The Third Reviewer is a website for those of us who would rather show up to a journal club late, beer in hand and in their pajamas. Which means basically 100% of all scientists I know. TTR pulls feeds form multiple journals, and posts the abstracts on its site for us to comment upon; anonymously if so wished. The site is called The Third Reviewer, since most papers are reviewed by two people, and the third would be the rest of the scientific community. From their Welcome page:



The Third Reviewer is a forum for scientists to share opinions about recently published research. It’s like journal club, but…

• Faster.  No need to set aside an hour of your time.
• Convenient. Check in from home or at lab, at 5 a.m. or 10 p.m.
• Comprehensive. Browse papers from lots of journals, all on one site.

Reviewers #1 & #2

TTR started with Neurobiology papers only. Now they added microbiology, so it’s nice to see that there is some interesting science going on there too… (Ow, owwww, ow… Kidding. KIDDING!!!).

Check it out.

Bora Zivkovic, the BUCA (Best Universal Common Ancestor) of science bloggers has tagged this blog with with a Blog of Substance award. As a grateful recipient of this award I am obligated to do two things:
1. Sum up my blogging motivation, philosophy and experience in exactly 10 words.
2. Pass this award on to 10 other blogs.

Of course, I never do anything without researching it first, because I am such an awesome scientist, or detail-oriented !@#*^, depending on whether you ask me or my students. So I looked up “substance” in the Merriam-Webster dictionary. Here is what I found:

Main Entry: sub·stance
Pronunciation: \ˈsəb-stən(t)s\
Function: noun
Etymology: Middle English, from Anglo-French, from Latin substantia, from substant-, substans, present participle of substare to stand under, from sub- + stare to stand — more at stand
Date: 14th century

1 a : essential nature : essence b : a fundamental or characteristic part or quality c Christian Science : god 1b
2 a : ultimate reality that underlies all outward manifestations and change b : practical importance : meaning, usefulness
3 a : physical material from which something is made or which has discrete existence b : matter of particular or definite chemical constitution c : something (as drugs or alcoholic beverages) deemed harmful and usually subject to legal restriction

4 : material possessions : property

Hmmm… 2a and 2b seem to be relevant. Perhaps 3c should be too, as my blogging could be construed harmful to other more productive activities, which I am obviously not engaged with at this moment. Actually you, gentle reader,  are not engaged in more productive activities either right now. Be that as it may, the word substance does seem to have an air of permanence about it, which is contrary to the perceived ephemeral nature of blogging. Bora is actually one of the people who are doing something about making blogs less ephemeral by publishing The Open Laboratory collection (full disclosure: I’m published in the 2009 book) and by supporting science bloggers, blogging and activities wherever they may be. This makes me so happy to be among Bora’s chosen 10 (OK, 11, he cheated a bit) among the hundreds of blogs he must be reading. Thanks Bora!

I do wonder though, eighty-five years from now, how many of us science bloggers would be remembered for our blogging? Well, maybe not as individuals, but what kind of impact are we having now, and how much will it remain 85 years from now? Hopefully as a collective, science bloggers are impacting the understanding of science, which is one of the reasons I am blogging. Hopefully, we do have substance, as a group if not as individuals.

Why eighty-five years? Well, the answer to that brings me to the main topic  (substance?) part of this post, which is the  anniversary of the Scopes trial. This month, 85 years ago, a schoolteacher in Tennessee was convicted of a high misdemeanor for violating the State of Tennessee’s Butler Act which prohibited the teaching of evolution in any of the state’s public schools and universities. He was fined $100.

PUBLIC ACTS

OF THE

STATE OF TENNESSEE

PASSED BY THE

SIXTY – FOURTH GENERAL ASSEMBLY

1925

________

CHAPTER NO. 27

House Bill No. 185

(By Mr. Butler)

AN ACT prohibiting the teaching of the Evolution Theory in all the Universities, Normals and all other public schools of Tennessee, which are supported in whole or in part by the public school funds of the State, and to provide penalties for the violations thereof.

