July 30, 2015

It’s that time again, Dear Reader.

This post is a meme for you, the readers of this blog, to take more than the usual spotlight you enjoy here in the comments. This is especially for you lurkers (in case you didn’t notice, the email field can be filled with nonsense like For the the veterans, yes I know who you are but feel free to update us on any changes in the way you interact with the blog…especially if you’ve lost touch with the content, been dismayed or just decided that I’m not who you thought at first, ideas-wise.

1) Tell me about yourself. Who are you? Do you have a background in science? If so, what draws you here as opposed to meatier, more academic fare? And if not, what brought you here and why have you stayed?

2) Have you told anyone else about this blog? Why? Were they folks who are not a scientist?. Ever sent anything to family members or groups of friends who don’t understand your career?

3) How did you find us and how do you regularly follow us? through Twitter, Facebook and/or other beyond-RSS mechanisms?

If you blog, and I know many of you do, go ahead and post your own version of this. Take the time to get to know your audience and ask the lurkers to come out and play. You’ll be most pleasantly surprised how many take you up on it.

[This is all the fault of Ed Yong. Head over the the last iteration to see all the gory details and links to prior comment threads.]

h/t: Namaste_ish

StructureFig-mdma-vs-cathinones450A new Case Report verifies the lethal potential of methylone (PubMed). This drug is also known as beta-keto-MDMA (bk-MDMA; Wikipedia) or 3,4-methylenedioxycathinone. In short, this is the closest cathinone cousin to MDMA, aka Ecstasy.

Barrios L, Grison-Hernando H, Boels D, Bouquie R, Monteil-Ganiere C, Clement R. Death following ingestion of methylone. Int J Legal Med. 2015 Jun 13. [Epub ahead of print]

The decedent was a 21 year old man reported to ingest methylone and cannabis. Friends placed him in a “nearby children’s paddling pool” upon report of breathing difficulty and polypnea (rapid breathing, panting).

By the time emergency medical services made contact he was in cardiac arrest.

Investigators were able to procure a sample of the powder the decedent consumed, represented to him as ecstasy upon purchase.

The toxicological screening was negative for alcohol or “medication”, opiates, cocaine and amphetamines (including MDMA, MDA, MBDB and MDEA). This individual was positive for THC. The screening for substances by GC/MS identified a substance with characteristics identical to the seized material which the decedent had ingested- methylone with a purity of 83.3%.

Now admittedly a cardiac arrest with labored breathing is not right down the main line of clinical findings in MDMA overdose cases. So this is a bit strange. However, “sudden collapse” or “found unresponsive” is not atypical as the triggering observation that the person on MDMA is in trouble. There are also numerous studies showing adverse effects on MDMA on aspects of cardiac function. Similarly, cardiac implications are common with methamphetamine-related deaths– both acutely and apparently as a consequence of longer term use.

So there is every reason to think that methylone might be cardiotoxic.

The finding of cardiac arrest triggered a vague memory and luckily these authors cited the paper I was remembering:

Carbone PN, Carbone DL, Carstairs SD, Luzi SA. Sudden cardiac death associated with methylone use. Am J Forensic Med Pathol. 2013 Mar;34(1):26-8. doi: 10.1097/PAF.0b013e31827ab5da.

Now in this case a 19 year old man collapsed while jogging and had a much lower blood level of methylone (0.007 mg/L) compared with the 6.64 mg/L blood levels in the Case reported by Barrios et al. No other drugs were detected, however:

No other drugs were detected in the urine or central blood, including pseudoephedrine, ephedrine, amphetamine, methamphetamine, MDMA, 3,4-methylenedioxyamphetamine, phenylpropanolamine, or cocaine and metabolites. Analysis was also negative for several other bath salts including flephedrone, n-ethylcathinone, mephedrone, methedrone, ethylone, butylone, MDPV, and naphyrone.

This was presumably not an effect of acute overdose intoxication but perhaps a lingering effect on heart function caused by the methylone consumed hours before. Hard to know without controlled studies, particularly given the exercise this person was engaged in.

Nevertheless, this new Case Report serves as a reminder that methylone, which is increasingly replacing MDMA in the US market, represents a risk for immediate and lasting adverse health consequences.
Related Reading:

It was the methylone that killed him.

Methylone, or beta-keto-MDMA, also causes fatality

Various posts on MDMA-related fatality and morbidity

Citation practices

July 27, 2015

I think that at some point, protracted refusal to cite relevant work amounts to scientific misconduct.

Tell me that doesn’t look a little bit funny to you.



