2015

(by drugmonkey) Dec 19 2014

My plan is to stir up some trouble.

What do you have on tap for 2015?

29 responses so far

H-index

(by drugmonkey) Dec 18 2014

I can't think of a time when seeing someone's h-index created a discordant view of their impact. Or for that matter when reviewing someones annual cites was surprising.

I just think the Gestalt impression you generate about a scientist is going to correlate with most quantification measures.

Unless there are weird outliers I suppose. But is there is something peculiar about a given scientist's publications that skews one particular measure of awesomeness....wouldn't someone being presented that measure discount accordingly?

Like if a h-index was boosted by a host of middle author contributions to a much more highly cited domain than the one most people associate you with? That sort of thing.

25 responses so far

The proof is in the budgeting

(by drugmonkey) Dec 17 2014

When we last discussed Representative Andy Harris it was in the wake of an editorial he published in the NYT. It consisted of a call to put hard targets on the NIH for reducing the average age of the first R01, standard Golden Fleece style carping about frivolous research projects and a $700M "tap" of the NIH budget. I speculated that this last was the real target because the "tap" is money appropriated to the NIH that then goes to "program evaluation" and the AHRQ. There is the possibility that this is a covert attack on the ACA ("Obamacare").

The recent appropriation to the NIH passed by the Congress is interesting because it addresses these three issues. According to Jocelyn Kaiser at ScienceInsider:

The report also directs NIH to pay more attention to the age at which new NIH investigators receive their first research grant... but lacks that specific target.

So toothless verbiage, but no more.


Lawmakers also address a perennial concern: that the amount NIH spends on specific diseases doesn’t take into account the burden that disease creates or death rates. The report “urges NIH to ensure research dollars are invested in areas in which American lives may be improved.” It also tells NIH “to prioritize Federal funds for medical research over outreach and education,”

"urges". Again, this is totally impotent. Two strikes on Rep Harris.

One recent concern about NIH’s budget—that each year some money is skimmed off for other Department of Health and Human Services (HHS) agencies—is remedied in the bill. It says that the $700 million that NIH is set to contribute to the “tap” this year will come back as $715 million for the agency.

Well that seems like Rep Harris got a win on the tap, no? And his goal was what again?

For one thing, we need to eliminate a budget gimmick, known as the “tap,” that allows the Department of Health and Human Services to shift money out of the N.I.H. budget into other department efforts. The N.I.H. lost $700 million to the “tap” in 2013 alone. Instead, the money should be placed under the control of the N.I.H. director, with an explicit instruction that it go to young investigators as a supplement to money already being spent. If we don’t force the N.I.H. to spend it on young investigators, history has shown that the agency won’t.

"lost". "supplement to money already being spent". This creates the strong impression that Rep Harris was trying to increase the NIH budget by $700M. And yet. The overall NIH appropriation only increased by $150M.

So in point of fact Rep Harris took three strikes.

Or so it appears.

Of course, if his agenda was to go after those agencies that received their support from the tap, perhaps he didn't strike out after all. We'll have to see if those agencies got all their money in this budget and, more importantly, if they remain this way in subsequent years. It is not impossible that breaking the previous recipients of the "tap" down into individual line items in the budget will allow them to be eliminated one by one.

One thing is for sure, Rep Harris didn't do anything concrete to help out the young investigator issue at the NIH in this budget appropriation.

UPDATE: Actually I screwed this up. If there is no net decrease in the budget and the NIH no longer loses $700M to the tap obligations, I guess this is a net gain. My bad.

15 responses so far

Writing

(by drugmonkey) Dec 17 2014

The paper I am working on.

The paper I should be working on as my top priority.

The paper I can't wait to work on once the last bit of data we are waiting for arrive.

The paper I shouldn't bother working on until one of the manuscripts under review comes back with comments.

Only two of these refer to the same manuscript.

8 responses so far

Thought of the Day

(by drugmonkey) Dec 17 2014

This blog is as much about succeeding in the world as we find it as it is about complaining about the bad things.