Section 1. Be it enacted by the General Assembly of the State of Tennessee, That it shall be unlawful for any teacher in any of the Universities, Normals and all other public schools of the State which are supported in whole or in part by the public school funds of the State, to teach any theory that denies the story of the Divine Creation of man as taught in the Bible, and to teach instead that man has descended from a lower order of animals.

Section 2. Be it further enacted, That any teacher found guilty of the violation of this Act, Shall be guilty of a misdemeanor and upon conviction, shall be fined not less than One Hundred $ (100.00) Dollars nor more than Five Hundred ($ 500.00) Dollars for each offense.

Section 3. Be it further enacted, That this Act take effect from and after its passage, the public welfare requiring it.

Passed March 13, 1925

W. F. Barry,

Speaker of the House of Representatives

L. D. Hill,

Speaker of the Senate

Approved March 21, 1925.

Austin Peay,

Governor.

Seems incredible at this day an age… or maybe not so incredible given recent events in Louisiana.

William Jennings Bryan, counsel for the prosecution, attacking evolution

The city of Dayton as the organ grinder profiting from the Scopes trial

The trial, which originated as something of a publicity affair for the town of Dayton, Tennessee, quickly became a battleground for evolution vs. creation. In the short term, the trial actually increased the number of anti-evolution bills proposed in different state legislatures in the US. In the long term, however, Tennessee vs. Scopes is seen as a watershed moment in the teaching and public acceptance of evolution, and has had long terms ramifications in the US and internationally. Scopes himself  spoke only once at the trial, was not called to testify, and only had this to say when granted a statement after sentence was passed:

Your honor, I feel that I have been convicted of violating an unjust statute. I will continue in the future, as I have in the past, to oppose this law in any way I can. Any other action would be in violation of my ideal of academic freedom — that is, to teach the truth as guaranteed in our constitution, of personal and religious freedom. I think the fine is unjust.

Now that is substance.

Back to the award;  I still have some conditions to fulfill:

1. Sum up your blogging motivation, philosophy and experience in exactly 10 words.

¹Blogging ²motivation, ³philosophy ⁴and ⁵experience ⁶cannot ⁷be ⁸summed ⁹in ¹⁰ten ¹¹words.

2. Pass this award on to 10 other blogs

Given the 10ⁿ growth rate of tagged blogs, chain-letter fashion, I wonder about how this Blogging with Substance award has originated. Search engines was no help, as so many blogs are now tagged with the Blogging with Substance. If someone has an answer, let me know. Anyhow, here are my 10 tags, based on what I am reading nowadays, ephemerality of blogging substance, and all that jazz. Tough choices though, so many good blogs out there:

1. Blue Collar Bioinformatics

2. Sandwalk

3. Thoughtomics

4. The Loom

5. Mike the Mad Biologist

6. Genomics, Evolution and Pseudoscience

7. Circle of Complexity

8. Buried Treasure

9. The Tree of Life

10. Mystery Rays form Outer Space

Final word: if this post seems a bit confused, and you are not sure that you are “getting it”, well, that’s this post’s substance.

It seems like there is no institution that is more criticized in science than that of the peer-review system — an no one that is less mutable. While published paper evaluation metrics are being  revised (such as the recently introduced PLoS article level metrics, or the Australian National Health and Medical Research Council abandonment of the Thomson Reuters impact factor system), the peer review system seems like it is here to stay. When asked, most scientists would probably paraphrase Churchill: “peer review is the worst system for judging science, except all others that have been tried from time to time”. (However, Churchill did have other working state models to compare with Democracy, whereas peer-review seems to have no, um, peers.) The latest diagnostic comes from Errol Friedberg (no relation to me), editor in chief of DNA Repair.

