RIP Fig Newton!

August 31, 2010

The great French cycling champion Laurent Fignon has died at the age of 50 from cancer.
As Velonews notes, he was French National Champion in 1984, took the Milan-SanRemo in 1988 and 1989 and Fleche Wallonne in 1986.
Fignon won the Tour de France in 1983 and 1984 and the Giro de Italia in 1989.

1989 Tdf, final stage (source)

Great rider, very classy.
He also had the honor of participating in one of the very best moments in sport, ever. The final day of the 1989 TdF found Fignon ahead of Greg Lemond by 50 seconds. That year the final day was a 25 km time trial- single riders against the clock, no drafting involved. Watching that stage coverage was certainly the greatest moment in sports that I have ever watched. Lemond beat Fignon by 58 seconds to win the 1989 Tour, as it happens, but Fignon was visibly battling the whole way. It was epic.

Hard and Soft Science

August 30, 2010


Seriously! Who does GMP think she’s fooling?

She puts up a post and a series of polls asking where are all the “hard” STEM bloggers. And writes extensively distinguishing “hard” STEM from “soft” STEM. This latter, apparently constitutes all the bio-medical types.

Leaving aside the hilarious fact that GMP somehow failed to notice all the geo-science, math geeks, computer science nerds, fizzycysts, engineers and assorted other “hard” science bloggers, I note that GMP felt compelled to put up this corrigendum:

Some people dislike the hard STEM/soft STEM distinction as it seems to imply that one of them is hard as in difficult and the other one is not. I most certainly don’t think that and I don’t know anyone who does. I simply use the above distinction as equivalent to a non-bio STEM/bio STEM field distinction, and I think most people do the same. But, as Namezia says below, you can alternatively consider it the physical/biological sciences distinction, although I am not sure where this type of classification leaves math and CS people or people who are engineers.

Heh. heh. HAHAHAHAHAHAHAAH!!! oh, masterful!

Here’s the thing, GMP. Nobody who is in biology, neuroscience, psychology… or (gasp) social sciences….favors this distinction. That in and of itself should tell you how it is used. The only “most people” who use this distinction are so called “hard” STEM people who are, yes, most certainly trying to run down other scientific disciplines as less rigorous, less precise and favored by smarter undergraduates who do not require grade inflation.

So please. Spare us your disingenuous corrections. Just sack up and FWDAOTI like a proper member of the “hard” STEM disciplines! We can take it….

A Finding of Misconduct Notice in the NIH Guide today (NOT-OD-10-130) holds more than the usual interest, Dear Reader.

Elizabeth Goodwin, PhD, University of Wisconsin-Madison: Based on the report of an investigation conducted by the University of Wisconsin-Madison (UW-M) and additional analysis conducted by ORI in its oversight review, the U.S. Public Health Service (PHS) found that Elizabeth Goodwin, PhD, former associate professor of genetics and medical genetics, UW-M, engaged in scientific misconduct while her research was supported by National Institute of General Medical Sciences (NIGMS), National Institutes of Health (NIH), grants R01 GM051836 and R01 GM073183. PHS found that the Respondent engaged in misconduct in science by falsifying and fabricating data that she included in grant applications 2 R01 GM051836-13 and 1 R01 GM073183-01.

The recent Marc Hauser misconduct case has been widely reported to have depended on or been triggered by whistleblowers from within his own lab. Comments in several places have praised the laboratory members for their bravery and willingness to take the inevitable career hit (possibly irrecoverable hit) in the service of correcting the scientific record.

Remember the profile in Science a number of years ago which described a group of trainees who blew the whistle on Elizabeth B. Goodwin?

Chantal Ly, 32, had already waded through 7 years of a Ph.D. program at the University of Wisconsin (UW), Madison. Turning in her mentor, Ly was certain, meant that “something bad was going to happen to the lab.” Another of the six students felt that their adviser, geneticist Elizabeth Goodwin, deserved a second chance and wasn’t certain the university would provide it. A third was unable for weeks to believe Goodwin had done anything wrong and was so distressed by the possibility that she refused to examine available evidence.

