tag:blogger.com,1999:blog-10781944.post3857430437256540978..comments2024-03-28T00:36:36.460-07:00Comments on The Tree of Life: Rated my first paper in PLoS OneJonathan Eisenhttp://www.blogger.com/profile/07953790938128734305noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-10781944.post-57494767653112364732007-09-26T22:45:00.000-07:002007-09-26T22:45:00.000-07:00I don't think we need a reward system. I just thin...I don't think we need a reward system. I just think that if you plan submit a paper to a journal, the journal should require all of the authors to review or comment on a paper first, so that there is some balance in the system.<BR/><BR/>Amazon is playing a different kinda game probabilistically. For example, let's assume "Harry Potter and the Deathly Hallows" sold 15 million copies (an underestimate for sure). Amazon has 2705 reviews for this book, so less than 1 in 5000 of those buying the book reviewed the book. At such a rate, I'd guess most PLoS One papers will never be read by enough people to accumulate 4-10 decent comments.<BR/><BR/>But I hope your right. Hopefully I am just one of the doubters in the new generation of blogging web 2.0 students.Jhttps://www.blogger.com/profile/02818497841390003056noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-54991395557756249892007-09-25T21:40:00.000-07:002007-09-25T21:40:00.000-07:00JI get your point and it is a valid one --- the qu...J<BR/><BR/>I get your point and it is a valid one --- the question of how we get people to do peer review is difficult. Everyone is really busy and this is just one more thing. So we need a better reward system for reviews - sure that might help. <BR/><BR/>But I am not so sure that the limitations are as large as you seem to think. The new generation of students seems eager to do for science what they do in all other aspects of their life with blogs and Web 2.0, etc. I think it is likely they will be very open about peer review and about participating in things like PLoS One. Sure - it would be good to have more carrots. But I am not convinced that PLoS One have the problems you suggest. It is pretty new. Give it time. After all, it took time for Amazon and other ratings systems to get used and now they are a key part of online sales.Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-14269869792201946942007-09-25T20:09:00.000-07:002007-09-25T20:09:00.000-07:00While it's noble that a few folks are starting to ...While it's noble that a few folks are starting to promote an open, continuous discussion of the published literature. I think this PLoS One experiment is doomed to failure. To really be useful, a large number of articles need a large number of comments and that just isn't happening until were forced to do it. I don't think most editors have folks knocking down their doors asking to review papers; no, they have to seek out reviewers; and then they have to remind them and remind them to turn the reviews in on time.<BR/><BR/><A HREF="http://blog-di-j.blogspot.com/2007/09/towards-richer-scientific-literature.html" REL="nofollow">I think we need a new system where comment and discussion are integrated and part of the publication process rather than optional add ons.</A>Jhttps://www.blogger.com/profile/02818497841390003056noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-52723485278944141602007-07-17T06:11:00.000-07:002007-07-17T06:11:00.000-07:00Well, I think it is relevant to understand barcodi...Well, I think it is relevant to understand barcoding to compare it to rRNA diversity studies where people are using a single gene to attempt to identify, count and classify organisms. As for delineate clusters in need of a formal description that is basically one of the main points of rRNA PCR based identification of OTUs (operational taxonomic units - also known as phylotypes). Furthermore this is directly relevant to metagenomics because one of the main goals of metagenomics is to connect those same rRNA clusters to the biology of the organisms, possible through genome sequencing. <BR/><BR/>As for a standardized reference system for all animals - that would be nice but again there are parallels to rRNA here as when you publish a new description of a bacterial or archaeal species there one is in essence forced to show it is a novel rRNA type.Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-16539549011794671022007-07-17T05:31:00.000-07:002007-07-17T05:31:00.000-07:001) DNA barcoding is not phylogenetics.2) I fail to...1) DNA barcoding is not phylogenetics.<BR/><BR/>2) I fail to see why it is relevant whether someone has already been doing a similar thing in a totally different context. DNA barcoding is meant to allow the recovery of existing formal species names (which don't exist in the rRNA system you're talking about for the most part), and to delineate clusters potentially in need of formal description. Of course the idea is not entirely new to use DNA sequences for identification -- but a standardized reference system for all animals sure is.T Ryan Gregoryhttps://www.blogger.com/profile/17028390880937952573noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-34428699023273447682007-07-17T04:57:00.000-07:002007-07-17T04:57:00.000-07:00As I was reading your post, I was getting ready to...As I was reading your post, I was getting ready to comment on how F1000 is not open access . . . and then you went and mentioned it yourself!<BR/><BR/>I agree with you that of course individual mt genes will be consistent with each other -- they're all on a molecule with, essentially, no recombination. What's more important is whether mtDNA genes are consistent with nuclear genes and whether individual nuclear genes are consistent with each other. Doing any evolutionary analysis (whether it be phylogenetic or popgen) with a single marker is not advisable -- and an entire mt genome is still just a single marker.RPMhttps://www.blogger.com/profile/00344508931818143159noreply@blogger.com