“—if peer review is so central to the process by which scientific knowledge becomes canonized, it is ironic that science has little to say about whether it works.” — J.P. Kassirer and E.W. Campion, Peer review: crude and understudied, but indispensable, JAMA 272 (1994), pp. 96–9

The conclusion that was reached after a few annual scientific conferences published in the Journal of the American Medical Association as to the merit of peer-review were: “(i) blinding reviewers to authors’ identity does not usefully improve the quality of reviews, (ii) there is no association between reviewers signing their reviews and the quality of the review, (iii) passing reviewers’ comments to co-reviewers has no obvious effect on the quality of review, (iv) reviewers aged under 40—-write reviews of slightly better quality, (v) appreciable bias and parochialism exists in the review system. Finally, and perhaps most significantly, developing a useful instrument(s) to measure manuscript quality remains a huge challenge“.  [and in the final analysis peer review]   “can screen out [studies] that are poorly conceived, poorly designed, poorly executed, trivial, marginal, or uninterruptable.” No mean feat, really. But many scientists maintain that peer -review is a screen for quality and impact, not just for screening out bad science for funding agencies and for journals.

Neither Errol Friedberg, nor the authors of the congress proceedings seem to suggest alternatives. Rather, they present examinations of the process and its effect upon the final outcome.  Friedberg also suggests that one constraint, that of page numbers in a journal, has been essentially removed with the advent of electronic publication, and thus more meritorious articles can now be published. Interestingly enough, many scientists — and journals — seem to value publication quotas, as those add prestige to those papers that do get accepted.

However, there are two things of which I’m certain: change, if any, will not come soon, but also we have not heard the last critique of the peer-review system.

Friedberg, E. (2010). Peer review of scientific papers—A never-ending conumdrum DNA Repair DOI: 10.1016/j.dnarep.2010.03.003

I have written about the Journal of Serendipitous and Unexpected Results before and now this just popped in my inbox from JSUR’s Google group. Apparently JSUR is now open for business.

JSUR Call for Participation

Submit your short (2-4page) and full length manuscripts to the Journal
of Serendipitous and Unexpected Results.

Over the past month we’ve received a great amount of press and
publicity for the Journal of Serendipitous and Unexpected Results
(JSUR). Thanks to everyone who helped spread the word, please keep it
up!

In Richard Feynman’s 1966 Nobel Lecture, he said, “We have a habit in
writing articles published in scientific journals to make the work as
finished as possible, to cover up all the tracks, to not worry about
the blind alleys or describe how you had the wrong idea first, and so
on. So there isn’t any place to publish, in a dignified manner, what
you actually did in order to do the work.”

We’re writing to invite you to solicit short (2-4page) and full length
submissions to JSUR.  Why not prepare a 2-4 page writeup discussing
side-investigations, alleyways, or false-starts in your latest
published or unpublished research? Papers of this length place a
minimal burden on the authors, while providing extremely valuable
research insights to a broad audience.

Journal website: http://www.jsur.org

Sincerely,
The JSUR Editorial Board

Yes! Why should the evolution people have all the fun with their blog carnival? (After all, it is only a theory.) It’s time for bioinformaticians to show what we are made of, and to have a carnival of our own. Bio::blogs had a good run some time ago. I decided to reconnect what is hopefully now a larger and more networked community under the title of Bioinformatics Blog Carnival.

Northampton: monument to Francis Crick, born in Northampton. Copyright Ian Rob, licensed for reuse.

Programming

For many new bioinformatic programmers, there is a question of which Bio* package to choose from. The Bio* packages (Biopython, BioPerl, BioJava and BioRuby) are open source licensed packages which are used heavily in bioinformatics coding. They contain parsers for bioinformatic data file, file format converters, SQL interfaces and other goodies that make a biohacker’s life manageable. Walter Jessen presents a rapid-fire no-nonsense review of Open Source Programming with Bio* Libraries on Expressing Scientific Insight. Finally, if you would like to do everything wrong, Manuel Corpas presents 10 Sarcastic Rules on How to Be a Bioinformatician posted at Manuel Corpas’ Blog.

