…and this is a 
I have to call your attention to this article, Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees, just published in PLoS One. It's cool in itself; it's about the analysis of metagenomic data, which may have exposed a fourth major branch in the tree of life, beyond the bacteria, eukaryotes, and archaea…or it may have just exposed some very weird, highly derived viruses. This is work spawned from Craig Venter's wonderfully fascinating work of just doing shotgun sequencing of sea water, processing all of the DNA from the crazy assortment of organisms present there, and sorting them out afterwards.
But something else that's special about it is that the author, Jonathan Eisen, has bypassed his university's press office and not written a formal press release at all. Instead, he has provided informal commentary on the paper on his own blog, which isn't novel, except in its conscious effort to change the game (Eisen has also been important in open publishing, as in PLoS). This is awesome, and scientists ought to get a little nervous. It maintains the formality and structured writing of a standard peer-reviewed paper, which is good — we don't want new media to violate the discipline of well-tested, successful formats. But it also adds another layer of effort to the work, in which the author breaks out from the conventional structure and talks about the work as he or she would in a seminar or in meeting with other scientists. A paper provides the data and major interpretations, but it's this kind of conversational interaction that can let you see the bigger picture.
I say scientists might want to be a little bit nervous about this, because I can imagine a day when this kind of presentation becomes de rigueur for everything you publish, just as it's now understood that you could give a talk on a paper. It's a different skill set, too, and it's going to require a different kind of talent to be able to address fellow scientists, the lay public, and science journalists. Those are important skills to have, and this kind of thing could end up making them better appreciated in the science community.
Are any of your grad students and post-docs blogging? You might want to think about getting them trained in this brave new world now, before it's too late. And you might want to consider getting started yourself, if you aren't already.
Life Science
Technology
Comments
Posted by: Fuck this... I'm getting Tacos!!!
|
March 19, 2011 9:06 AM
Um yeah I'm going for a BFA, so I'm just going to walk away now...
No but really I all ways learn some thing new every time I come on here.
Posted by: Mapariensis
|
March 19, 2011 9:23 AM
There's a typo in this one:
"de rigeuer" should be "de rigueur"
Posted by: DN King
|
March 19, 2011 10:03 AM
Makes me happy I'm an English Language (Linguistics side rather than Literature) major turned Microbiology / Ecology major.
So far, all of my science professors have complimented me on my ease of writing, except that they often miss glaring errors because the writing flows right over them.
Posted by: Sven DiMilo
|
March 19, 2011 10:06 AM
oh, definitely.
In fact, everybody should blog about everything.
I'm working on today's grilled-cheese-for-lunch post right now.
Posted by: inflection
|
March 19, 2011 10:08 AM
An application of the principle that "you don't really understand it unless you can explain it to an undergraduate," perhaps.
I work in math, and on my own departmental web page, I post short explanations of my papers next to their links, a bit less formal than the abstract -- although I had intended them as summaries for potential search committees! I've seen some smaller departments make a point of listing their faculty members' papers; since there isn't really a central directory for finding scientists' blogs unless they're linked from their faculty page, perhaps an institutional blog summarizing papers could be a place for this sort of presentation. The department could simply request that, when you get a paper accepted, you pass the secretaries a blog post on it.
Posted by: https://me.yahoo.com/a/6xJPW9glmf7Zlo6KJ5aEcT5ybmIC9p.cTh8-#69d8e
|
March 19, 2011 10:29 AM
This is a great step in science becoming more accessible to the general public. This blog in itself a manifestation of that accessibility. Good stuff, thank you for posting.
Posted by: Cor (formerly evil)
|
March 19, 2011 10:33 AM
PZ - Have you considered doing this here? Maybe dust off something you've already published and give us a dose we'll understand without a degree in biology? Might be a neat experiment for Pharyngula.
Posted by: SWH
|
March 19, 2011 10:35 AM
Putting a link to the blog location in the text of the manuscript might be seen as good practice. Perhaps in the acknowledgments section might be a good place. Otherwise it's only there if you happen to know about it or follow the specific blog (essentially I agree with inflection #5 on this - I looked for a link in this paper, gave up and did an electronic search within the pdf and still don't find it)
Bypassing the institutional press office is something that should be practiced at every opportunity! So few papers are worth a press release, and the good ones get attention anyhow.
Posted by: TWood
|
March 19, 2011 10:47 AM
Have you seen the infrastructure that the company called Blackboard has set up? Imagine taking that to the next level and letting professors record their lectures on video, and sell them to students at other universities. Now that talented professor of string theory at MIT who is SO good at explaining things can sell his lectures to students anywhere in the world. Apply that across disciplines and the very best professors will make a mint, finally.
