This post originally appeared at the old site May 22, 2007.

Lots of bashing of the peer review process lately. Admittedly Orac has a nice counter, directed at forces external to science but highly relevant to on-the-bus complainers. [Update: another comment on peer review from NeuroLogica]
I have some unusually un-cynical thoughts today.

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This post originally appeared at the old site Oct. 4, 2007.

Many academic honor codes boil down to two essential statements, namely “I will not cheat and I will not tolerate those who do“. For “cheat” you may read any number of disreputable activities including plagiarism and research fraud. My alma mater had this sort of thing, I know the US military academies have this. Interestingly a random Google brings up some which include both components (Davidson College, Notre Dames, Florida State Univ (which as been in the academic cheating news lately), and some which do not (CU Boulder, Baylor); Wikipedia entry has a bunch of snippet Honor Codes. The first component, i.e. “don’t cheat” is easily comprehended and followed. The second component, the ” I will not tolerate those who do” part is the tricky one.

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Our good blogfriend JuniorProf has launched a campaign to explain why pain research matters. I am already learning lots of stuff from his older posts. Also from observations such as this one at Almost Diamonds and this one from Zuska.
The thing that caught my eye recently, though, was this post:
Drug discovery in academia and NIH, a new type of U01

This brings us to the bane of drug discovery: absorption, distribution, metabolism and excretion (ADME). This is something that industry does very well.

ADME in academia, well, let’s just say, not so much. The reasons for this are likely pretty simple: its an important area of drug development but not the most exciting, by any stretch of the imagination (sorry you ADME specialists), and it often requires all sorts of rather expensive testing in model organisms that aren’t used often in academic labs. Its also highly compound-specific and this makes grant writing very hard (or so I hear).

JuniorProf then goes on to make an argument for why drug development should be done in academia and how that might work best. He then describes a recent NIH initiative that is trying to support some academic drug development effort.
Go read. Follow @juniorprofblog on Twitter or perhaps just the #painresearchmatters hashtag.

The banner

July 26, 2010

Huh, you know what? The original plan was to get started here on ScienceBlogs with a plain banner and then after a few weeks have one of those banner contests so the brilliant and creative readers could come up with something.
Wow, has it been so long? And the first time I changed the banner was for the strike.
Now it is starting to grow on me. What do you think?

Midsummer Blogrolling

July 26, 2010

Ok, while I’m on housekeeping chores, might as well get this one out of the way. Been a little light on the Latest 24 Hrs channel lately hasn’t it? What with all the people leaving ScienceBlogs and the Strike and all there has not really been the same level of activity around here.
So I have a charge for you. Take a look down the blogroll (appended below), yes even if you are a regular reader. Find a link that is new to you, click over there and find us all something interesting to read. Bring it back over here and drop a link in the comments, eh? Oh, and make a comment on that site about what great stuff you think it is, will ya? (only please, DearReader, do not leave one of those assy comments saying “I came over here from DrugMonkey” because those make my skin crawl.)
If you’ve read every thing on the blogroll and can’t find any blogs you haven’t seen before, well, give me something new for the blogroll!

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A design change

July 26, 2010

I’m anticipating making some design changes for ye old swagge shoppe in the near future. Since it is just the free version of Cafepress I’ll have to take down the old designs to do so.
Thought I’d put out a last call on the old stuff for a week or so. They look like the following.
In case you didn’t know, you can also get items related to, Adventures in Ethics and Science, On Becoming a Domestic and Laboratory Goddess, A Blog Around the Clock, Greg Laden’s Blog and Digital Biology.
The in situ images are after the jump.

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This pretty much tells it as it is.

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Gerty-z of Balanced Instability blog posed an age-old problem in post-graduate education.

I was talking to a graduate student the other day. It was a hallway interaction, she had not searched me out for advice. I have known this grad student for several years, and she is one of the superstars in a highly-ranked graduate program. By every metric, she should be graduating. Now. Turns out, her advisor has been suggesting that she stick around for another year or two.

ruh roh! Conflict of Interest raises its ugly head.
I bring this up because this is not the first time I’ve heard a similar story. In fact I’ve heard of what appears to be at least one entire department that is riddled with this tendency to prolong the graduate school interval as long as possible, seemingly only to extract more value out of productive trainees.

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Rob Knop has a series of observations up on Galactic Interactions that struck a chord with me. He’s talking about Linden Labs and the Second Life dealio, about which I know next to nothing. I barely understand all that stuff. However, he starts with this observation:

I think often the way to kill a business is to over-monetize it. I remember the 1990’s, and Web search engines. The pattern was repeated over and over again. There’d be one that was the best. They’d realize they were the best, and they’d either get sold or they’d try to monetize their business. The page would go from being relatively clean, to being a cluttered mess of ads… and the search results, being increasingly paid, would become less and less useful. So we’d all move on to another engine. That ended with Google, who had the vision not to try too soon to over-monetize their search, and who recognized when they did monetize it that they had to do it in a way that didn’t completely undermine what brought people there in the first place.