Databases

Morgan Langille talks about BioTorrents – a file sharing resource for scientists posted at his blog Beta Science. My take on BioTorrents is that it is a cool idea, but as most institutes block BitTorrent along with other peer-to-peer sharing utilities, I doubt there is a critical mass of feeders to make BioTorrents viable. Things can change though: institutes might decide to set up dedicated servers to Torrent scientific data, just like there are legitimate Torrent servers for Linux distros. George presents Bio-graphics, BioSQL and Rails part 1 posted at Biorelated. He talks about how to quickly add graphics support to a bioinformatics database rails application.

Brad Chapman’s Blue Collar Bioinformatics is a treasure-trove of useful bioinformatics methods. Brad is very thorough in his writing, and he covers a wide variety of topics. I particularly enjoyed reading about his adventures at the biohackathon 2010 in Tokyo, and the resulting Python query interface to BioGateway SPARQL endpoint and InterMine.

Genomics

Nick Loman from Pathogens: Genes and Genomes gives some excellent tips for de-novo genome assembly. He also gives the necessary scripts,which are great companions to Velvet, the popular short read assembler. Luke Jostins writes about AGBT: Speculating on Third Gen Tech posted at Genetic Inference, “An investigation into what data from various third generation sequencing technologies may look like.” SM presents Resources for Exome sequencing annotation posted at Organizing the Strands of Curiosity.

Structural biology

Sean Seaver talks about the retraction of several protein structure papers published by one group at the University of Alabama, Birmingham. Structuregate was reported both in the media and in the blogosphere. Sean walks us through how it might have been done, and how structural bioinformatics techniques found out the wrong structures in Origin and Orientation posted at P212121. Maria Hodges talks about how difficult it is to explain structural genomics to the man in the pub. Menachem Fromer presents Tradeoff between stability and multispecificity in the design of promiscuous proteins. Promiscuous proteins are proteins which bind different partners (ligands, or other proteins). However, the more partners they are able to bind, the less stable they are, as shown in a series of simulated evolution studies, summarized at Nir London’s Macromolecular Modeling Blog. OK, promiscuity and and a pub. There must be a joke somewhere there.

Credit: Iddo Friedberg & 3D chem for the Anthrax toxin lethal factor image

A common lament among bloggers and other enthusiastic adopters of Web 2.0 technology is the lack of mainstream uptake of these tools by active scientists. A recent report from University of California Berkeley confirmed this: “The advice given to pre-tenure scholars was consistent across all fields: focus on publishing in the right venues and avoid spending too much time on public engagement, committee work, writing op-ed pieces, developing websites, blogging, and other non-traditional forms of electronic dissemination (including online course activities)“. Maria Hodges argues that Web 2.0 thrives where journals don’t, and that the NMR community might be the first to reach the tipping point, where your career is harmed by not contributing. She talks of two wikis used by the NMR community. It is a small community, which has a need for sharing methods that are generally not publishable in peer-reviewed journals. The wiki venue makes for an ideal dissemination method for this community. On the subject of data sharing, and how it can backfire: here is an interesting connection between the history of the PDB, and the email affair known as ‘climategate’.

Some interesting events cropped up recently. The Marco Island Advances in Genome Biology and Technology meeting was heavily tweeted and blogged about.  Pacific Biosciences unveiled their third generation sequencer. Ostensibly, it can sequence reads of 20,000 length, but the fraction of actual long reads in a run, and their quality is still a bit hazy. The most interested to me is the Ion Torrent. Being rather low on budget, this seems like the family budget car of high throughput sequencing: cheap, reliable, and does not offer more than I really need. $50,000 for a sequencer with $500 runs with 160MB/hr? Nice. Genetic Inference has a great summary of the various technologies presented.

