Websearch your CongressCritter and navigate to the email / reply form. Then give him or her an earful (eyeful) about the attempt by Reps Maloney and Issa to discontinue the requirement for public funded science to be made publicly available (by the Omnibus Appropriation passed in Mar 2009).

Please. Put your Critter on alert that this is bad legislation that is bad for taxpayers. Additional detail is after the jump. Read the rest of this entry »

Truth Vigilante

January 12, 2012

A recent editorial by the NYT Public Editor is drawing a lot of fire on the Twitts and blogs.

He asks if journalists should be “Truth Vigilantes” and places it in the context of verifying political assertions. In place of the usual cowardly he-said/she-said stenography that has almost entirely replaced the sadly lost profession of journalism.

Pfaah! I spit on stenographic media.

I invite you, dear reader, to relate your own moments of clarity where the stenographic replacement became crystal clear to you.

For me it was when then President George H. W. Bush came out of the back door of his Kennebunkport retreat and told the media that the best possible, most qualified person to fill a vacant seat on the Supreme Court of the united States was Clarence Thomas. His blatant falsehood went entirely unchallenged.

Eventually, I was able to close my mouth.

Hott Shoe of the Week

January 11, 2012

It’s gotten a little stale around here muffins, so it’s time for a little diversification in the blogging. Welcome to a new feature on fashion. And we’ll start off with this lovely little number. Read the rest of this entry »

Remember the Ginther et al. (2011) report on NIH Grant awards to Principal Investigators sorted by race and ethnicity? The one that showed African-American PIs suffered worse success rates even when controlling for a number of obvious potential contributing factors?

A new Notice (NIH-OD-12-031) seeks input on diversity in the NIH system.

The critical background:

The Advisory Committee to the NIH Director (ACD) has established a working group to examine diversity in the biomedical research workforce (see http://acd.od.nih.gov/DBR.asp for charge and roster) and provide concrete recommendations to the ACD and the NIH Director on ways to enhance diversity throughout the various research career stages, particularly with regard to underrepresented minorities, persons with disabilities, and persons from disadvantaged backgrounds. The Working Group on Diversity in the Biomedical Research Workforce has considered the evidence presented in “Race, Ethnicity, and NIH Research Awards” published in the August 2011 edition of Science and additional data provided by the NIH. This data shows that R01 applications from Black or African American PhD applicants between 2000 and 2006 did significantly worse than those applications from White applicants, even after controlling for observable characteristics. The article and a corresponding policy piece by NIH Director Francis Collins and NIH Deputy Director Lawrence Tabak can be found at http://www.sciencemag.org/hottopics/race-nihfunding/.

I offered solutions before, after expressing skepticism about the Advisory Panel approach.

Now it is time for all of us to offer our insight and possible solutions (or reasons why this is a non problem) to the Working Group.

UPDATE: The CPDD Blog review of the recent ACNP meeting notes that a question was asked about this situation in a session featuring a number of NIH IC representatives. Insel, NIMH Director, polled the crowd as to how many people knew what the Ginther report found. There were probably less than 5 hands raised that I could see. I’m not great at room estimates but there were easily over a hundred folks sitting there, probably less than 200. Folks who bothered to attend a session from NIH representatives so likely people with more than average interest in NIH matters.

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For your convenience, a few links from last August when this arose:

Sally Rockey, Office of Extramural Research
Tom Insel, NIMH
Updated:
Bashir
Chronicle of Higher Ed
National Public Radio

SciCurious has a post up today, rambling on about some apparent bugaboo of the trainee set. There’s a survey and everything so go read it.

What I take away from this is that there is some aspect within the culture of science in which there are some bragging rights to be obtained on the basis of how many papers you read. “Read“.

This is asinine.

Some commenter named ‘brian’ irritated me with:

I disagree with these definitions of reading. An abstract and figures are in no way reading a paper. To truly grasp what authors are trying to say you need to have a working knowledge of the entire article, intros and discussions are critical since bad assumptions and wrong interpretations are the most likely errors in any paper. Abstract and figures and a quick skim of the discussion are a cop out way of upping your read list.

This comment seems to personify that subject which is SciCurious original motivation. People in science who are really, really focused on how many articles they read and the nature of the “reading” of such articles.

Bollocks.

Science is about apprehending what has and has not been demonstrated on a particular subject. About understanding what has been supported by evidence, what may be provisionally inferred and what has been provisionally (or repeatedly) rejected. As a practicing scientist, this understanding permits us to design better or more interesting experiments, make better or more interesting interpretations of our data and set better or more interesting provisional inferences. There is no score card for “how many papers I have read”. There is only a scorecard for how great your science chops are.