Posted by: Antiochus Epiphanes
|
March 19, 2011 10:59 AM
@Fuck this... I'm getting Tacos!!!
I was about to set up a blog with that^ name. Back to the drawing board for me.
Posted by: Glen Davidson
|
March 19, 2011 10:59 AM
It could be experimental DNA that the Designer is playing around with just for fun. Maybe this is the way in which ID will finally become experimental, catch the Designer in the act.
This is every bit as likely as that we can catch the Designer's work by making up probability figures, which is IDiocy's closest approach to science yet.
Glen Davidson
Posted by: David Marjanović
|
March 19, 2011 11:08 AM
Huh? Everything that bypasses science journalism is good.
And while giving a talk is indeed a different skill set, it's more difficult than writing a blog post, because talks always have to be squeezed into too little time, and if you do manage to leave time for questions, you may not be able to answer all of them immediately to everyone's satisfaction because you don't have time to think about the answers much.
Posted by: Tak
|
March 19, 2011 11:14 AM
Like DN King above, I'd be ready, being a writing/cell biology double major! Of course, in the short term, that just means that I get to write everyone's group paper since just about everyone else in these classes write and cite like sixth-graders. Joy.
Posted by: hillaryrettig
|
March 19, 2011 11:48 AM
>>>It's a different skill set, too, and it's going to require a different kind of talent to be able to address fellow scientists,
including, probably, the talent to give up more control over our work and how it's used. that's a bigger barrier for many people than it seems - certainly for me, and I'm a free software/free culture advocate. But it's hard to let things go.
on another note, I can't believe there's a fourth major branch of life coming. I'm still getting used to the archaea and learning how to spell them...
Posted by: jonathan.eisen
|
March 19, 2011 11:59 AM
Glad people generally like what I did here with the paper. I am getting so sick of press releases myself I figured I should try to experiment with alternative ways ...
I note, for PLoS One and other PLoS papers, one can post comments and even links to the online version of the paper to point out blog posts. That is what I did for this paper on the article page at PLoS One . The commenting / notes system PLoS have is not ideal but it does at least allow one to post such links to the paper. I would like to formalize this so that there is a section in the online version of the paper for the "Story behind the story" by the authors. But still working on that so for now this posting notes/comments will have to do.
Posted by: rubberband
|
March 19, 2011 12:50 PM
What happens to editorial process and peer review? I just got through leading a group of 9th graders into databases (Lexis-Nexus, JSTOR, Science Resource Center), and it was nearly impossible to convince them that the content on these was somehow superior to the random websites they could find so much more easily. I am concerned that most of them will never appreciate the difference between whatever they get from a Google search and the information found in scientific journals. I am totally in favor of actual scientific papers becoming more easily available, but there needs to be some sort of way to separate them from opinion, lies, etc. that LOOKS legit online, but lacks any of the rigorous filtering processes inherent in the formal journal publishing world.
Or are my stodgy old ideas outdated and quaint?
Posted by: theophontes (θεός γαμώτο)
|
March 19, 2011 1:01 PM
@ jonathan.eisen #15
Through a lack of training in biology (particulary at the level of the gene) a lot of what you write goes over my head here. Much of it comes down to my ignorance of the language used. Though on the face of it the article looks fascinating, I can only see it as a blur - perhaps you really need to bundle it with a "press release" style simple summation for the lay person. (Perhaps something that could inspire a young person to want to follow in your footsteps or allow a more public discussion.)
There is a problem of specialisation (as Feynman noted) that makes much of what is special in science difficult to discuss publicly. If each new publication could give a simple down to earth precise we could go a long way to bringing work like yours into the public interest.
Posted by: Marc Abian
|
March 19, 2011 1:11 PM
It's not affected at all. The paper is published as normal*, but in addition Eisen has explained the paper on his blog and also elected to skip the press release.
*Actually PLoS One isn't quite normal because while there is peer review it is much less stringent than regular journals, including other PLoS journals. This is intentional; the idea is to place more emphasis on the type of review that happens after publication i.e. what other scientists in the field think of the paper.
You and me both buddy. Public Library of Science was set up to achieve just that.
Posted by: https://www.google.com/accounts/o8/id?id=AItOawlngOyskkM_yD-3stJ22NSWcL3trBLLfpw
|
March 19, 2011 1:33 PM
In fact PLoS One is just as stringent about the quality of the science it publishes as any other journal. It differs in not requiring that the research be 'important' or 'groundbreaking' or 'a breakthrough'.
