A query came in through the email box:

Do you use ELNs in your lab? Is that something that you think would make a useful blog post? I haven’t found much elsewhere in the blogosphere about ELNs. Maybe you will find this to be a shining example of why you have stuck with paper and pen.

I don’t use one so I’m turning this over to you folks. Any recommendations for your fellow Reader?


The Legislative Mandates have been issued for FY 2014.

The intent of this Notice is to provide information on the following statutory provisions that limit the use of funds on NIH grant, cooperative agreement, and contract awards for FY2014.

It contains the usual familiar stuff, of pointed interest is the prohibition against using grant funds to promote the legalization of Schedule I drugs and the one that prohibits any lobbing of the government. With respect to the Schedule I drugs issue, for a certain segment of my audience, I remind you of the critical exception:

(8) Limitation on Use of Funds for Promotion of Legalization of Controlled Substances (Section 509)
“(a) None of the funds made available in this Act may be used for any activity that promotes the legalization of any drug or other substance included in schedule I of the schedules of controlled substances established under section 202 of the Controlled Substances Act except for normal and recognized executive-congressional communications. (b)The limitation in subsection (a) shall not apply when there is significant medical evidence of a therapeutic advantage to the use of such drug or other substance or that federally sponsored clinical trials are being conducted to determine therapeutic advantage.”

I wouldn’t like to find out the hard way but I would presume this means that research into the medical benefits of marijuana, THC and/or other cannabinoid compounds are just fine. I seem to recall reading more than one paper listing NIH support that might be viewed in this light.

What I found more fascinating was a little clause that I had not previously noticed in the anti-lobbying section.

(3) Anti-Lobbying (Section 503)

(c) The prohibitions in subsections (a) and (b) shall include any activity to advocate or promote any proposed, pending or future Federal, State or local tax increase, or any proposed, pending, or future requirement or restriction on any legal consumer product, including its sale or marketing, including but not limited to the advocacy or promotion of gun control.”

there is also another stand-alone section in case you didn’t get the point:

(2) Gun Control (Section 217)
“None of the funds made available in this title may be used, in whole or in part, to advocate or promote gun control.”

I was sufficiently curious to go back through the years and found out that this language did not appear in the Notice for FY 2011 and was inserted for FY 2012. This was part of the “FY 2012 the Consolidated Appropriations Act, 2012 (Public Law 112-74) signed into law on December 23, 2011“. I didn’t bother to go back through the legislative history and try to figure out when the gun control part was added but it looks like something similar that affected the CDC appropriation was put into place in 1996.

So I guess we should have expected the anti-gun-control forces to get around to it eventually?

PubMed Commons has finally incorporated a comment feature.

NCBI has released a pilot version of a new service in PubMed that allows researchers to post comments on individual PubMed abstracts. Called PubMed Commons, this service is an initiative of the NIH leadership in response to repeated requests by the scientific community for such a forum to be part of PubMed. We hope that PubMed Commons will leverage the social power of the internet to encourage constructive criticism and high quality discussions of scientific issues that will both enhance understanding and provide new avenues of collaboration within the community.

This is described as being in beta test version and for now is only open to authors of articles already listed in PubMed, so far as I can tell.

Perhaps not as Open as some would wish but it is a pretty good start.

I cannot WAIT to see how this shakes out.

The Open-Everything, RetractionWatch, ReplicationEleventy, PeerReviewFailz, etc acolytes of various strains would have us believe that this is the way to save all of science.

This step of PubMed brings the online commenting to the best place, i.e., where everyone searches out the papers, instead of the commercially beneficial place. It will link, I presume, the commentary to the openly-available PMC version once the 12 month embargo elapses for each paper. All in all, a good place for this to occur.

I will be eager to see if there is any adoption of commenting, to see the type of comments that are offered and to assess whether certain kinds of papers get more commentary than do others. All and all this is going to be a neat little experiment for the conduct-of-science geeks to observe.

I recommend you sign up as soon as possible. I’m sure the devout and TrueBelievers would beg you to make a comment on a paper yourself so, sure, go and comment on some paper.

You can search out commented papers with this string, apparently.

In case you are interested in seeing what sorts of comments are being made.

On showing the data

September 5, 2013

If I could boil things down to my most fundamental criticism of the highly competitive chase for the “get” of a very high Impact Factor journal acceptance in science, it is the inefficiency.

GlamourDouchery of this type is an inefficient way to do science.

This is because of several factors related to the fundamental fact that if the science you conduct isn’t published it may as well never have happened.

Science is an incremental business, ever built upon the foundations and structures created by those who came before. And built in sometimes friendly, sometimes uneasy collaboration with peers. No science stands alone.

Science these days is also a very large enterprise with many, many thousands of people beavering away at various topics. It is nearly impossible to think of a research program or project that doesn’t benefit by the existence of peer labs doing somewhat-related work.

Consequently, it is a near truism that all science benefits from the quickest and comprehensive knowledge of what other folks are doing.