It therefore follows that the nature of reading a scientific paper may vary tremendously in the service of the real goal. The nature of this reading may not be the same across different scientists (who are interested in different things) or even within scientist across time. Some details in a paper may be irrelevant to one person, but highly pertinent to another. Details of methodology (who gives a crap what kind of rat they used…a rat’s a rat….until I happen to be interested in a strain difference, that is) or of outcome (quarter-log, half-log shift in the dose-response function, who cares? we’ll just up the starting point for the clinical, titrated dose.) and especially of the interpretation (dude, I don’t care one bit whether this drug is likely to be abused recreationally, it’s just a good probe for the endogenous system…) will vary.

For the trainees, I sympathize.

I understand, I think, how you come to this misunderstanding of paper count as a measure in and of itself of scientific acumen. It is because over the course of a scientist’s lifetime, she reads a hella lot of papers and draws together a hella lot of stories. So for the noob(ier) scientists, the scope of understanding of the most impressive and vigorous scientists seems a little daunting. Intimidating. Because you are looking at what seems an unbounded ability to reel off citations of relevant papers in the service of some point the Big Swinging type is making. But this is natural accumulation. It builds up over time.

And here’s a little hint. The brilliant types with seemingly unbounded ability to reel off citations don’t “read” all the literature in the way brian, above, would have it either. They read in a variable fashion.

Sometimes it is just a glance at Figure 2. Sometimes it is the deepest of deep readings and pondering the paper over several days that is required. Sometimes it is a series of re-reads over months or years. Always, in service of the real goal which is to understand how the data presented in a paper fit into a scientific story that is of interest.

Never in service of bragging to one’s peers about how many papers one has “read’ this month.

I mean Jesus, do you even listen to yourselves? Doesn’t that sound insane?

There is another reason for the quick glance-at-the-Figures level of reading which trainees find incomprehensible because it is so damn insulting. I really don’t care what you think about your data. I care what I think about your data.

This is a horrible realization for trainees that spend many, many long hours crafting their rationale and interpretation in the Discussion section. Who have also spent many long hours arguing with their PI and lab mates (and peer reviewers) about the design of studies, which ones will create the story, what can be included in a manuscript, etc. You have sweated bullets over this! And all the reader wants is to see the Figure? AAAAAaaaaaauuuggggghh!

Yeah, you need to get over that.

A new post by Erick Schonfeld up at techcrunch points to some data from online comment management system DISQUS.

The take home as interpreted by Schonfeld:

According to the data, 61 percent of all Disqus comments are made via pseudonyms, versus 35 percent anonymous and 4 percent using real names (i.e. Facebook). People with pseudonyms also comment 6.5 times more than those who comment anonymously and 4.7 times more than commenters who use real names.

Okay, but what about the trolls? Disqus maintains that only does allowing pseudonyms produce more comments, but the quality of the comments is also better, as measured by likes and replies. Disqus maintains that 61 percent of pseudonymous comments on its system are positive in that regard, versus only 34 percent positive for anonymous comments (I knew it!) and 51 percent positive for comments made using real names. People who use pseudonyms post better comments on Disqus. Their comments are liked more and generate more discussion.

There you have it folks. Data to prove what I’ve maintained nearly constantly since starting a pseudonymous blog that allows anonymous commentary. And, more specifically, since I’ve started pointing out that online venues that 1) overtly desire vigorous commentary and 2) require real name registration are shooting themselves in the foot….after tying one hand behind their back.

A recent blogpost from NIMH Director (and Acting NCATS Director) Tom Insel details the grim future for private sector development of drugs for the brain and behavior disorders.

But change is coming from another direction as well, especially for psychiatric medications. Over the past year, several companies, including Astra Zeneca, Glaxo-Smith-Kline, Sanofi Aventis, and recently Novartis, have announced either a reduction or a re-direction of their programs in psychiatric medication R&D. Some of these companies (such as Novartis) are shifting from clinical trials to focus more on the early phases of medication development where they feel they can identify better targets for treating mental disorders. Others are shifting from psychiatry to oncology and immunology, which are viewed by some as lower risk.

There are multiple explanations for these changes. For instance, many of the blockbuster psychiatric medications are now available in inexpensive generic form. In addition, there are few validated new molecular targets (like the dopamine receptor) for mental disorders. Moreover, new compounds have been more likely to fail in psychiatry compared to other areas of medicine. Studying the brain and the mind has proven to be much more difficult than the liver and the heart. Most experts feel the science of mental disorders lags behind other areas of medicine. The absence of biomarkers, the lack of valid diagnostic categories, and our limited understanding of the biology of these illnesses make targeted medication development especially difficult for mental disorders.