Emphasis added. Now I’m not so much afeeerd of monetizing but it appears an axiomatic truth to me that you cannot kill the function that brings people to your online site or business. That is really the key to Google’s world dominance as a search engine. I had the exact same frustration expressed by Rob with Web engines in the 1990s and I bet most of you did too. It still boggles my mind that you go to the root Google page and you get what you need- a search box and an entry button. Sans extra crap.

It really is sad that Twitter is trying as hard as they can to miss the point of Google. but I digress..

Rob has another observation about Linden that sounds hauntingly familiar:

Alas, the company as a whole didn’t realize this. What they should have been focusing on was promoting virtual worlds. Instead, they… well, to be honest, I’m not really sure what they were focusing on, but they didn’t direct substantial effort towards promoting virtual worlds in general.

I return to the Google example. I mean sure, the Internet was going to explode anyway. I get this. But by making the internet useful for people (some of us do remember the Web before search engines were so ubiquitous, fast and so damn good, you know), all people-even our grandparents- Google made themselves indispensible. This is what Rob is getting at I think. If you want to be an online entity that relies on low fractional payment from a vast audience, you need to concentrate your efforts on the audience. And when an audience doesn’t exactly exist yet, you are not trying to steal marketshare, you are trying to build up the whole dang market.

This is where I personally think that has gone a bit astray and where I routinely criticize the approach of Nature Networks. I look at it this way. I’ve been blogging for over three years now and experienced both negligible-audience privateer blogging and the heady heights of the Pharyngula driven traffic. Comments and personal communications to PhysioProf and I suggest that our focus on academic careerism for grant funded scientists is of interest even beyond biomedical disciplines. Our traffic is quite pleasing and the commentariat of decent size. But here’s the thing. If I look at the IP numbers coming in from the domains of easily identified research Universities and research institutes we still only draw one or maybe 5 repeat viewers from a given institute. That spells one heck of a lot of untapped audience to me.

The funny thing is that Sb says all the right things about engaging the broader audience. And Nature Publishing Group routinely tries to tell all scientists reading their flagship publications (and this is a good fraction of all scientists) to go online, to comment on papers and, gasp, to blog.

Their hearts are in the right place but their execution could use some re-thinking.

The following is a more casual description of a stream of thought I had about these posts I’ve been writing on the MDMA/PTSD paper.

ok, so there’s this paper that has finally come out. I’ve been bashing away at the project itself on the blog since, oh, forever. I finally had a chance to get around to blogging the paper. no biggie.
takehome message, MDMA is good for treating PTSD if given in the therapy session.
one of the features of such a study is that it is going to get media attention. I was ignoring that all week so that I could blog the paper unmolested.
Trolling around the media coverage I started on a slow burn.
Going through Google hits, there was a great deal of emphasis on PTSD caused by combat stress. Angles on the story which suggested we have a big ol’ problem looming (true dat) and won’t it be great to have some new hope (true dat) and then doing a less than complete cockup of the facts of the paper.
Problem is that it is a small study as it is, 12 MDMA-treated, 8 placebo controls, but only ONE had combat trauma as the index trauma. ONE. The rest were mostly sexual assault, crime (not further specified) and childhood trauma (sexual assault and physical neglect). Me, I was happily bashing away at the overselling of the single combat PTSD case in my draft.
On the way home it hit me.

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I am disappointed in the mainstream, and not so mainstream, media coverage of the Mithoefer et al, 2010 paper on MDMA-assisted therapy for Post-Traumatic Stress Disorder. I had been holding off reading any of it because I suspected it might distract me from actually discussing the paper.
After writing up my thoughts on the paper, I went strolling around the Google News hits for MDMA to see what had been written about this paper. There was a whole lot of of really bad journalism. Sure, for the most part they got the basic facts right, but I noticed a consistent issue having to do (I assume) with journalism’s penchant for selling a story they’d like to tell over the story that exists.
Let us start with the more venerable news organizations.
ABC News Ecstasy may help traumatised veterans
See the title? Pretty common to see something abut veterans or combat PTSD in the title as well as in the article body.

found that the drug seems to improve the effects of therapy in military veterans

No, there was one combat stress case. I noted that this stuck out as odd in my post on the paper. Well, now you can see why the authors might have been so keen to include this single warfighter subject. They enjoyed much wider press and nobody called them out for this scientific distraction
(This part of the ABC report caused me to laugh though:

The researchers, led by Dr Rick Doblin of the Multidisciplinary Association for Psychedelic Studies

Of course this is true, the driving force behind getting these studies rolling is the recreational legalization Trojan outfit MAPS. It looks better though, if you ask me, when they credit the therapist Mithoefer as being the leader of the project and MAPS as only providing support and assistance. )

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ecstasypills.jpgMy readers will recall that I have blogged now and again about ongoing efforts to get 3,4-methylenedioxymethamphetamine (MDMA), the psychoactive compound preferentially sought as Ecstasy in recreational users, approved as a medication to be used in psychotherapy. The initial attempts have focused on the treatment of Post-Traumatic Stress Disorder. PTSD is a seriously debilitating condition and we may not have sufficient resources and knowledge to deal with, e.g., an anticipated uptick due to the current wars that the US is prosecuting.
I introduced the MDMA/PTSD Phase I clinical trials here, noting

The short version of the theory is that the subjective properties of MDMA (empathic, inhibition lowering, etc) are consistent with helping people in difficult psychotherapeutic situations (such as for post-traumatic stress disorder (PTSD) and, supposedly, end stage cancer anxiety) make therapeutic breakthroughs during a limited number of treatment sessions of talk therapy. This is not proposed as a chronic medication like a selective serotonin reuptake inhibitor (SSRI). The funny thing is, I approve of the concept of moving forward with clinical trials based on the available evidence.
Why not? I mean PTSD can be a very devastating psychological issue and if there are treatment-resistant cases that can benefit from a limited number of MDMA exposures, great.