The “get” of an extremely high Impact Factor Journal article acceptance requires that the authors, editors and reviewers temporarily suspend disbelief and engage in the mass fantasy that this is not the case. The participants engage in the fantasy that this work under consideration is the first and best and highly original. That it builds so fundamentally different an edifice that the vast majority of the credit adheres to the authors and not to any part of the edifice of science upon which they are building.

This means that the prospective GlamourArticle authors are highly motivated to keep a enormous amount of their progress under wraps until they are ready to reveal this new fine stand-alone structure.

Otherwise, someone else might copy them. Leverage their clever advances. Build a competing tower right next door and overshadow any neighboring accomplishments. Which, of course, builds the city faster….but it sure doesn’t give the original team as much credit.

The average Glamour Article is also an ENORMOUS amount of work. Many, many person years go into creating one. Many people who would otherwise get a decent amount of credit for laying a straight and true foundation will now be entirely overlooked in the aura of the completed master work. They will never become architects themselves, of course. How could they? Even if they travel to Society Journal Burg, there is no record of them being the one to detail the windows or come up with a brilliant new way to mix the mortar. That was just scut work for throwaway labor, don’t you know.

But the real problem is that the collaborative process between builders is hindered. Slowed for years. The dissemination of tools and approaches has to wait until the entire tower is revealed.

Inefficiency. Slowness. These are the concerns.

Sure, it is also a problem that the builders of the average Glamour Article tower may not share all their work even after the shroud has been removed. It would be nice to let everyone know just where the granite was found, how it was quarried and something about the brand new amazing mortar that (who was that anonymous laborer again? shrug) created. But there isn’t really any pay for that and the original team has moved on. Good luck. So yes, it would be good to require them to show their work at the end.

Much, much more important, however, is that they show each part of the tower as it is being created. I mean, no, I don’t think people need to work with a hundred eyes tracking their every move. I don’t think every little mistake has to be revealed, nor do I think we necessarily need to know how each laborer holds her trowel. But it would be nice to show off the foundation when it is built. To reveal the clever staircase and the detailing around the windows once they are installed. Then each sub-team can get their day in the sun. Get the recognition they deserve.

[And if they are feeling a little oppressed, screw it, they can leave and take their credit with them. And their advances in knowledge can be spread to another town who will be happy to hire this credentialed foundation builder instead of some grumpy nobody who only claims to have built a foundation.]

The competition for Glamour Article building can’t really catch up directly, after all it takes a good bit of work to lay a foundation or create a new window design. They can copy techniques and leverage them, but there is less chance of an out and out scoop of the full project.

So if the real problem is inefficiency, Dear Reader, the solution is most assuredly the incremental reveal of progress made. We don’t need to watch the stirring and the endless recipes for mortar that have been attempted, we just need to know how the successful one was made. And to see the sections of the tower as they are completed.

Ironically enough, this is how it is done outside of GlamourCity. In Normalville, the builders do show their work. Not all of it in nauseating detail but incrementally. Sections are shown as they are completed. It is not necessary to wait for the roof to be laid to show the novel floorplan or for the paint to be on to show the craft that went into the floor joists.

This is a much more efficient way to advance.

It has to be, since resources are scarce and people in Society Burgh kind of give a shit if one of their neighbors is crushed under a block of limestone. And care if an improperly supported beam cracks and they have to get a new one.

This is unlike the approach of Glamour City where they just curse the laborer and draft three new ones to lift the block into place. And pull another beam out of their unending pile of lumber.

Show me the data, Jerry!!!!!!

September 3, 2013

Today’s Twittsplosion was brought to you by @mbeisen:

he then elaborated



There was a great deal of distraction in there from YHN, MBE and the Twitteratti. But these are the ones that get at the issue I was responding to. I think the last one here shows that I was basically correct about what he meant at the outset.

I also agree that it would be GREAT if all authors of papers had deposited all of their raw data, carefully annotated, commented and described (curated, in a word) with all of the things that I might eventually want to know. That would be kickass.

And I have had NUMEROUS frustrations that I cannot tell even from methods sections what was done, how the data were selected and groomed, etc in many critical papers.

It isn’t because I assume fraud but rather that I find that when it comes to behaving animals in laboratory studies that details matter. Unfortunately we all wish to overgeneralize from published reports….the authors want to imply they have reported a most universal TRUTH and other investigators wish to believe it so that they don’t have to sweat the details.

This is never true in science, as much as we want to pretend.

Science is ever only a description of what has occurred under these specific conditions. Period. Including the ones we’ve bothered to describe in the Methods and those we have not bothered to describe. Including those conditions of which we have no knowledge or understanding that they might have contributed.

Let us take our usual behavioral pharmacology model, the 10 m Hedgerow BunnyHopper assay. The gold standard, of course. And everyone knows it is trivial to speed up the BunnyHopping with a pretreatment of amphetamine.

However, we’ve learned over the years that the time of day matters.

Until…finally….in its dotage seniority. The Dash Lab finally fesses up. The PI allows a trainee to publish the warts. And compare the basic findings, done at nighttime in naive bunnies, with what you get during the dawn/dusk period. In Bunnies who have seen the Dash arena before. And maybe they are hungry for clover now. And they’ve had a whiff of fox without seeing the little blighters before.