Which makes its high impact factor (4.31 for its first year!) all the more impressive.
Posted by: PZ Myers
|
March 19, 2011 1:37 PM
Yes -- PLoS quickly became one of my regular reads, along with Nature and Science and Development and Bioessays and a few others. There are some journals I make a point of browsing every time they come out, and others that are just storage spaces for articles I find in searches...PLoS is one of the consistently good ones.
Posted by: Marc Abian
|
March 19, 2011 2:50 PM
Exactly right, but I consider this to be "less stringent." Perhaps I'm using the wrong word.
Posted by: rubberband
|
March 19, 2011 3:42 PM
Well, it's good to know that there are at least a few places that Google might hit that are also filled with quality, peer reviewed information! I will not only bookmark "PLoS. . .Nature and Science and Development and Bioessays", but put links to them on the course webpage.
In fact, is there a 'list of links' that would be recommended to send bright High School Bio students to?
Posted by: DaveH
|
March 19, 2011 5:35 PM
@ rubberband:
Google or Google Scholar? Because I find the latter very handy for finding papers...
Posted by: Warm Little Pond
|
March 19, 2011 6:01 PM
Too cool! Jonathan Eisen was my professor last quarter! It's awesome to see my prof getting some mention here. Too cool.
Posted by: jonathan.eisen
|
March 19, 2011 9:38 PM
@theophontes
Yes, I completely agree --- I also wanted to do the simple version of the blog posting to explain to others. But then Carl Zimmer wrote a post and well, he is f*$&% brilliant at doing exactly that. So I simply added a link to his post.
Posted by: Fuck this... I'm getting Tacos!!!
|
March 19, 2011 11:20 PM
@Antiochus Epiphanes
All part of my evil plan...
Posted by: theophontes (θεός γαμώτο)
|
March 20, 2011 12:08 AM
@ jonathan.eisen # 25
F*$&% brilliant! Yes, that is a great link, thank you. The writer has made matters a lot clearer for me at least. If all new published research had such a great summation linked to it, I think something extremely worthwhile will have been achieved. Suddenly a lot of otherwise arcane knowledge will become accessible to a far larger audience. I am sure this will be very empowering and serve to expand the reach of science and reason.
Posted by: j-brisby
|
March 20, 2011 7:59 AM
It's fascinating how often PZ and Roger Ebert overlap.
Posted by: DN King
|
March 20, 2011 9:34 AM
Tak, and other good writers here, I wonder if there'll soon be a market for research publication writers. Rather than writing up their own research paper, the scientist could call upon another scientist in that field, versed in the specific terms and with some clue what the research is discussing, and with a skill in writing papers, to write the paper for them.
I'm just curious, because this might be a great way to pay the bills during grant dry spells.
Posted by: David Marjanović
|
March 20, 2011 10:47 AM
The paper is much more cautious and offers viruses, particularly the recently discovered mimiviruses, as an alternative suggestion.
In huge, rich molecular-medicine labs, this already happens: the paper is written by a "technical writer", who is the only person who touches the paper or research but does not end up in the long list of coauthors.
LOL! All your potential employers are in the same dry spell, so they can't afford to hire you! In fact, unless they work in an extremely rich lab as described above, they can't afford to hire you at any time!
I have never even seen a technical writer. Dude, I did my PhD at an institution that couldn't afford online access to Nature or Science, never mind the Journal of Systematic Palaeontology.
Posted by: vincentfleury
|
March 20, 2011 12:44 PM
So you mean that blogging is going to replace books?
Sounds unlikely to me.
Posted by: PZ Myers
|
March 20, 2011 12:57 PM
Damn, Fleury, I knew you were an idiot...but do you really have to make comments that prove it?
Posted by: Topsailsman
|
March 20, 2011 2:32 PM
@#22 "Well, it's good to know that there are at least a few places that Google might hit that are also filled with quality, peer reviewed information! "
I recall in the 90's I would do searches using a compiler called Dogpile and results would be mostly scientific papers that were difficult for me to understand and were fairly narrow topics. I recall wishing I would get results that were more general and easy to understand.
Now I do similar searches and get "ehow" or "answers.yahoo.com" and other crap sites that are empty-headed opinion postings. Now I'm wishing I could find more scientific papers even if they are narrow and harder to understand.
Posted by: Horace
|
March 20, 2011 5:11 PM
>I can't believe there's a fourth major branch of >life coming. I'm still getting used to the >archaea and learning how to spell them...
There is a lot of wierd stuff out there in microbial metagenomes. I amplify environmental DNA using various primer sets. Often the primers amplify stuff that they are not designed for. Sometimes we get amplicons that when we BLAST them match nothing in the database.