As I may have mentioned already, this sort of change in the development “system*” gives me a better reason to agree with the creation of NCATS and the earlier noises about the NIH taking a more active role in therapy development. There are lots of indications that don’t receive enough attention because there is no route to sufficient profit. Drug abuse is one of those indications. Part of the reason we aren’t more advanced in pharmacotherapy for substance abuse is on us, the basic science folks. Sure. But a big part is also on private industry which never saw where the paycheck was going to come from. So there was never much enthusiasm for pursuing anti-substance abuse programs. No program, no drugs. Remember, estimates run some 10-20,000 compounds evaluated in a drug development pipeline to arrive at each approved medication.

I don’t believe the NIH can improve this by being smarter, that is a foolish conceit of many. But not having to seek blockbuster returns does change the calculus for what indications are worthy of serious drug development effort.

And that would be a GoodThing.
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*such as it is

PIs on screen

January 5, 2012

The Professor guy in Congo really didn’t seem too broken up about his postdoc getting ripped apart by beasts. People complain about maniacal slave driver bosses like MooMing Poo and Scott Kern but c’mon…could be worse.

RIP Jon Driver (1962-2011)

January 3, 2012

I have just discovered a blog which notes the untimely passing of Professor Jon Driver. Driver was a central figure in cognitive psychology for much of my career and has contributed many papers investigating the way the human brain pays attention to things and fails to pay attention to other things. His work was mostly concerned with the processing of visual information and included work in both neurologically damaged patient groups and normal, healthy control subjects.

The blog indicates that he passed away unexpectedly.

Jon Driver died suddenly on 28th November 2011. Jon was a wonderful individual; a loving son, husband and father; and an irreplaceable friend and colleague.

This is a place for everyone who knew Jon to share our memories of him and through this to help celebrate his life.

If you would like to add a description of your memories of Jon to this blog please contact g.rees@ucl.ac.uk with the text you would like posted. We welcome any contribution, from short snippets to longer pieces. Please bear in mind this is a place to remember Jon and to help celebrate his life.

He will be missed.

I might be a plagiarist…

January 3, 2012

When it comes to performance enhancing drugs (PEDs) in sports, aka doping, I’m a confirmed cynic. Each case of a later life confession for prior doping habits, when the person wasn’t ever caught by the system, just reinforces cynical suspicion about other athletes. Suspicions based on mostly circumstantial evidence in the absence of a confession.

Marion Jones...before and after


The circumstantial evidence will depend on the sport….in some sports it is the player’s amazing physical transformation. In others it is the amazing, short-duration transition from from a relatively pedestrian* level of performance to the top of the heap. In other cases it may be sustaining top level amazing performance for a longer duration of time than seems reasonable. Additional grist is added via comparing athletes to those who are confessed dopers and concluding that if Manny, Moe and Sarah doped, those who were competitive with them likely doped too.

Common Man has been cracking me up lately. For those that don’t follow @commnman, he styles himself as some sort of baseball pundit. Big baseball fan. Seems like a decent dude, other than this clear character deficit (no?)

Common has been holding his fellow baseball writers’ feet to the fire over cynical suspicion about suspected PED use in baseball, specifically related to the Hall of Fame voting for one Jeff Bagwell.

We asked you to find us more writers who believed, without evidence, that Jeff Bagwell was too “suspicous” to have naturally played baseball so well, knowing that it would be equally fair for all of us to collectively suspect those writers of being dirty, stinking plagiarists based on the same lack of evidence they use to punish Jeff Bagwell for his big arms and for the era in which he played.

The original complaint:

The point of this exercise is obviously not that we should hang the lot of them. It’s that trying to play this game of who played with whom and asking whether or not that should make us suspicious is a stupid one, especially when, by The Common Man’s count, just 42 clubs out of 408 436 possible teams (bah, I included from 1992-2006, just 10.3 9.6% of clubs, were devoid of players who have thusfar been accused of PED use. It touched every single franchise in Major League Baseball, and presumably every single player.

By the ridiculous standards used by many of baseball’s HOF voters, no one is enough above suspicion to warrant consideration. Just stop everyone. Stop. It was an era of rampant cheating in which relatively few players actually got caught. We cannot ignore an entire era of baseball history, and we cannot delegitimize the Hall of Fame by refusing to recognize some of the greatest players of all time for nothing other than our own suspicious natures.