Overall, we are starting to see a divergence in sequencing technologies, as each tech concentrates on having clearly defined advantages and potential applications that differ from all others. This means that the scientists themselves can more closely tailor their choice of tech to fit their situation. Are you a small lab that needs 10 high-quality genomes on a budget? Go to Complete. Want a cheap, fast machine for library validation? Use Ion Torrent. Setting up a pipeline for sequencing thousands of genomes? Go Illumina.

The review article on metagenomics I recently published in PLoS Computational Biology (yeah, yeah, shameless plug) already starts to feels somewhat outdated on the sequencing technology front.

Carnival of Evolution #21 the superstar edition is up: check it out. It’s a nice and detailed one,. Some posts I liked included talking about how human fingers evolved, and why it is important to consult evolutionary biologists when making decision about conservation.

An interesting email I got yesterday: PubGet, a search engine for PDFs of scientific articles, is no linked to PLoS. PubGet is a very useful service that gets  you the article PDF immediately, without going through he usual clickeroo via Google,  pubmed, publisher’s gateway, journal gateway and then squinting along the sidebar to find the PDF link. Nice to see that these two are teaming up.

Finally, two reminders. First, Ada Lovelace day, a blogging day celebrating the achievements of women in science and technology is coming up, March 24. Go ahead, pledge and blog! Second, the Byte Size Biology will be hosting a Carnival of Bioinformatics. Quite a few posts have been submitted already, please submit yours, deadline: March 9.

Haiku:

A finer book of

Blog posts the world has not seen

Buy: you won’t regret

The fine print: one of my posts is published in this anthology

To-day we have naming of parts. Yesterday,
We had daily cleaning. And to-morrow morning,
We shall have what to do after firing. But to-day,
To-day we have naming of parts. Japonica
Glistens like coral in all of the neighboring gardens,
And to-day we have naming of parts.
— Henry Reed “Naming of Parts”

To-day we have  Henry Reed’s birthday. Henry Reed, who wrote one of my favorite poems: Lessons of the War. Reed published this poem in the New Statesman and the Nation August 1942. Superficially, the poem is a soldier’s griping in the ill-equipped British army of WWII.  But there is also the dark undercurrent of a man yanked from everyday life and forced to face his own mortality.  Lessons of War has six parts, and it gets more somber as the poem progresses. The “naming of parts” he talks about in the excerpt above is the all-too-familiar experience in basic training: getting to know your personal weapon.

Here is part II: Judging Distances.

LESSONS OF THE WAR

II. JUDGING DISTANCES

Not only how far away, but the way that you say it
Is very important. Perhaps you may never get
The knack of judging a distance, but at least you know
How to report on a landscape: the central sector,
The right of the arc and that, which we had last Tuesday,
And at least you know

That maps are of time, not place, so far as the army
Happens to be concerned—the reason being,
Is one which need not delay us. Again, you know
There are three kinds of tree, three only, the fir and the poplar,
And those which have bushy tops to; and lastly
That things only seem to be things.

A barn is not called a barn, to put it more plainly,
Or a field in the distance, where sheep may be safely grazing.
You must never be over-sure. You must say, when reporting:
At five o’clock in the central sector is a dozen
Of what appear to be animals; whatever you do,
Don’t call the bleeders sheep.

I am sure that’s quite clear; and suppose, for the sake of example,
The one at the end, asleep, endeavors to tell us
What he sees over there to the west, and how far away,
After first having come to attention. There to the west,
On the fields of summer the sun and the shadows bestow
Vestments of purple and gold.

The still white dwellings are like a mirage in the heat,
And under the swaying elms a man and a woman
Lie gently together. Which is, perhaps, only to say
That there is a row of houses to the left of the arc,
And that under some poplars a pair of what appear to be humans
Appear to be loving.

Well that, for an answer, is what we rightly call
Moderately satisfactory only, the reason being,
Is that two things have been omitted, and those are very important.
The human beings, now: in what direction are they,
And how far away, would you say? And do not forget
There may be dead ground in between.

There may be dead ground in between; and I may not have got
The knack of judging a distance; I will only venture
A guess that perhaps between me and the apparent lovers,
(Who, incidentally, appear by now to have finished,)
At seven o’clock from the houses, is roughly a distance
Of about one year and a half.