9 responses so far

On the credibility of a Ferguson witness

(by drugmonkey) Dec 16 2014

In case you need to argue with some dumbass on the internet or family member at holiday dinner about Ferguson, you should really review the saga of Witness 40.

The DA in the case let this dumpsterfire lying ass racist psycho go up before the Grand Jury and perjure herself. This is, apparently, where the "charging like a football player" bullshit came from. Important, because this particular claim is important to justify why Wilson shot Brown in the top of the head- the alternative account is that Brown was already falling on his face when Wilson shot him in the top of the head as some sort of coup de grace.

The smoking gun report:

DECEMBER 15--The grand jury witness who testified that she saw Michael Brown pummel a cop before charging at him “like a football player, head down,” is a troubled, bipolar Missouri woman with a criminal past who has a history of making racist remarks and once insinuated herself into another high-profile St. Louis criminal case with claims that police eventually dismissed as a “complete fabrication,” The Smoking Gun has learned.

Oh, how so?

Sandra McElroy did not provide police with a contemporaneous account of the Brown-Wilson confrontation, which she claimed to have watched unfold in front of her as she stood on a nearby sidewalk smoking a cigarette.

Instead, McElroy (seen at left) waited four weeks after the shooting to contact cops. By the time she gave St. Louis police a statement on September 11, a general outline of Wilson’s version of the shooting had already appeared in the press. McElroy’s account of the confrontation dovetailed with Wilson’s reported recollection of the incident.

How convenient. Wait, why was she even there in the first place?

Before testifying about the content of her notebook scribblings, McElroy admitted that she had not driven to Ferguson in search of an African-American pal she had last seen in 1988. Instead, McElroy offered a substitute explanation that was, remarkably, an even bigger lie.

McElroy, again under oath, explained to grand jurors that she was something of an amateur urban anthropologist. Every couple of weeks, McElroy testified, she likes to “go into all the African-American neighborhoods.” During these weekend sojourns--apparently conducted when her ex has the kids--McElroy said she will “go in and have coffee and I will strike up a conversation with an African-American and I will try to talk to them because I’m trying to understand more.”

Sure.

The opening entry in McElroy’s journal on the day Brown died declared, “Well Im gonna take my random drive to Florisant. Need to understand the Black race better so I stop calling Blacks Niggers and Start calling them People.” A commendable goal, indeed.

What a peach of a person she is.

Shaun King at Daily Kos:

Sean Hannity, with a popular drive-time radio show and highly rated prime-time television broadcast, is one of the two or three most important voices in conservative America. Love him or hate him, what he says matters to millions of Americans. What he says over and over again, particularly to an audience that often sees him as a primary source of news, actually matters a great deal. While he may not shape culture for you, he shapes and informs culture for millions of Americans.

This is why, among many reasons, it is so troubling that he regularly quotes and leans on one particular "witness" in the August 9 shooting death of Ferguson teenager Mike Brown by Officer Darren Wilson. This so-called witness, a middle-aged white woman, known only to us as "Witness #40," openly stated to FBI investigators a litany of bizarre and disturbing facts about herself, including that she regularly calls African Americans "niggers and apes," helped start a support group for Darren Wilson encouraging kids to make him Christmas cards, and that she only happened to be on Canfield Drive—which is not even in the town she lives in—the exact moment Darren Wilson killed Mike Brown, on a whim "to understand the black race better so I can stop calling Blacks niggers and start calling them people."

And it wasn't just Hannity either. It was the DA. More Shaun King at Daily Kos:

Sandy McElroy was never near Canfield Drive on August 9. She completely fabricated her entire story weeks after Darren Wilson killed Mike Brown. During their interrogation of her, Sandy McElroy was completely shredded by the FBI as a racist, a liar, unstable, and more. They proved in their own interview, with evidence, that McElroy lied about ever being there, about how she left the scene, about key details of the case that she claimed she witnessed, and more.

Furthermore, Sandy McElroy, beyond being a convicted felon, had a record in St. Louis of interfering with investigations and making preposterous claims about connections she had to cold cases. All of this was known to St. Louis officials. Her extreme racism was not private, but public, and was discussed at great length with the FBI before she was ever allowed to testify before the grand jury.

