed As-DNA band</i>. If so, the higher measured As is the As DNA band (27 vs. 15) is utterly meaningless.<br /><br />Can this really be what they did?jlcnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-4995643958492574542010-12-26T15:19:39.460-08:002010-12-26T15:19:39.460-08:00FWS is pushing herself out front on this.FWS is pushing herself out front on this.EliRabetthttps://www.blogger.com/profile/07957002964638398767noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-8110759380490727932010-12-26T07:10:18.040-08:002010-12-26T07:10:18.040-08:00Besides nucleic acids, there are other needs for P...Besides nucleic acids, there are other needs for P in a cell, in particular, for the phospholipids in a cell membrane. However, I believe that arsenolipids have been previously described in biology (in fish, such as cod), so if they were present in this bacterium, this could free-up some scarce P for nucleic acids. Also, as a microbiologist with some experience with electron microscopy, the "vacuoles" shown in the electron micrograph look to me more like granules of poly-beta-hydroxybutyrate (PHB), a carbon storage polymer. PHB is often formed when carbon is in excess and especially so when carbon is in excess and cells are growth-limited for some other nutrient. Perhaps P starvation has triggered PHB formation?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-68860054750653938142010-12-23T13:31:39.685-08:002010-12-23T13:31:39.685-08:00Dave:
"Shoutfests" are nothing new in s...Dave:<br /><br />"Shoutfests" are nothing new in science, occurring way before social media was invented. Of course they used to be limited by the physical constrains of the lab, conference room or hall.ALL Florida Bee Removalhttps://www.blogger.com/profile/13726310600387220227noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-52884754338515076072010-12-23T09:33:13.339-08:002010-12-23T09:33:13.339-08:00After my early reaction (Arsenic and Odd Lace), I ...After my early reaction (<a href="http://www.starshipreckless.com/blog/?p=3544" rel="nofollow">Arsenic and Odd Lace</a>), I wrote a more extended critique of the successive gatekeeping failures that accompanied this paper, from the researchers to the reviewers to Science to NASA: <a href="http://www.starshipreckless.com/blog/?p=3668" rel="nofollow">The Agency that Cried "Awesome!"</a><br /><br />After I had written it, the authors' FAQ appeared. Most of the items you list in this post jumped at me. Particularly egregious was the "PCR requires highly purified DNA" statement. It makes me wonder if they comprehend all the techniques they used as well as they seem to (not) comprehend this one.<br /><br />To those who insist that Rosie is doing something inappropriate, think again. To let this paper sail by unchallenged would be a grave disservice to the scientific process. Let's just hope that the struggling discipline of astrobiology survives it.Athena Andreadishttp://www.starshipreckless.com/noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-27254769178598641742010-12-23T07:54:09.016-08:002010-12-23T07:54:09.016-08:00Dear Dave, please try to remain objective and reas...Dear Dave, please try to remain objective and reasonable about this discussion. In this case, remaining objective means admitting that this study is a pile of unsubstantiated and contradictory ramblings.<br /><br />A very strong response by other scientists was the only suitable course of action in this case, as it ensured that at least some of the criticism was picked up by the mainstream media. Claiming an illusory moral high ground from which to watch and be dismayed is naive at best; while a calm and measured discourse may be desirable and laudable, this is not how the world actually works, and will not get your voice publicly heard. This discussion is not about the scientific process or scientific publishing, but about the responsibilty of scientists to have the courage to stand up publicly to defend scientific integrity. I have no evidence to show that there are no intelligent woodlice on Mars, but that doesn't make it alright to go on TV and claim that I've found them.<br />That is pretty much what the authors did, or can you give an example of convincing evidence for P/As exchange? Just one?<br /><br />-jjAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-47585311445208649812010-12-22T11:06:31.269-08:002010-12-22T11:06:31.269-08:00There are plenty of scientists not involved with t...There are plenty of scientists not involved with the work who have watched with dismay the way our scientific process and discussion has devolved. As a society we have become too accepting of the idea that every debate must be a cable news style shout fest where one attacks not only the messenger but everyone and everything associated with him/her, along with the message.