You can read all six parts of Lessons of the War here.

Byte Size Biology will be hosting the first edition of the bioinformatics blog carnival. All you bioinformatics bloggers, submit your entries by Mar 9, 2010 23:59:03  EST. Note the 3 second extension I have already given. There will be no more deadline extensions, I’ve been generous enough as it is. The carnival will be posted here by March 15, 2010.

Any blog posts that have to do with the computational aspects of: genomics, nextgen sequencing, sequence analysis, gene expression, systems biology, ontologies, databases, structural biology, metagenomics, phylogenetics, function prediction and I probably forgot a few other categories so don’t hold it against me, just submit. Early and often. Your own posts and others that you liked. Nothing too old please, 1/1/2009 and later. I reserve the right to be a less-than-benevolent dictator and screen out posts. This applies especially to commercial plugs with no other merits.

Please retweet, reblog, rebuzz and remember:  submit to the bioinformatics blog carnival!

If you have a cool logo for this carnival, email bioinfo.blog.carnival AT gmail.com OhOne and OhToo will pick the winning logo to be displayed on the carnival. Likewise, if you would like to host the next edition, let me know. Do not submit posts by email, only via blogcarnival.com.

Happy carny-ing.

A  small spike on my blog traffic yesterday led me to look for the source via Google Analytics. (If you are a blogger, you should really use this tool, lots of useful traffic information.) Seems like most of the traffic came from the page of a high school science teacher at Badin High School in Hamilton, OH. Apparently the students were to be quizzed today on two of my posts about endosymbiosis (and one from 80Beats; I’m in good company.) So they were very busy Sunday. It’s encouraging to know that some of my posts are accessible enough for high school science. Finally, quite a few Miami students come from Hamilton (we’re close). So I might see some of them next year.

Muahahaha!

My post The Incredible Shrinking Genome was selected for publication in Open Laboratory 2009. The Open Laboratory books are anthologies of 52 posts from various science blogs selected annually by a panel of judges . This year the judges waded through 470 740 nominations (thanks for catching this Bora), so it is great to be selected! How on Earth did they go through 740 posts?

You must buy the book once it’s out, office and home copies. Don’t forget your spouse, lover, friends, colleagues, children and pet hamster, for they will all be deeply offended if you do not get them a copy of Open Laboratory 2009, which may have serious ramifications.  I will link to the book once it is out, in a month or so. In the meantime, you should seriously  consider purchasing the 2008, 2007 and 2006 editions.

Floated in my email inbox recently. Bears blogging.

Dear Editor,

I would like to thank the editorial board and the referees for their comments and contributions to our manuscript. We have carefully considered the comments when rewriting the manuscript, and believe it to be much improved now…

…Oh, screw this. Let’s cut the bull. Mmkay?

Referee #1 did not even bother to read the paper. He basically glanced at the references, realized he was not cited enough to his taste, got pissed off, and attached a Pubmed dump of his papers in the last 10 years. All three of them. There is a reason none of these papers went beyond a single digit number of citations: they suck! Also, I fail to see how a paper discussing semantic distances as applied to an “endoplasmatic reticulum membrane elasticity ontology” has anything to do with my paper. Or with anything of interest, for that matter.

Referee #2 requested reanalysis of our data, using Boyle-Scott statistics. Applying Boyle-Scott statistics to our work would be like draping a hornet’s nest with clingwrap while wearing a bathing suit: a long and painful process which is utterly pointless. B-S statistics are exactly what they are, and if you think I will be bothered to do that, with my grad student finally graduating and taking off, you’re as delusional as Dr. Boyle was when he was researching REM sleep in cannabis-treated amphibians just before he went completely schizo and had to be locked up.

Referee #3 Actually read the manuscript carefully. Which is both commendable and rare. Unfortunately, judging by the comments presented, it was not my manuscript.