Posted by: vincentfleury
|
March 20, 2011 6:01 PM
@32 You have very little sense of humor.
Posted by: PKMKII
|
March 20, 2011 7:22 PM
@12
Actually, I could see this change revolutionizing science journalism. Having the paper's author available in such a quick form of communication(s) could* mean instant feedback on any and all question pertaining to the paper. The journalist could even run his or her rough draft past the author to make sure there are no glaring errors or misrepresentations.
*Obviously, it would require that the science journalist gives a damn about producing quality work. But that's a problem with every specialization in journalism, not just science.
Posted by: Nerd of Redhead, OM
|
March 20, 2011 7:29 PM
Pot, Kettle, Black. Now fuck off troll...Posted by: Horace
|
March 20, 2011 8:37 PM
>Pot, Kettle, Black. Now fuck off troll...
Nerd, you could save everyone a lot of time by developing an algorithm that automatically posted obscenities and demands for peer reviewed literature.
Posted by: vincentfleury
|
March 21, 2011 5:03 AM
But something else that's special about it is that the author, Jonathan Eisen, has bypassed his university's press office and not written a formal press release at all. Instead, he has provided a book, which isn't novel, except in its conscious effort to change the game. This is awesome, and scientists ought to get a little nervous. Books maintain the formality and structured writing of a standard peer-reviewed paper, which is good — we don't want books to violate the discipline of well-tested, successful formats. But it also adds another layer of effort to the work, in which the author breaks out from the conventional structure and talks about the work as he or she would in a seminar or in meeting with other scientists. A paper provides the data and major interpretations, but books can let you see the bigger picture.
Posted by: The Tim Channel
|
March 21, 2011 6:34 AM
If this method of operation becomes more standard you can be sure that there will be "an APP for that" shortly thereafter, eliminating all the heavy lifting whatever the blog tech adds to the equation.
Also, glad to see the site back up.
Enjoy.
Posted by: Nerd of Redhead, OM
|
March 21, 2011 7:03 AM
VF, you can write a book now if you can find a publisher. Why don't you do so, and stop trolling this blog with your idiocy. You add zero to the discussion, as you are years behind in what is possible.
Posted by: jonathan.eisen
|
March 21, 2011 11:19 AM
A bit of shameless self promotion here but for those interested Newsy.Com did a video story about the paper and about PZ's blog post / my press release.
Posted by: theophontes (θεός γαμώτο)
|
March 21, 2011 1:07 PM
Thanks for the link.
Posted by: Horace
|
March 21, 2011 2:18 PM
Jonathan,
How long were the reads in this metagenomic library ?
Do you thing that you could develop primers that are specific to these novel fourth domain sequences and use them to screen other metagenomic libraries ? Ideally fosmid libraries so that you could get longer sequences.
Posted by: jonathan.eisen
|
March 22, 2011 3:22 AM
Horace
The reads were longish --- Sanger reads about 800 bp plus there were paired end with a small insert size so they might overlap from the ends
But yes you could use them to screen ... Kept thnking I would do this which is why we waited and waited to write this up
Then realized I would probably never get to it so we decided to write up the paper as is ...
Posted by: Horace
|
March 22, 2011 1:57 PM
Jonathan,
I would have thought that 800bp would be enough to say if the 16S sequences were from a novel domain or not. Perhaps you could use these sequences to design primers that were trully universal and find environments where this group was more common than in seawater.
Anyway enough of telling you how to do your work, I should get back to my own.
all the best and thank you for posting on Pharyngula.
Posted by: jonathan.eisen
|
March 22, 2011 10:41 PM
Horace
We went after rRNA first using the same logic as you ... seemed to us that the Sanger reads should be long enough. Alas, with the methods we used things did not work out so well. There are three main explanations for why our rRNA analysis was, well, not so useful. 1) The 800 bp is a random read. Most of the time you do not get all 800 bp inside the small subunit rRNA gene --- much of the time you get only a few hundred bp plus flanking sequence 2) Novel rRNA sequences were/are hard to align accurately to other rRNAs because the secondary structure is what is conserved not the sequence and with fragments of rRNAs we could not model the full secondary structure. And 3) Maybe there were no novel rRNAs ... Since we could not rule out difficulties with 1 and 2 we could not tell if 3 was true or not.
Posted by: jonathan.eisen
|
March 22, 2011 10:44 PM
Oh and - to be honest - am honored to be written about here. So am very happy to respond to comments/questions. Or post comments on the paper site or my blog ... only problem with that is Pharyngula gets like 1000x the traffic ...