You must understand, then, that Sandy McElroy, whose testimony matches that of Darren Wilson's better than any witness who testified, was only called to the grand jury, not once, but twice, and allowed to present concocted physical evidence at that, because she was a neutron bomb for this case. Not ONE PIECE OF EVIDENCE proving that she was there could be found and scores of evidence that she made the entire thing up was presented weeks before she was ever allowed to testify before the grand jury, but it was all deliberately ignored.

So yeah. When you run up against some Klown that wants to explain to you about "credible" testimony and how the DA and the Grand Jury process was all on the up and up, you go ahead and ask them about Witness 40.

12 responses so far

Blog networks

(by drugmonkey) Dec 15 2014

Blog networks appear to have a life cycle. Today it is Scientific American that is blowing up its blog network.

Dave Winer, one of the medium’s pioneers, once defined a blog as, “the unedited voice of a person.”

sure.

It’s an honorable notion of what a blog should be, which suits independent bloggers just fine. News outlets, however, have unique responsibilities to their readers and to the public and as such their standards must differ.

So... maybe don't pretend to have blogs? Just call them columns like you used to?

First, we are publishing a new set of Blog Network Guidelines so that everyone, bloggers and readers alike, is fully aware of our basic operational ground rules and protocols.

To make the most of these new guidelines, we are also reshaping the network to work more closely with our blogggers, create an improved balance of topic areas and bring in some new voices.

One of those statements is believable, anyway.

On down to a comment from what I guess is a staffer?

The reduction in the size of the network is not a statement about the quality of bloggers’ work—any more than any periodic update in any magazine’s content offerings is such a statement. Our decisions involved a variety of factors, including frequency of posts and traffic.

and adherence to the new Guidelines?

ah well. Like I said at the top, networks appear to have a natural life-cycle. The ones that are tied up to a traditional publishing entity perhaps are on a short burn from the start. They are just waiting for enough little kerfuffles to build up into a profound nervousness on the part of the suits upstairs. Then down comes the hammer.

7 responses so far

Health report from Colorado: Recreational marijuana harms

(by drugmonkey) Dec 15 2014

a Reader put me onto a new Viewpoint in JAMA:

Monte AA, Zane RD, Heard KJ. The Implications of Marijuana Legalization in Colorado.JAMA. 2014 Dec 8. doi: 10.1001/jama.2014.17057. [Epub ahead of print][JAMA; PubMed]

The authors are from the Department of Emergency Medicine, University of Colorado and the Rocky Mountain Poison and Drug Center. They set out to describe a few health stats from before and after the recreational legalization of marijuana.

Interesting tidbits:

However, there has been an increase in visits for pure marijuana intoxication. These were previously a rare occurrence, but even this increase is difficult to quantify. Patients may present to emergency departments (EDs) with anxiety, panic attacks, public intoxication, vomiting, or other nonspecific symptoms precipitated by marijuana use. The University of Colorado ED sees approximately 2000 patients per week; each week, an estimated 1 to 2 patients present solely for marijuana intoxication and another 10 to 15 for marijuana-associated illnesses.

This one is obviously frustratingly anecdotal in that there is no real measure of the rate before legalization.

The one on cyclic vomiting syndrome is better:

The frequent use of high THC concentration products can lead to a cyclic vomiting syndrome. Patients present with severe abdominal pain, vomiting, and diaphoresis; they often report relief with hot showers. A small study at 2 Denver-area hospitals revealed an increase in cyclic vomiting presentations from 41 per 113 262 ED visits to 87 per 125 095 ED visits (prevalence ratio, 1.92) after medical marijuana liberalization (A. A. Monte, MD, unpublished data, December 2014).

We've discussed the phenomenon of cannabis hyperemesis before on the blog. One thing we do have to be careful about is that since it has only been recently that the medical community has been alerted to the possibility of cannabis hyperemesis, we should expect the detection rate to increase. Thus, even against a stable rate of cannabis hyperemesis I would expect the reported rate to be increasing.

