tag:blogger.com,1999:blog-3522311.post6452677874113653683..comments2024-03-12T03:23:42.976-04:00Comments on NeuroDojo: Reporting on that non peer reviewed stuffZen Faulkeshttp://www.blogger.com/profile/07811309183398223358noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-3522311.post-24769381790562738652012-02-07T18:21:29.659-05:002012-02-07T18:21:29.659-05:00More to the point, the physical chemistry is reaso...More to the point, the physical chemistry is reasonably well-understood. DNA with an arsenodiester backbone is not chemically plausible. The half-life of an arsenoester bond in water at 25° C is 60 milliseconds. That's for one bond. <br /><br />The half-life of a phosphoester bond -- used as the DNA backbone in all known organisms -- is about 30,000,000 YEARS under the same conditions. <br /><br />http://pubs.acs.org/doi/pdf/10.1021/cb2000023<br /><br />An back-of-envelope calculation: the E. coli genome has about 10 million phosphodiesters in the two backbones of its ~5 Mbp chromosome. If they were all arsenodiesters, a new break would appear in the DNA backbone roughly once every 10 nanoseconds. Something like 6 trillion backbone breaks a minute. <br /><br />Arsenic? You're going to need a bigger DNA repair system.Alex Merznoreply@blogger.comtag:blogger.com,1999:blog-3522311.post-591424067650547922012-02-07T06:40:02.640-05:002012-02-07T06:40:02.640-05:00Did anyone bother to read Redfield's paper? Sh...<i>Did anyone bother to read Redfield's paper? She couldn't replicate the growth rate reported by FWS, yet still went ahead with the arsenic assays to determine if it was incorporated. </i><br /><br />I did read it. You're wrong, she could get the growth rate to replicate. She had to add a little phosphate to get it, but she replicated it.<br /><br />Did the phosphate concentration replicate that contaminating the FWS paper? We don't know, because they didn't report that (or, probably, test it). They were sloppy; Redfield was not.<br /><br />You seem to be arguing that sloppy, careless science can stand forever, because it's not reproducible. Is that really what you want to say? <br /><br />It's not that Redfield failed to replicate FWS. It's that FWS generated non-reproducible work. Non-reproducible work is bad science, and shouldn't get a pass <i>because</i> it's bad science.<br /><br />(If you're just saying that FWS will blow it off and claim that it doesn't count, I'm sure you're right; and I'm sure her claims will be ignored by the vast majority of scientists, because her non-reproducible work doesn't stand up.)iayorkhttps://www.blogger.com/profile/10717810444752993915noreply@blogger.comtag:blogger.com,1999:blog-3522311.post-72543933275366191652012-02-06T12:36:26.389-05:002012-02-06T12:36:26.389-05:00Did anyone bother to read Redfield's paper? Sh...Did anyone bother to read Redfield's paper? She couldn't replicate the growth rate reported by FWS, yet still went ahead with the arsenic assays to determine if it was incorporated. The rebuttal for the Redfield work is going to be, "Well, they couldn't get the cells to grow correctly, so that's why they couldn't replicate our findings." Reporting on this paper as if it has killed arsenic life, which is what numerous outlets have done, really isn't responsible. It's going to take more work from more labs or a retraction from FWS to finally nail this story. I'm not saying the results of the original paper are right, or that peer review is some holy grail, but reporting on a negative result this early as some kind of perfect validation is not what science reporting should be about. I agree that science and peer review is a process and it should be reported on in a similar manner. I'd be much happier if the stories guarded these initial results with something like, "First results hint that arsenic life is not real, further work needed."<br /><br />I'm not sure that FTLN illustrate your argument very well. That's a perfect example of another story that NEVER should have been reported on in MSM until researchers were able to validate the results. Peer review would have saved an incorrect story from hitting the airwaves. Which headline are readers going to remember? The one on the front page in big bold print that says "NEUTRINOS TRAVEL FASTER THAN LIGHT" or the rebuttal a week later on page 12 next to the obituaries that reads "Mathematical error, neutrinos not super"Brian Kruegerhttps://www.blogger.com/profile/13456672262242780223noreply@blogger.comtag:blogger.com,1999:blog-3522311.post-74686345611897891012012-02-03T20:14:35.711-05:002012-02-03T20:14:35.711-05:00But that's an issue with the level of care in ...<i>But that's an issue with the level of care in the reporting, rather than ethical issue of reporting on something that isn't peer reviewed. </i><br /><br />Exactly! Careless, sensationalist reporting is bad, no matter what the status of the paper supposedly being reported on.Blake Staceyhttps://www.blogger.com/profile/13977394981287067289noreply@blogger.comtag:blogger.com,1999:blog-3522311.post-3326426085200481292012-02-03T09:48:03.047-05:002012-02-03T09:48:03.047-05:00Pretty much everything medical (especially society...Pretty much everything medical (especially society-related) that I know of is reviewed, but I can't use specifics here...Dr. Dad, PhDhttps://www.blogger.com/profile/00244148018964711614noreply@blogger.comtag:blogger.com,1999:blog-3522311.post-59670081261039707342012-02-02T14:45:21.628-05:002012-02-02T14:45:21.628-05:00I believe peer reviewing conference presentation a...I believe peer reviewing conference presentation abstracts is common in engineering.<br /><br />In contrast, I know of no conference in biology that peer reviews abstracts.<br /><br />I'll grumble if I see sensational reports that don't mention, "This is a conference presentation." But that's an issue with the level of care in the reporting, rather than ethical issue of reporting on something that isn't peer reviewed.Zen Faulkeshttps://www.blogger.com/profile/07811309183398223358noreply@blogger.comtag:blogger.com,1999:blog-3522311.post-51055112026640163202012-02-02T14:32:56.225-05:002012-02-02T14:32:56.225-05:00One quick thing to point out is that abstracts sub...One quick thing to point out is that abstracts submitted to conferences are usually peer-reviewed (at least in my specialty), but not as intensely figure-driven as journals. Data (even p-values) are usually included in the abstracts.<br /><br />As a side note, I've often seen reports from meetings often frame findings as being preliminary, but this may be discipline-specific. <br /><br />I think the big problem is when partial stories are framed as complete. Omitting the status of the data source (published, under review, from a meeting) is critical information that needs to be reported and may even be more important than any supposed "findings."Dr. Dad, PhDhttps://www.blogger.com/profile/00244148018964711614noreply@blogger.com