July 24, 2015

Often times in academics we are anticipating a job change in the near future. Postdocs, in particular, since this is supposed to be a temporary job. But faculty occasionally anticipate a job change too. On the market b/c you fear tenure won’t fall, to leverage progress into a better job, to jump out of the rat race, to join Administration. 

I give advice based on Yoda’s wisdom. 

Yoda: Ready are you? What know you of ready? For eight hundred years have I trained Jedi. My own counsel will I keep on who is to be trained. A Jedi must have the deepest commitment, the most serious mind. This one a long time have I watched. All his life has he looked away… to the future, to the horizon. Never his mind on where he was. Hmm? What he was doing. Hmph. Adventure. Heh. Excitement. Heh. A Jedi craves not these things. You are reckless. 

No, not the paternalistic grouch stuff. In this he is worse than a greybeard of science. 

No it is the part about doing a good job on what you are currently doing. To me this is the basis for making the future stuff more likely to go your way.  

No matter how removed the anticipated job category, the candidate who has been successful in her previous job is going to look better. 

I entertained the McKinsey thing at one point during my training. Looked into it, saw who they hired and spoke to a friend of a sibling who went that way. They did not want people who had a disappointing career in science up to that point. They knew what CN or S publications meant. They wanted excellence.

Now of course plenty of people get alternative career jobs after a disappointing career as grad student or postdoc. But I think the take away message is that you should maximize your success in whatever job you are doing now. Don’t just slack because you plan to be out-o-here in a year. 

Success now increases the chances of getting into whatever next job lies over the horizon. 

There is also the consideration that you may find yourself staying in the job you have much longer than anticipated or desired. A year from now, you don’t want to look back and wish you had finished that experiment, paper, grant application or whatever.

Work based on the idea you may still be in this job in a year or three. Sometimes things happen. Maybe the local institution finally steps up and does you a solid. Maybe that firm job offer elsewhere is denied by the Dean or P&T committee. Maybe the University System puts down a hiring freeze.

You’ll be better off if you are taking care of business in your existing job.

Wow. I last used the BRDPI estimate of inflation in the cost of biomedical research to illustrate how the full modular grant ($250K direct) had not changed and therefore purchasing power had eroded.

Jeff Mervis at Science has a blockbuster observation.

To remind you, the BRDPI is this:

The annual change in the Biomedical Research and Development Price Index (BRDPI) indicates how much the NIH budget must change to maintain purchasing power. The BRDPI was developed and is updated annually by the Bureau of Economic Analysis (BEA), Department of Commerce under an interagency agreement with the NIH.

That link also leads you to the data tables where you find the annual rates stretching back to the 50s.

The Mervis article highlights the historical low for FY2012 and reminds us of the cut in the salary cap (maximum amount of an Investigator’s salary that can be charged to NIH grants)

Congress passed a spending bill in December 2011 that lowered the salary ceiling for investigators on a standard NIH grant from $199,700 to $179,700.

and concludes with a caution:

NIH enjoys strong support in Congress, and the realization that biomedical inflation largely tracks salary trends, not the sticker price of essential lab equipment and supplies, is unlikely to have a major impact on policy debates. Still, it may behoove biomedical lobbyists to think twice before citing the cost of high-tech science as a rationale for pumping up NIH’s budget.

Yeah, I hear that. Let’s peer a little closer though.

The NIH Office of the Budget January 2015 overview [PDF] futher anticipates that salary cap is a major driver of the inflation index.

The modest BRDPI growth rate of 2.0 percent for FY 2014 reflects the effect of the NIH extramural investigator salary limitation (“cap”) of $181,500 and an increase on salaries of Federal civilian employees of 0.75 percent for that fiscal year.
The projected 2.2 percent growth for FY 2015 assumes a one percent increase for Federal salaries starting in January 2015, as well as an increase on the extramural investigator salary cap to $183,300.

OK, let’s route ourselves back to the NIH Office of the Budget report from January 2013 [PDF] which indeed draws an explicit link.

The modest BRDPI growth rate of 1.4 percent for FY 2012 reflects the effect of the reduction of the NIH extramural investigator salary limitation (“cap”) from $199,700 to $179,700 for that year and the continued freeze on salaries of Federal civilian employees.