The University of Colorado burn center has experienced a substantial increase in the number of marijuana-related burns. In the past 2 years, the burn center has had 31 admissions for marijuana-related burns; some cases involve more than 70% of body surface area and 21 required skin grafting. The majority of these were flash burns that occurred during THC extraction from marijuana plants using butane as a solvent.

This is the e-cigarette and vape market at work people. In South Florida they apparently call it 'Budda'.

Apparently some basic pharmacology 101 would be of help to the good citizens of Colorado.

Edible products are responsible for the majority of health care visits due to marijuana intoxication for all ages. This is likely due to failure of adult users to appreciate the delayed effects of ingestion compared with inhalation. Prolonged absorption complicates dosing, manufacturing inconsistencies lead to dose variability

Interesting. I recall the language in the original initiative was very vague about product testing, labeling, etc. Looks like this is a problem.

Ten to 30 mg of THC is recommended for intoxication depending on the experience of the user; each package, whether it is a single cookie or a package of gummy bears, theoretically contains 100 mg of THC. Because many find it difficult to eat a tenth of a cookie, unintentional overdosing is common. Furthermore, manufacturing practices for marijuana edible products are not standardized. This results in edible products with inconsistent THC concentrations, further complicating dosing for users. According to a report in the Denver Post, products described as containing 100 mg of THC actually contained from 0 to 146 mg of THC.8

Oh, and the children. Don't forget about the children.

The most concerning health effects have been among children. The number of children evaluated in the ED for unintentional marijuana ingestion at the Children’s Hospital of Colorado increased from 0 in the 5 years preceding liberalization to 14 in the 2 years after medical liberalization.3 This number has increased further since legalization; as of September 2014, 14 children had been admitted to the hospital this year, and 7 of these were admitted to the intensive care unit. The vast majority of intensive care admissions were related to ingestion of edible THC products.

This Viewpoint certainly draws attention to the edibles/consumables products as being a problem. Seems pretty clear that maturation of product regulation would be a start, so that people are informed about what they are getting. This should probably be supplemented with some sort of public information campaign on the pharmacokinetics of ingested products compared with smoking marijuana. And, you know, keep it away from your kids.

13 responses so far

Authorship decisions

(by drugmonkey) Dec 12 2014

Deciding who should and should not be on the author line of a science publication is not as simple as it seems. As we know, citations matter, publications matter and there are all sorts of implications for authorship of a science publication.

A question about this arose on the Twitts:

Of course, we start from a very basic concept. Authorship of a scientific paper is deserved when someone has made a significant contribution to that paper. I can't distill it down any more than that. Nice and clean.

The trouble comes in when we consider the words significant and contribution.

This is where people disagree.

I also rely on another basic concept which is that someone should try to match, to a large extent, the practices within the subfields from which similar work is published. This can mean the journal itself, the scientific sub-domain or the institution type from which the paper is being submitted.

On to the specifics of this case.

First, do note that I understand that not everyone is in the position to wield ultimate authority when it comes to these matters. @forensictoxguy appears to be able to decide so we'll take it from that perspective. I will mention, however, that even if you are not the deciderer for your papers, you can certainly have an opinion and advocate this opinion with the person in charge of the decision making.

My first observation is that there is nothing wrong with single-author papers. They might be rare these days but they do occur. So don't be afraid to offer up a single-author paper now and again.

With that said, we now move on to the fact that the author line is a communication. Whether you are trying to convey a message about yourself as a scientist or not, your CV tells a story about you. And everything on there has potential implications for some audiences.

ethical, schmethical. Again, you don't throw someone on a paper "just because", you do it because they made a contribution. A contribution that you, as the primary/communicating/deciderering author, get to determine and evaluate. It is not impossible that these other people referred to in the Tweet made, or will make, a contribution. It could be via setting the environment (physical resources, administrative requirements, funding, etc), training the author or it could be through direct assistance with crafting the manuscript after all the work has been done. All of these are valid as domains for significant contribution.