Two days before winter break, as the moral compass of all six swung in the same direction, they shared their concerns with a university administrator. In late May, a UW investigation reported data falsification in Goodwin’s past grant applications and raised questions about some of her papers. The case has since been referred to the federal Office of Research Integrity (ORI) in Washington, D.C. Goodwin, maintaining her innocence, resigned from the university at the end of February.

2006. My how time has flown. There was a brief note from someone in the student’s department indicating that other laboratories had helped them to bring at least one paper to press.

Most noteworthy are the young scientists who worked so hard on the paper at early stages of their careers–because they are victims of this unfortunate situation and are doubly victimized if the conclusion the scientific community reaches is that this paper has no merit. Although the scientific results are the most important component of the vindication of the work, I feel strongly that we owe it to our young scientists to draw attention to the verification.

Hmm, that appears to be the last paper published by O. Lakiza.

An update, which I missed, in Science from June of this year gave us a preview of the Notice.

Four years after a group of graduate students faced the agonizing experience of turning in their mentor for apparently falsifying scientific data, she has pleaded guilty to a criminal charge in the case. Elizabeth Goodwin, who was a biologist at the University of Wisconsin (UW), Madison, until resigning in February 2006, admitted “that she included manipulated data” in a grant progress report “to convince reviewers that more scientific progress had been made with her research than was actually the case,”

it also says this about the fate of the trainees.

But the outcome for several students, who were told they had to essentially start over, was unenviable. One, Chantal Ly, had gone through 7 years of graduate school and was told that much of her work was not useable and that she had to start a new project for her Ph.D. (The reason wasn’t necessarily because of falsified data but rather, Ly and the others thought, because Goodwin stuck by results that were questionable.) Along with two of the others, she quit graduate school. Allen moved to a school in Colorado. Just two students chose to stay at UW.

One hopes the outcome is slightly better for the Hauser trainees…

Another interesting thing that popped up in the Hauser affair was the mention of involvement from the US Attorney’s office. Maybe I’m so focused on the misconduct that I usually ignore any mention of legal penalties. But the Science bit on Goodwin emphasizes that the Department of Justice press release (pdf) indicates a $50,000 fine to the HHS has already been issued. Furthermore:

Goodwin will be sentenced on 3 September on the charge of making false statements and faces up to 1 year in jail and a $100,000 fine.

Again, I can’t recall seeing these before but I may just have missed it. I’m wondering if this represents a new stance in these prosecutions, or perhaps if the PIs in question were just so egregious in their misconduct and obstinate in their defense that the BigGuns were brought to bear.

Ethan Siegel has a highly topical observation up over at his blog, Starts with a Bang. It is as simple as this:

But we do not let fear dictate what we are free to do. Syed, Atiyah, Freida, and all the other Muslims I grew up with are no more or less American than any of us, and it is the right of every Muslim-American to expect the exact same freedoms that we have.

Glenn Beck’s little #Whitestock rally for racist #teabaggers at the Lincoln Memorial may have fizzled in terms of numbers but it really should be a wake up call for RealAmericans. You know, the ones who actually believe in the Constitution, the Bill of Rights and the ensuing body of Constitutional jurisprudence. The ones who actually believe in what has always made the United States special, democratic and progressive, rather than longing for the worst of our past.
The theme of the idiots from Glennbeckistan was “Restoring Honor”. What, you might wonder, in the hell is that supposed to mean?
There’s a nice explanation over here at Balloon Juice.

Citation practices

August 28, 2010

A simple question for my Readers about their behavior when drafting a manuscript or grant proposal or creating scientific presentation. How often do you consider, in any way, the identity of the journal in which a finding was published when making your choice?

An ethical scenario was forwarded to the blog today with a request for the wisdom of the crowd. I can but oblige. The query has been lightly modified for anonymity purposed.