<br /><br />I'm not F.W.S., and for the record I agree with many of the criticisms leveled at the paper. However, I also understand that this is a preliminary report of what would be a very new phenomenon. The authors can't be expected to have searched down every possible avenue. They probably thought that they had enough to support and put forth their interpretation, and it would seem that the reviewers agreed. People could (and possibly will) spend years on further work. Really, the interesting question for everyone to take away from this is when do you have enough evidence to publish and when do you continue to hold off for more and different analyses? We all know that there is a rush to publish, and the authors may be guilty of "least publishable unit" syndrome here. Presenting enough to support their conclusion to reviewers and deferring other lines of investigation for future pubs. That was a big mistake for something of this magnitude. Its easy enough to make these points without turning in to Bill O'Riley and calling people pinheads.Davenoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-70925875543718195132010-12-21T17:29:53.835-08:002010-12-21T17:29:53.835-08:00Dave, Dr. Redfield just owned Wolfe-Simon, and eve...Dave, Dr. Redfield just owned Wolfe-Simon, and everyone in the know agrees the Science paper was poorly done. Deal with it.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-48882944221567906052010-12-21T09:45:55.692-08:002010-12-21T09:45:55.692-08:00Dave is Wolfe-Simon? Looks like.Dave is Wolfe-Simon? Looks like.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-56864271319182289502010-12-21T07:42:11.114-08:002010-12-21T07:42:11.114-08:00@Dave,
There are a lot of reasons why some scream...@Dave,<br /><br />There are a lot of reasons why some screaming is warranted in this situation and I'm glad there are people like Rosie that are willing to do so. Take a look at the news agencies that are still publishing stories that are clearly spoon-fed from the NASA press machine. But thanks to blogs like Rosie's, most news is taking a more balanced view of this.<br /><br />Imagine the embarrassment when it's found out that the DNA in these bugs ISN'T made with As instead of P.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-64114911567428522742010-12-20T19:37:03.275-08:002010-12-20T19:37:03.275-08:00@Anonymous at 10:45, my last post was meant to be ...@Anonymous at 10:45, my last post was meant to be sarcastic so yes I realize quite well that scientists often post their CV online. I also realize that others see these CVs and take them at face value because its impossible to check every entry to make sure the person isn’t being *deliberately misleading*. Thank you for validating my premise.<br /><br />As for my point in bringing it up, I think it goes to motive. Let’s leave it at that.<br /><br />@Anonymous at 12:33, it would be a lot easier to avoid getting lost in the delivery if the delivery wasn’t so over-the-top personal, vehement, and insulting. I’m especially referring to the nature of the quotes that were given to anyone in the media who was willing to put a “microphone” in front of Dr. Redfield. Yes, it does dilute your message if you do business this way. It was true before the internet and it’s still true now, in all places except the cesspool that is the blogosphere.Davenoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-79556937717271870272010-12-20T13:22:29.410-08:002010-12-20T13:22:29.410-08:00See the criticism of Wolfe-Simon paper on Facult o...See the criticism of Wolfe-Simon paper on Facult of 1000:<br />http://f1000.com/6854956Michael Galperinhttps://www.blogger.com/profile/10862430008395724632noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-54894364729930260762010-12-20T12:33:49.267-08:002010-12-20T12:33:49.267-08:00Thanks Rosie for keeping up the fight, even with j...Thanks Rosie for keeping up the fight, even with jerks like Dave around. People are getting caught up in the delivery and not the message (i.e. the science). <br /><br />Someone along the way in the comments asked what us skeptics would think if this result is validated? That question exposes a key misunderstanding of the scientific method that is unfortunately shared by the general public. That the authors conclusions are poorly supported by their data is a fact that won't be changed by subsequent work.<br /><br />Another person asked how such a flawed paper could have gotten past peer-review. Peer review is imperfect for many reasons but is the best system that we know of for screening shoddy science. Bad papers do get through sometimes so the publication of a paper is not a guarantee that it is good science (conclusions following from data).Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-45151399695933507462010-12-20T10:54:33.241-08:002010-12-20T10:54:33.241-08:00Dave, professors and scientists that are far more ...Dave, professors and scientists that are far more reputable than you have personal and lab websites with their CV's posted.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-78804403988570257002010-12-19T12:17:50.344-08:002010-12-19T12:17:50.344-08:00^