And it turns out these minor methodological changes actually matter.

We also know that dose response curves can be individual for amphetamine and if the dose is too high the Bunny just stims (and gets eaten by the fox). Perhaps this dose threshold is not identical so we’re just going to chop off the highest dose because half of them were eaten after that dose. Wait…individuals? Why can’t we show the individuals? Because maybe a quarter are speeded up by 4X and a quarter by 10X and now that there are these new genetic data on Bunny myocytes under stressors as diverse as….

So why do the new papers just report the effects of single doses of amphetamine in the context of this fancy transcranial activation of vector-delivered Channelrhodopsin in motor cortex? Where are the training data? What time of day were they run? How many Bunnies were aced out of the study because the ReaChr expression was too low? I want to do a correlation, dammit! and a multivariate analysis that includes my favorite myocyte epigenetic markers! Say, how come these damn authors aren’t required to bank genomic DNA from every damn animal they run just so I can ask for it and do a whole new analysis?

After all, the taxpayers paid for it!

I can go on, and on and on with arguments for what “raw” data need to be included in all BunnyHopping papers from now into eternity. Just so that I can perform my pet analyses of interest.

The time and cost and sheer effort involved is of no consequence because of course it is magically unicorn fairy free time that makes it happen. Also, there would never be any such thing as a protracted argument with people who simply prefer the BadgerDigger assay and have wanted to hate on BunnyHopping since the 70s. Naaah. One would never get bogged down in irrelevant stuff better suited for review articles by such a thing. Never would one have to re-describe why this was actually the normal distribution of individual Hopping speeds and deltas with amphetamine.

What is most important here is that all scientists focus on the part of their assays and data that I am interested in.

Just in case I read their paper and want to write another one from their data.

Without crediting them, of course. Any such requirement is, frankly my dear, gauche.

There’s a new post up over at Speaking of Research that documents The Double Life of Dr. Lawrence A. Hansen. The most astonishing thing is that this AR wackanut has the gall to hold research funding as PI and publish papers that, you guessed it, involve animal research. Including a study in “mongrel dogs” [cited 21 times including twice in 2012] which he first authored some ten years before hitting the scene in outrage over med school physiology labs which used canine models.

Go Read.

23andme and the Cold Case

August 15, 2013

By way of brief introduction, I last discussed the 23andme genetic screening service in the context of their belated adoption of IRB oversight and interloper paternity rates. You may also be interested in Ed Yong’s (or his euro-caucasoid doppelganger’s) results.

Today’s topic is brought to you by a comment from my closest collaborator on a fascinating low-N developmental biology project.

This collaborator raised a point that extends from my prior comment on the paternity post.

But, and here’s the rub, the information propagates. Let’s assume there is a mother who knows she had an affair that produced the kid or a father who impregnated someone unknown to his current family. Along comes the 23 and me contact to their child? Grandchild? Niece or nephew? Brother or sister? And some stranger asks them, gee, do you have a relative with these approximate racial characteristics, of approximately such and such age, who was in City or State circa 19blahdeblah? And then this person blast emails their family about it? or posts it on Facebook?

It also connects with a number of issues raised by the fact that 23andme markets to adoptees in search of their genetic relatives. This service is being used by genealogy buffs of all stripes and one can not help but observe that one of the more ethically complicated results will be the identification of unknown genetic relationships. As I alluded to above, interloper paternity may be identified. Also, one may find out that a relative gave a child up for adoption…or that one fathered a child in the past and was never informed.

That’s all very interesting but today’s topic relates to crimes in which DNA evidence has been left behind. At present, so far as I understand, the DNA matching is to people who have already crossed the law enforcement threshold. In fact there was a recent broughha over just what sort of “crossing” of the law enforcement threshold should permit the cops to take your DNA if I am not mistaken. This does not good, however, if the criminal has never come to the attention of law enforcement.

Ahhhh, but what if the cops could match the DNA sample left behind by the perpetrator to a much larger database. And find a first or second cousin or something? This would tremendously narrow the investigation, wouldn’t it?

It looks like 23andme is all set to roll over for whichever enterprising police department decides to try.

From the Terms of Service.

Further, you acknowledge and agree that 23andMe is free to preserve and disclose any and all Personal Information to law enforcement agencies or others if required to do so by law or in the good faith belief that such preservation or disclosure is reasonably necessary to: (a) comply with legal process (such as a judicial proceeding, court order, or government inquiry) or obligations that 23andMe may owe pursuant to ethical and other professional rules, laws, and regulations; (b) enforce the 23andMe TOS; (c) respond to claims that any content violates the rights of third parties; or (d) protect the rights, property, or personal safety of 23andMe, its employees, its users, its clients, and the public.

Looks to me that all the cops would need is a warrant. Easy peasy.

h/t to Ginny Hughes [Only Human blog] for cuing me to look over the 23andme ToS recently.