A member of my department informed me that a collaborator, another faculty member in our department, gave, without this person’s knowledge or permission, quantitities of unique compounds that synthesized by the lab to an investigator outside our university. That external researcher has recently published work based upon those compounds, and included in that paper an acknowledgement of the collaborator as the source of those materials.

The rest of the note indicates that the person who had synthesized the compounds was not informed by the departmental collaborator or the external investigator. This person only learned about it through a roundabout way that boiled down to “hey, have you seen this paper about this stuff you are working with?”
This is entirely simple, as depicted. Nowadays it is nearly impossible that an investigator would not know that anything sent to a collaborator external to the University requires a Materials Transfer Agreement. Everything. Compounds, reagents, mice, tissues. Everything.
Now true, many times people sort of overlook this for the small stuff. Or overlook it until something actually works out and it looks like a publication is ahead. But c’mon. How can you not know?
Furthermore, everyone knows that you don’t get to screw a collaborator and doing so in your own department is incredibly stupid. It will come out and you will look like a jerk. Particularly when you have failed to file the right MTA paperwork. And, depending on your University policies, you may be in a world of local hurt for letting intellectual property that belongs (formally speaking) to the University into a competing institution’s hands without protecting the intellectual property rights.
(Look, I don’t make the rules and I actually think they are bad for science. But the roots of this go back a long, long ways. Universities have a structural stance toward intellectual property that is highly corporate.)
My view is that the fault here is almost exclusively with the in-house collaborating investigator because s/he could have told the external collaborator that it was all coolio and conveniently neglected to mention that a third lab had actually made the compound in question. Maybe a *slight* possibility that the external collaborator had proceeded to publication without appropriate notification of the in-house collaborator who provided the (third lab’s) compound.
What do you think DearReader? Straightforward? or am I missing something?

We pay some degree of special attention to the doings of the University of California system because it is so huge when it comes to US NIH-funded biomedical research. Policies that exist at the UC campuses affect a large percentage of our target audience and for that matter, many of our colleagues and friends. There is also an assumption on my part that the very size of the UC means that it has an influential effect on policies across the US and maybe even worldwide.

The UAW recently announced that they had reached an agreement with the University of California system (provost confirmation) and about ~6,500 postdoctoral researchers/fellows represented by the UAW.

The UAW and the University of California today jointly announced that UC postdoctoral scholars voted to ratify their first union contract. The union announced that postdocs approved the contract by an overwhelming vote of 2588 to 121, or 96 percent in favor, in balloting that concluded Aug. 11. The postdocs’ union, Postdoctoral Researchers Organize/UAW, and UC reached a tentative agreement on July 31.

No word on whether hilarious Congressional threats to investigate UC uses of federal money had any effect on the process.

An overview of the agreement can be found in this pdf.

One main outcome of this initial agreement is to put the UC postdocs on the NIH NRSA salary scale as a default minimum ($37,740 / yr for new postdocs with less than a year’s experience at present). It seems to be phased in for existing postdocs and in immediate effect for any new hires.

There are also some points about benefits but since I’m not particularly familiar with existing UC postdoc benefit policies I’m not going to comment on that.

I’m viewing this settlement/agreement as a good first step. I’m on record as saying I favor the NIH / NRSA scale as a minimum for all postdoctoral fellows so this more or less ratifies my position.


August 25, 2010

Since there are several traffic meters running here at DM on Scientopia, I was curious as to how the GoogleAnalytics, Sitemeter and WordPress in house statistics compare. Read the rest of this entry »

A fascinating vignette into the glorious future of online commenting on papers was passed along to me by a reader.

Laurén and colleagues published a paper in Nature in February 2009 describing a phenomenon related to understanding the process of Alzheimer’s disease and a possible role for prion. From the Abstract we can glean the essentials.