Finally, I would request that you as an editor grow a brain. Did you even read their comments before passing them on to me? Shipping out papers to referees, then getting them back, pasting them together and slapping on some boilerplate text from your journal’s editor’s site is not editorial work. In fact, a middle school student that volunteers in my lab wrote up a script yesterday that does just that. We are thinking of installing it in your esteemed journal’s author’s website and waiting to see if this editorial version of the Turing test would pass. We are very optimistic about the results, and we plan to write a paper about them.

Sincerely,

Prof. I. M. Irritated

In no particular order or context. No personal stuff and by no means a complete list:

WordPress (like, duh).

Wikipedia (default for looking up new stuff)

Wikis in general (great lab management tool. Don’t need LIMS)

Open Access Publishing and Creative Commons licensing.

FLOSS licensing (90% of the software I use, and 100% of what I write)

Science Bloggers (too numerous to link)

Science tweeters and FriendFeeders (too numerous to link. That’s how I keep up with things)

BLAST (Sometimes it feels like bioinformatics is should be renamed to blastology)

LaTeX (Wrote my dissertation in LaTeX, and never looked back)

OpenOffice.org (because not everyone uses LaTeX).

CiteULike (Keeping my reference library up to date and in good order)

Delicious (Keeping my bookmarks up to date and in good order)

Gmail (because finding that document you sent me a month ago would be impossible otherwise)

Google Scholar (For standing on the toes of Hobbits. Or something like that)

GIS (for blogging and making class slides)

Vim (because emacs blows)

Python (ease & power)

Biopython (OK, conflict of interest here, since I contributed a bit)

Friendly colleagues (They certainly are!)

Good students (gotta make my lab page).

Goulash for dinner. Can’t stand oven Turkey.

Music. Especially the latest song that is going around in my head:

I didn’t write this one, but I wish I did. I found it on Science after Sunclipse. I guess that a CC license can be safely applied to anonymous chain letters.

Today CBSG continues with its pointers for budding scientists with the second part on serving as a peer reviewer for papers and grants.

Okay, you’ve decided that you are going to reject a manuscript. The naive reviewer might think that it is enough to simply state the reasons for the rejection as clearly and succinctly as possible. But this overlooks a major issue: ensuring that the authors do not know that it is you who rejected the manuscript.

Because the peer review process is anonymous, this may seem like no concern, as long as you extirpate all references to your own work to keep your identity secret. Wrong! You have to keep in mind that no matter how crappy the paper is, the authors are going to be pissed that it is rejected, and they are going to immediately begin wracking their brains to identify referees who might have done the dirty on them. Most will form a list of at least 5 or 6 people that they think are likely to have screwed them. Since most papers are reviewed by no more than 2-3 reviewers, this means you have a good chance of being on the list even if you were NOT the reviewer. Thus, particular pains must be taken to direct the authors ire elsewhere. Several different means to accomplish this are described below:

1. Pretend that you are British. (Note — this does not work well if you actually are British).

Just a few decades ago, it was enough to include a liberal sprinkling of “rathers” and “doubtlesses” throughout the review, and convert all colors to colours, analyze to analyse, polymerize to polymerise, etc. However, the increasing intellectual and cultural cross-pollination brought by the internet has rendered such limited measures ineffective. Thus, you need to be au courant with all the most specific idioms available to the average Brit.

For example, you might want to refer to a poorly run gel as being “dodgy”, “gammy” or “a bit pear-shaped”. Especially effective are slang terms derived from cricket. This is because no self-respecting American knows anything about this sport (indeed, outside the British Commonwealth, cricket is universally reviled as the one sport even more boring than baseball). Here are some cricket-based phrases worked into sentences that you might include in a review. Instead of writing “Some of the data presented by the authors are mutually contradictory” write “The authors seem to have gotten themselves into a bit of a sticky wicket”.