If you want to see the raw data from TCM’s study, you’re welcome to click here. The second sheet on that spreadsheet will give you the team-by-team breakdowns.

Mark McGwire, before and after ?


And then the shit got totally, hilariously funny with

Plagiarist who (might) write among us

This led The Common Man to the realization that, if it was fair for writers to penalize Bagwell* because of their own suspicions that they were apparently too busy to investigate during Bagwell’s playing career, it was equally fair to suspect them of being plagiarists.** After all, sports reporters tend to write an awful lot, and so many of them seem to be writing about the same topics and coming to the exact same conclusions. Are we really so naïve as to think that they are doing this naturally?

These plagiarists, who violate the public trust and unfairly compete against their fellow writers on a daily basis, need to be called to account in a public forum. And thanks to our friend LeoKitty of The Girl Who Loved Andy Pettitte and her Hall of Fame voting tracker, TCM was able to find several writers who seem incredibly suspicious.*** Until they are able to definitively prove otherwise, the following writers are hereby suspected plagiarists:

Which of course put some people into a terrible snit, which I am inferring from the content of this:

Every so often, I get an objection in the comments or on Twitter about my use of a pseudonym, especially when I use this forum to criticize others who are not similarly pseudonymous. This happened to me the other day, in fact. It’s an entirely reasonable and justified objection to raise, and my reasons for remaining pseudonymous are not easily explained in 140 characters or less. So I thought it would be appropriate to have a place to which I can point people to explain my decision. If you are not at all interested in why I choose to write as The Common Man…well…feel free to skip this post.

You will recognize the above topic as being of interest to me. I am fascinated, as always, that people who find themselves on the pointed end of sharp criticism feel the need to go after the person who is criticizing them, rather than the critique itself. Especially when the criticism is so. damn. obviously. correct.

Which brings it back to me. I’m totally guilty of the charge Common is making. Overly suspicious of athletes without direct evidence of PED use. An unshakeable belief that despite the limitations of circumstantial evidence analysis, dammit, those dudes clearly doped. So I’d better take it in good humour if someone like Common called me out for it.

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*don’t get me wrong, anyone who makes the professional ranks, olympic or other serious international “amateur” level is an amazing athlete. But not everyone can be a superstar.

ah, a tragic conundrum emerges from the thickets.

Carl Zimmer (yeah, science writer! blogger! our dude! woot.) has published a new profile of Neil deGrasse Tyson (popular science! woot! one of the bigger media presences on science right now, yay!!!).

Then @MiriamGoldste noticed that there was some objecting going on in commentary to her Gplus (which nobody sees cause nobody is on the geeeplus). And she asked,

Should respectable authors publish in Playboy? http://bit.ly/w3ARtA

My kneejerk response was “No.”. No, I do not think that respectable authors should participate in the continue oppression of women that is instantiated by the laddie-mag, porn-lite, “lifestyle magazine” or whatever you care to call Playboy. The magazine that, articles or not, sells based on youngish women appearing naked and air-brushed and photoshopped to a fair-thee-well.

In both the gplus discussion and in a Twittply to me, @miriamgoldste seems to be pursuing the thesis that Playboy itself is so irrelevant and dinky at this point, not to mention kinda tame, compared with internet pR0n and other sources, we should not be getting our knickers in a twist over this.

So I’m conflicted. I tend to agree that Playboy is tame stuff, the print magazine (even pR0n!) is dying a slow, inevitable death and as far as such venues go…it is semi respectable. However, given that it is the granddaddy of mainstream legitimized pornography, we also have to appreciate the role that this magazine has played in normalizing the pornification of culture. Also the resulting impact on women.

Which ain’t good.

Despite the way I sound, I’m not particularly prudish on this issue. One ideal of Playboy, that of releasing all of us from puritanical restrictions on our sexual beings, is not half bad. I’m down with that. Problem is, the impact seems not to have been as good as it could have been. We’re still fighting the whole woman-expresses-the-sexxah-and-was-asking-for-a-rapin’ thing. And the grown ass men who are fixated on a single age-range of extremely young women as their only appropriate sex target. Not to mention lots of women trying to fit themselves into the 1% plus cosmetic surgery body type/image with a lot of resulting disorders of affect, behavior and eventually metabolism and physiology.

Not being a social scientist, I’m uncertain as to the direction of causality…so I turn to you, Dear Reader. Is our revered scribe off science Carl Zimmer off the reservation on this one? Should he have thought twice?

Should we recognize that free lance writers have to take their pay where they can?

Should we be happy for the opportunity to present something, anything about science to the Playboy audience?