Here we identify the cellular prion protein (PrPC) as an amyloid-β-oligomer receptor by expression cloning. Amyloid-β oligomers bind with nanomolar affinity to PrPC, but the interaction does not require the infectious PrPSc conformation. Synaptic responsiveness in hippocampal slices from young adult PrP null mice is normal, but the amyloid-β oligomer blockade of long-term potentiation is absent. Anti-PrP antibodies prevent amyloid-β-oligomer binding to PrPC and rescue synaptic plasticity in hippocampal slices from oligomeric amyloid-β. Thus, PrPC is a mediator of amyloid-β-oligomer-induced synaptic dysfunction, and PrPC-specific pharmaceuticals may have therapeutic potential for Alzheimer’s disease.

This is grand stuff. Treatment for AD continues to be a holding/rearguard action to slow progression and maintain cognitive function as long as possible. Our treatments are not so great, even at that limited role. So any new therapeutic targets, particularly ones that interfere with the pathological processes (as opposed to treating the symptoms of such unrelenting processes), are a BigDeal (or BFD as the US Vice President would have it).

However, a “brief communication arising” which has just been published in Nature says “uh-uh, not so fast”. Kessel et al (2010) conclude the following from their results:

Laurén et al. suggested that binding between oligomeric amyloid-β … and the cellular prion protein (PrPC)8 is necessary for synaptic perturbations. Here we show that PrPC is not required for amyloid-β-induced synaptic depression, reduction in spine density, or blockade of LTP; our results indicate that amyloid-β-mediated synaptic defects do not require PrPc.

Laurén et al provided a response, in Nature, to possibly explain the different outcomes.

Great, right? Big new idea/finding, some people jump on it and either confirm or question the results. These get published, and a dialog results. Happy, happy, amirite?

Well, somebody isn’t too thrilled and has offered a comment on the Kessels et al paper. A. Aguzzi congratulated the group on their study and then points out that they scooped him. Not by getting their first in offering a counterpoint to Laurén et al

on May 19th, 2009, I have reported my lab’s finding indicating that the Prnp genotype (Prnp+/+ vs +/-, /, and overexpressors) exerts no influence on LTP degradation in APPPS1 transgenic mice at the CDD conference in Rome.

but by being the first to be able to publish a counterpoint in Nature.

Marie-Therese Heemels, Nature editor, attended the talk and asked me (during the lunch break) to send her my findings to be considered for publication as ?brief matters arising? in Nature. (3) Following Dr. Heemels? request, we rapidly submitted our paper (Calella et al.). The paper was rejected on August 21, 2009 despite largely positive referees? comments (which I shall be happy to post separately if the blog editor allows for sufficient space). (4) because of the favorable, encouraging comments we opted to perform additional experimentation and to resubmit a further version of our paper, which was again rejected on May 5th, 2010 despite additional commendatory comments by the referees.

Our manuscript was then submitted to EMBO Molecular Medicine, where it received a rather enthusiastic reception and was finally published on July 21st, 2010

Yowsa! Now, I will admit right up front that I am unable to reasonably judge the quality of the papers of Kessels et al and of A. Aguzzi (Calella et al, 2010; EMBO Mol Med) so as to be able to determine why the one was worthy of Nature publication (as correspondence arising) and the other was not. Nor am I able to determine if one is a “better” criticism, counterpoint or elucidation of Laurén et al. But one thing does seem obvious to me. If the publication of Kessels et al in Nature was driven mostly by the mere fact it questioned or pared back the claims of Laurén et al then it would seem that Aguzzi’s work was similarly meritorious on this criterion.

I will be fascinated to see if Nature responds to this in any way, including deleting the comment. Clearly they are going to have to take the view that Aguzzi’s description of the reviews as largely positive and commendatory is a bit inaccurate. Right? Because beyond the scientific view of the reviewers, the only possible role for nonscientific professional editors is to judge hotness, relevance, impact and all that. And clearly since they published Kessels et al (which Nature received 22 Feb 2010 and accepted 01 Apr 2010), they think critique of Laurén et al is sufficient justification. If Aguzzi’s contention that Nature rejected his second submission 05 May 2010 is valid, obviously the journal had both of these criticisms of Laurén et al in hand at the same time and chose to publish one but not the other.