However, it also goes on to note other contributions:

The BRDPI growth rate was also adjusted for the growth of stipends and related expenses on fellowships and training awards. In addition, the FY 2012 BRDPI growth is lower than the growth for FY 2011 because the rate of growth of prices for several input categories slowed down in FY 2012 compared with the growth during FY 2011. For inside NIH activities, the categories with slower growth in prices include travel, transportation, printing and reproduction, ADP and other IT services, instruments and apparatus, laboratory supplies, office supplies, utilities, repairs and alterations of facilities, compensation rates for consultants and support contracts. For extramural activities, fringe benefits, travel, equipment, supplies, patient care alterations and indirect costs each showed slower price growth during FY 2012 compared with FY 2011.

Wait. Sooooo, everything contributes a little bit? This seems out of step with Mervis’ column. Wait, wait….the 2013 overview continues….

Primarily because of the freeze on Federal civilian employee salaries and the cap on compensation of extramural investigators, the rate of growth of the BRDPI during the years FY 2011 through FY 2013 has been relatively low compared with its historical relationship with general inflation as represented by the growth of the GDP Price Index.

Primarily. So that circles us right back to the reduction in the extramural cap and elimination of Federal civilian salary raises. [You might ask why the Federal civilians did not also suffer salary reductions, merely freezes, eh?] But if we take this as a valid and intended connotation then it would seem Mervis has it right. The salary issues are huge.

I wonder why they didn’t just find the dollar figure. How many Investigators funded by the NIH in a given year are paying up to the cap? Multiply that by you favored reduction or increase and boom, you can translate that into new R01s.

The annual Salary Cap numbers can be found here. It seemed to steadily increase from 2005-2010, including that 2008-2009 interval that produced the most immediately prior reduction in the BRDPI. So why didn’t salary cap drive the BRDPI that year?

ladeeeez men

July 15, 2015

After discussing this post at shakesville:

It’s difficult to describe what I mean when I say my husband likes women, because it’s so rare that we don’t even have words for it. And because any words I might use are corrupted by the urgent defense of patriarchal standards, which reject any dynamic that isn’t framed to center women as the objects of men.

with certain parties, I conclude that it is worth discussing on the blog.

My thought is this: Isn’t this familiar to everyone? I mean when you go to social events there are some men that gravitate towards talking with men and other men that gravitate towards talking with women. There are totally woman-guy and guy-guy phenotypes and they have been obvious since like middle school (and as this post mentions, not just because they are trying to hook up).


Mentoring and parenting

July 14, 2015

Like it or not, your mentoring behavior is intimately tied to the experiences you had as a scientific trainee. Let me rephrase that for emphasis. Tied to the way you experienced your training.

In the very general sense, if you thought something was good for you, you are going to tend to try to extend that to your trainees. And if something was bad for you, you are going to try to avoid that for your trainees.

Obviously, the ability that you have to emulate or avoid certain behaviors of your mentors-of-reference* is not going to be perfect. But let us assume for argument’s sake that you can make a fair stab at mentoring the way that you would intend yourself to mentor.

This is not all that dissimilar to parenting, I find. There are obvious ways in which I think my parents did an absolutely bang up job of raising me. They set me on a path of life that is in many ways ideal. A career that is fulfilling, a political and social stance that I am proud of, a strength of will and freedom from many of the family-drama related pathologies that plague many adults. I would hope to provide this type of parenting to my own children. Absolutely.
Read the rest of this entry »

Open Thread

July 14, 2015

Whatcha got for me today?

Science published a “Working Life” bit by Eleftherios P. Diamandis titled “Getting Noticed is Half the Battle

sciwo is not impressed

I’d sum it up like this: “If you were a man 30 years ago and ignored your family in favor of work, you might have been privileged enough to get a faculty position without an open search.

Arrgh Matey

July 13, 2015

There was a comment on a prior post suggesting that when postdocs are funded by a RPG, this prevents them from engaging in independent scholarship.


When I was a postdoc, regardless of source of my salary (variously grants, TG and individual fellowship), I was certainly constrained by the grants funding the lab. But I felt it was up to me to add value. To leverage my own interests to pursue extras and add-one that the lab head perhaps had not thought about as a strong interest. And whaddaya know, this direction turned into a funded R01. And eventually into publications.

I have always felt that my independent scholarship, such as it was, was at liberty to develop just so long as it was within the broad scope of contributing to the RPG.

Does true “independent scholarship” require something that does not contribute in any way to the goals of the grants funding the lab?


Lastly, there IS one way to experimentally test how much a PD is worth, at least to PIs, and you are promoting that test, whether you know it or not. And that is a PD strike. I would love to see you discussing how spoiled PDs are in between gel runs because your PD is really not there. I think 50K/yr wouldn’t sound that much then.

Go ahead dudes, you have nothing to lose but your chains.