I concluded that particular post with this observation.

As is general practice in medicine, sometimes there are going to be risks associated with therapy. Sometimes quite substantial risks can be acceptable if the alternative is bad. However we get ourselves into a world of trouble, sometimes even losing a perfectly helpful medication, if we are not as honest as possible, up front, over the actual risks.

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Now #NatNetFAIL?

July 23, 2010

A Twitt from @drisis alerted me to this post over at Nature’s blog empire. In it, one Ian Brooks muses:

Do i fit in Nature Network anymore? Is it time to consolidate and “out” myself and find a new Network to join.

I don’t know. I haven’t been around here for so long, I don’t know how Nature Network is holding up; I’ve lost touch with this place and most of the bloggers here (which I’m very sad about). I know some of the regular bloggers are frustrated with The Rules and the dreadfully slow log ins (it took me almost 2 minutes from entering The Network URL to start writing this post. That is an utterly unacceptable lag time).

Sounds a bit familiar to those of us on the side of the pond, doesn’t it? A vague sense of discomfort. Loss of community. “Why am I here?” reflections. And a sense that the complaints are many and varied, even if any given issue does not affect every single person. A storm is abrewing at Nature Networks, make no mistake.

I also enjoyed the comments that emerged in the wake of Ian’s post. Recall the sorts of snootery mooted about by these NatNet folks about the tawdry interest of Sb bloggers in their….traffic? Not to mention their difficulties with our lack of civility? And accusations that there ‘just isn’t enough science at, wot, wot old chap’?

Well now they are irritated by the Science-only dictum, bridling against the limits on cursing, complaining about a perceived pusillanimity of NPG about the infamous English Libel law and demanding, DEMANDING I SAY, their traffix stats. STAT!

All there in the comments and original post. Heck, even Henry Gee (you remember SpittleFest, right?) is whining about how he feels sadly unwelcome after his (female as it happens) boss chastised him for pissing on her carpet posting a (no doubt hilarious) blog entry about rejecting a manuscript on his iPhone from the loo.

[sidebar: I love the fact you can reference comments at NatNet now, bang up job on that at least.]

Brooks has more opinionating on Nature Networks here.

Oh and final note, Ian? You are no PhysioProf.

crossposting from

He has a new post up in response to a request for the full regression analysis. This analysis is tasty and here was the bit that drew my attention:

A principal component analysis reveals that a single principal component accounts for 71% of the variance in the overall impact scores. This principal component includes substantial contributions from all five criterion scores, with weights of 0.57 for approach, 0.48 for innovation, 0.44 for significance, 0.36 for investigator and 0.35 for environment.

A Twitt from Dirk Hanson, of the Addiction Inbox blog, pointed to the Mini Chill drink which purports to be:

..the world’s only drink guaranteed to make you feel great! Our all natural blend of herbs and aminos is Dr. formulated and proven to promote relaxation, improve mental focus and even boost your mood!

Dirk made some crack about this being an alcohol enhancer and, fascinatingly, the website for this product has a whole page for cocktail recipes. Mood enhancing, healthy…and a mixer! Oh joy…
MiniChillFACTS.pngAt any rate, I was searching for the Quack Miranda Warning when I clicked on the “Lab” page and I immediately noticed something funny. An icon right in the middle of the page is linked to the ingredients page which says the product contains:

four primary ingredients found in nature, all of which have been subjected to molecular research and clinical studies. These components are Valerian Root, Aminobutyric acid (GABA), Theanine and 5-HTP.

Oh this is a classic of misdirection and insinuation isn’t it? “Molecular research” and “clinical studies” eh? Yet I bet not one single clinical study showing that this product has the benefits that they claim. Just guessin there. Anyway I’d best leave the quack busting to the real experts like PalMD and Abel Pharmboy, so let’s return to the iconography.
ResearchBlogging.orgThat icon, linked to their supposed evidence mind you, reminded me of this icon. When you put them together like this it is obvious that the Mini Chill icon is not an exact duplicate. But still. It evokes the ResearchBlogging icon, does it not? Surely this is not just me?
If you will recall the ResearchBlogging icon is the descendant of a prior icon. The goal of this icon was, of course, to evoke rapid identification with the intent of itself. I.e., to form a sort of Good Housekeeping seal of approval that the post you were reading met certain basic standards.
If this is not simply a coincidence, I find it really interesting that some quack product would try to coopt the authority of Among other things it would seem that marketing donks think that the is actually meaningful to people. That’s good at least.
I never did find the Quack Miranda Warning.