I’d be interested to hear their thinking on that one.

I have a trainee running a study in which she is examining the effects of methamphetamine on Bunny Hopping using the established open field to hedgerow assay. The primary dependent variable is escape latency from stimulus onset to crossing the plane of the hedge.

She is examining the effects of a locomotor stimulant dose of methamphetamine derived from her pilot dose-response study versus vehicle in groups of Bunnies which have been trained for six weeks in our BunnyConditioning Model and age matched sedentary Bunnies. (The conditioning training consists of various sprint, long run, horizonal hop and vertical leap modules.)

So we have four groups of Bunnies as follows:
1. Conditioned, Vehicle
2. Conditioned, Meth
3. Sedentary, Vehicle
4. Sedentry, Meth

The trainee is actually a collaborating trainee and so these data involve the analytic input of multiple PIs in addition to the trainee’s opinio. We are having a slight disagreement over the proper analysis technique so I thought I would turn to the brilliant DM readers.

Our great blog friend Abel Pharmboy has a new home for one of my (and yours, Dear Reader, and yours) favorite blogs.
He has joined the stable of blogs in the Chemical and Engineering News site for blogging, CENtral Science.
Congrats to Abel and congrats to CENtral Science.

Our great blog friend Abel Pharmboy has a new home for one of my (and yours, Dear Reader, and yours) favorite blogs.

He has joined the stable of blogs in the Chemical and Engineering News site for blogging, CENtral Science.

Congrats to Abel and congrats to CENtral Science.

One of the more salient issues to me in the wake of’s PepsiBlog fiasco was the moderate schism it revealed between science bloggers (lower case) who self-identify as journalists and those who self-identify as scientists.

The uproar was driven in large part by the journalist types screaming about traditional journalist ethics and the supposed hard line that is drawn between the editorial and business sides of a media property.

My response to this was that as a profession and job sector this is nothing more than a convenient fiction. Recent history is rife with cases in which financial considerations clearly shaded, moved, biased or otherwise influenced content. Look, I get it. There are many cases in which the alleged Chinese wall works. Cases in which newsmedia entities published stories clearly against their own financial interest. And yes, there is a lot of print and J-school professor hot air wasted on devoted to the ethical line.

But at best, these forces for ethical hard lines are losing. Better bet is that the profession is just irretrievably conflicted and we are just going to have to muddle along.

But what really disturbed me was the eagerness of some otherwise respectable scientist-bloggers to start claiming that they (meaning “we) are quasi journalists. Claiming that they (and let’s be honest, “we”) actually should lean toward and adopt the supposed professional ethics of journalism.

An exchange I’ve been having on the Twitts today illustrates precisely why science bloggers should not only not adopt a journalist stance but should continue to disparage, correct and otherwise dissect journalistic “coverage” of a science-related story.

The news of the day is the judicial decision to block an executive order issued by President Obama to expand the number of stem cell lines which could be used in federally funded research. The NYT bit does a good job of summarizing the context.

For years, private financing has been used to create embryonic stem cell lines, mostly from discarded embryos from fertility clinics. The process destroys the embryos. President Bush agreed to finance embryonic stem cell research, but limited federally financed research to 21 cell lines already in existence by 2001.

Under the Obama administration, private money was still needed to obtain the embryonic stem cells, but federal money could be used to conduct research on hundreds more stem cell lines, as long as donors of embryos signed consent forms and complied with other rules.

See? This is by no means a complicated story. The grand hoopla over the original decision by President G. W. Bush to permit federal funding of research on a limited set of stem cell lines was a HUGE media storm. Really, even most lay people should be up to speed on the issues and rapidly appreciate the scope of the current judicial ruling.