Instead of writing “The documentation of morpholino efficacy by monitoring expression of exogenously provided target rather than the endogenous target is not quite fair” write “Using GFP-ponticulin as a read out for the morpholino effects is not quite cricket”. And, instead of writing “I was chagrined to see that the authors ignored the previous studies by the Jones lab”, write “the failure of the authors to cite the seminal studies of Jones and colleagues hit me for six”.

1B. Pretend that you are an American pretending to be British (Note: this does work if you are British, but does not work if you are American.) The strategy here is similar to #1 above, but instead of being a little bit subtle, you go straight over the top. Thus, instead of writing “I seriously doubt that anyone will believe …”: “Blimey! Blokes would have to be right daft if they were to believe …”

2. Pretend that you are Canadian. This is harder because the only major language difference between Americans and Canadians is that the latter tend to mispronounce words with the short O sound such that they rhyme with newt. Needless to say, this sort of thing is not manifest in written reviews.

However, the canny reviewer can draw on the one or two features of Canadian culture that are unique. Interestingly (in light of the cricket discussion above) most of these revolve around Canadian football. For example, you might allude to a paper not being ready for the Grey Cup yet (a reference to the Canadian equivalent of the Super Bowl), describe an experimental situation as being “3rd and long” (an allusion to the fact that there are only three downs in Canadian football) or argue that the authors need to “bring in a couple more coaches” (referring to the fact that Canadian football teams have 4 head coaches). Cite obscure Canadian journals: “J Can. Med. Assoc.” or “Can. J. Cardio.” No one outside of Canada reads these journals.

3. Pretend that you are German. This is even harder, because even if you know some German, you have to write your review in English for most journals. Be extremely precise and technical. You could also try simply putting the verb at the end of your sentences (as in “The experiments in figures 5 and 6 should repeated be”), however this runs the risk of having yourself labeled not as a German, but as an imbecile or an incarnation of Yoda. Alternatively cite organic chemistry articles from the late 19th and early 20th century that have never been translated into English. Cite German aricles during the 30s and 40s when the rest of Academia was trying its best to ignore German science.

3B. Pretend that you are an American pretending to be German; sprinkle the text with flavorful comments such as “Ach mein lieber!” or “Du spinnst!” Or, if a line of reasoning is particularly awful, “Ist gibt ein Blutbat en der Hoelle!” Stick umlauts on random words, and make liberal use of the eszett. Downside: the editor will conclude you have flipped.

4. Pick one of the people from you own list of 5-6 enemies and pretend to be that person. Heavily cite their work. Reference their obscure conference presentations. Arrogantly suggest that person’s methods in favor of the methods used in the paper, especially where they are clearly inapplicable

One problem that I am facing is convincing colleagues of the utility of an Open Access publication. The usual arguments: more visibility, retention of the right to re-use material, the Greater Good, taxpayer access to taxpayer-funded research and so on don’t stick very well when faced with a $1500-$2500 or higher publication fee. These can be very big expenses if one is working on medium to small size grants, and where publication fees are sought, in part, from the College. Note: in many case the OA fees are not unaffordable; one would not request, in good faith, that the fees be waived or discounted by the publisher. But if one can use this money to pay the summer salary of a couple of more students, go to a conference, or upgrade / repair equipment, then the utility of shelling out this money for a publication seems marginal and pying this money for publication fees seems almost frivolous. In the US, funding agencies require, at most, that publications resulting from their funding would, be available on Pubmed Central within a certain time period and many non-OA publications comply, or they would lose the ability to publish a large chunk of NIH/NSF funded research projects. But doing so is not really timely OA. The bottom line is, if the grant is smaller than R01 size, many applicants would rather budget the expected $8000 of OA fees for the 3-4 year grant period for other line items that have a more palpable payoff, so to speak.

I don’t really have a point to this post, other than raising a problem that seems to be ignored, or marginalized, by many OA advocates. Not everyone operates on large grants. Many lab budgets leave very little room to buy a new laptop, let alone pay for an OA publication (typically the price of two of said laptops).