Don't be a dick, Dave.^<br />Don't be a dick, Dave.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-28955826762359776922010-12-18T22:25:33.716-08:002010-12-18T22:25:33.716-08:00@Rosie, OK thanks for clarifying I thought that wa...@Rosie, OK thanks for clarifying I thought that was a copy of your CV but a website is not really used for academic purposes.Davenoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-57359853599863771822010-12-18T22:08:06.787-08:002010-12-18T22:08:06.787-08:00@ Dave: That Letter isn't on my CV, though it...@ Dave: That Letter isn't on my CV, though it is on the list of research I've published, on the 'What we've done' page of our web site. Sorry you were misled.Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-7057317773086104062010-12-18T19:19:38.901-08:002010-12-18T19:19:38.901-08:00Here's a question. Isn't it customary/expe...Here's a question. Isn't it customary/expected that if you publish a letter in the journal Science, and you want to put it on your CV with the Science citation, you should specify that the work in question is in fact a letter and not a full blown article?<br /><br />I mean, if you saw this on someone's CV:<br /><br />Redfield R. 2009. Looking to bacteria for clues. Science. 325(5943): 946 PDF<br /><br />you'd be inclined to think its a real paper, right? A letter would be expected to appear more like:<br /><br />Redfield R. 2009. Looking to bacteria for clues. Letters to Science. 325(5943): 946 PDF<br /><br />or<br /><br />Redfield R. 2009. Looking to bacteria for clues. Science (letter). 325(5943): 946 PDF<br /><br />Am I off base here? Well Rosie at least you provided the link for the PDF so its not intellectually dishonest or anything (heavens no).<br /><br />By the way, congrats on your upcoming NEW SCIENCE PAPER that you will be able to put on your CV if your latest letter makes it in.Davenoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-53386876690794596862010-12-18T16:46:08.961-08:002010-12-18T16:46:08.961-08:00@anonymous (the one at 3:17 pm)
I think that the ...@anonymous (the one at 3:17 pm)<br /><br />I think that the 16S rRNA segment they amplified was about 1500 bp long. If less than about 0.1% of the backbone phosphoruses were replaced with arsenic then the PRC polymerase would probably have had enough arsenic-free template DNA to copy. <br /><br />The reasons to think that DNA polymerases would not be able to use arsenic-containing templates are spelled out in the post that follows this one.Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-62043610447700650552010-12-18T15:17:16.373-08:002010-12-18T15:17:16.373-08:00"...for the phylogenetic analysis. This stro..."...for the phylogenetic analysis. This strongly suggests that the DNA from arsenate-grown cells has a normal phosphorus backbone. The polymerases used for PCR have very high fidelity and would not tolerate substitution of arsenic for phosphorus."<br /><br />Rosie, could PCR work if only a small proportion of P was substituted? What's the reason fro saying that PCR polymerases wouldn't tolerate arsenic substitution?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-35194678807342571182010-12-18T14:37:58.222-08:002010-12-18T14:37:58.222-08:00Anonymous: somehow you seem to forget that part of...<b>Anonymous</b>: somehow you seem to forget that part of the scientific process is open criticism and analysis of published results. If I were a graduate student or a posdoc, I wouldn't want you supervising my work, as you would be likely to push me to publish incomplete research and obviate stringent controls. Your anonimity and your relaxed attitude towards good experimental methodology make me seriously doubt your supposed work as a reviewer. Your acerbic defense of sloppy publishing, your talk of respectability behind the veil of anonimity and your implied threat of blocking funding approval (how respectable!) make me rather suspect some kind of involvement with Wolfe-Simon's work.Ribozymehttps://www.blogger.com/profile/00617035031357327037noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-37852657270896639992010-12-18T13:59:02.495-08:002010-12-18T13:59:02.495-08:00@Torbjörn Larsson, i review for these journals and...@Torbjörn Larsson, i review for these journals and magazines in question. i stand by what I said. No respectable scientist has taken this route of lashing on a young scientist in public. thats how the decorum of science works. Dr. Felisa might have done a mistake, but what this blogs author is doing is public assault. she has drooped to a level worse than just doing a scientific error. if blogs and public commenting is the reason for that, i shoud just say your community may not be ready for it yet. open sourced publications like arxiv have set a great example of quick dissemination and critical process. Your and this author's choice of words, choice of medium, lack of understanding of what affect an open washing of dirty laundry will have on the community utterly disappoints me. if you talk about funding, which this author mentions, i will love to see if acerbic fighting like this will lead to a single new student or funds in astrobiology. the funding reviewers and peer reviewers like me are watching the terms of this argument. most of my colleagues in private consider this style to be bad and when the time comes it will be made clear.Anonymousnoreply@blogger.com