And yet some respectable science blogger went ahead and Twitted this:

Yikes! Judge halts stem cell research

The link goes to the NYT piece, btw. Nice headline from @davemunger, right? A journalistic headline. The kind of headline that the typical author/journalist, when called on it’s inaccuracy, tends to (wink, wink) blame on the editor. “Not my headline (shrug)” they will say in faux apology.

Irritated by this inaccurate sensationalism which clearly implies to the naive reader that this judicial act actually blocked all stem cell research, I responded to Dave with:

halts Obma’s *expansion* of permitted use of *federal funds* RT: @davemunger: Yikes! Judge halts stem cell research

He came back with:

@drugmonkeyblog Sure, but not quite as exciting when you put it that way. The implications of the move are still drastic

Quite a tell, isn’t it? Typical journalistic approach and why we need scientist-bloggers to oppose this sort of inaccurate communication. Sensationalism that draws the eye is “exciting”. That is the justification. So what if the viewer/reader who just glances at headlines walks away with a totally inaccurate perception? He gave the link to the story, right? No fault of his if people don’t read it and immediately grasp the nuance…

Yeah, well I object to this journalist tradition/ethic.

This is what I absolutely detest about journalism, dude. Just say no to inaccurate hypage RT: @davemunger: not quite as exciting..

What I object to is this notion that the closest approximation of the truth is optional. Inconvenient. That the business exists to get attention and readers, no matter the cost to the accurate transfer of the best possible information. It is, quite simply, offensive to my professional sensibilities. Yes, we have some movements toward hype in scientific publication but this doesn’t mean I agree with it. In point of fact I draw parallels between journalism and GlamourMag science…and Dave Munger stepped right into the steaming pile of why this is so.

@drugmonkeyblog What is inaccurate about my statement?


the judge did not “halt stem cell research” dude. He reversed the *expansion* of what could happen with fed funds.


.@davemunger return to the Bush scenario in which fed funds could be used for *some* stem cell res. private/state funds used despite fed


@drugmonkeyblog TFA says It’s actually unclear whether the ruling reverses back to Bush’s compromise, or even rolls that back as well

Ahh, the typical journalist dodge-and-weave when called out on inaccurate reporting. No, this is not some discussion of he said / she said and what might possibly be the downstream implication. I might buy it if you’d started your comments with this or refined them. It is intellectually dishonest to claim you intended your initial Twitt to lead to this particular nuance. Bullshit. Sure, when backed into a corner you can find some loophole to try to weasel out of. Just like the next one…


@drugmonkeyblog And he did “halt stem cell research.” He may not have halted *all* stem cell research, but I didn’t say that.

HAHAHAHA! Classic journalism. Use an unmodified and bold statement. When called out for the inaccuracy of what you know damn well was going to be the overwhelmingly frequent perception of the statement, retrench to Clintonian parsing of syntax. “I didn’t say ‘all’, dude, not my fault if people inferred that from my unmodified statement. It could have easily meant ‘judge halts one experiment involving stem cells in one obscure lab’! HAHA!”

Bullshit. You should be ashamed of yourself when you find yourself in this ridiculous attempt at a defense.

Unless you want to, you know, be a journalist. Then I guess it is totes okay to create whatever inaccurate impression you want via selective quoting, selective phrasing and other tricks.

Pfah. I spit on this journalist tradition. This is why it is an absolute mistake for people who identify as science bloggers to move toward being “more like journalists”.

Their crappy practices are the very reason that we bother to blog about science!

How can you have forgotten this?

Remember James Sherley?

August 24, 2010

Remember the case of James Sherley? Tenure denial fight featuring all kinds of unpleasantness. Claims that his program was crippled by lack of space and other resources. Hints of politico-religious stuff involving the stem cell field he worked in?

Well juniorprof noticed something interesting about the recent lawsuit against the Obama administration’s stance on stem cells.

Data w000tang!!!

August 24, 2010

You know those weeks where every day the data keep getting more and more exciting? Yeah, I’m having one of those times three…w00t!!!!