This scenario of a private industry research lab appears, from the tweets, to be one where the colleagues and higher-ups are not intimately involved in pushing paper submissions. It appears to be a case where the author in question is deciding whether or not to even bother publishing papers. Therefore, the politics of ignoring more-senior folks (if they exist) is unfamiliar. I can't do much but read through the Tweet lines and assume this person is not risking annoying someone who is their boss. Obviously if someone in a boss-like status would be miffed, it is in your interest to find some way that they can make a contribution that is significant in your own understanding or to have a bloody discussion about it at the very least.

Leaving off the local politics, we can turn to the implications for your CV and the story of you as a scientist that it is going to tell.

If all you ever have are first-author publications it will look, to the modern eye, like you are non-collaborative, meaning not a team player. This is probably an impression you would like to avoid, yes, even within an industrial setting. But this is easy to minimize. I can't set any hard and fast rules but if you have some solo-author and some multiple-author pubs sprinkled throughout your timeline, I can't see this being a big deal. Particularly if your employment particulars do not demand a lot of pubs and, see above, the other people around you are not publishing. Eventually it would become clear that you are the one pushing publication so it isn't weird to see solo-author works.

Consider, however, that you are possibly losing the opportunity to burnish your credentials. The current academic science arc has an expectation for first-author papers as a trainee (grad student, postdoc) which is then supposed to transition to last-author pubs as a scientific supervisory person (aka professor or PI). Industry, I surmise, can have a similar path whereby you start out as some sort of lowly Scientist and then transition to a Manager where you are supervising a team.

In both of these scenarios, academic and industry, looking like you are a team-organizing, synthetic force is good. Adding more authors can be helpful in creating this impression. Looking like you are the driving intellectual participant on a sub-area of science is good. This concern looks like it votes for thinning your authorship lines- after all, someone else in your group might start to leech credit away from you if they appear consistently or in a position (read: last author, co-contributing author) that implies they are more of the unifying intellectual driver.

This is where you need to actually think about your situation.

I tell trainees who are worried about being hosed out of that one deserved first-author position or being forced to accept a co-contributing second author this
; You are in for the long haul. If you are publishing multiple papers in this area of science (and you should be) then for the most part you will have first-authors and in the end analysis it will be clear that you are the consistent and most important participant. It will be a simple matter for your CV to communicate that you are the ONE. So it may not be worth sweating the small stuff on each contentious author issue.

In a related vein, it costs you little to be generous, particularly with middle authors that have next to no impact on your credit for this work.

If you only plan to publish one paper, obviously this changes the calculation.

Do you ever plan to make a push for management? Whether of the academic PI or industry variety, I think it is useful to lay down a record of being the leader of the team. That can mean being communicating author or being last author. At some point, even in industry, an ambitious scientist may wish to start being last author even under the above-mentioned scenario.

This is what brand new PIs have to do. Find someone, anyone to be the first author on pubs so that they can be the last author. This is absolutely necessary for the CV as a communication device. Undergrad volunteer? Rotation student? Summer intern? No problem, they can be the first author right? Their level of contribution is not really the issue. I can see an industry scientist that wants to start making a push for management doing something similar to this.

As always, I return to the concept that you have to do your own research within your own situation to figure out what the expectations are. Look at what most people like yourself, in your situation, tend to do. That's your starting point. Then think about how your CV is going to look to people over the medium and long term. And make your authorship decisions accordingly.

92 responses so far

Supplementary Materials practices rob authors of citation credit

(by drugmonkey) Dec 11 2014

This is all the fault of qaz. And long time reader Nat had a blog post on this ages ago.

First, I shouldn't have to remind you all that much about a simple fact of nature in the academic crediting system. Citations matter. Our quality and status as academic scientists will be judged, in small or in large ways, by the citations that our own publications garner.

This is not to say the interpretation of citations is all the same because it most assuredly is not. Citation counting leads to all sorts of distilled measures across your career arc- Highly Cited and the h-index are two examples. Citation counting can be used to judge the quality of your individual paper as well- from the total number of cites, to the sustained citing across the years to the impressive-ness of the journals in which your paper has been cited.

Various stakeholders may disagree over which measure of citation of your work is most critical.

On one thing everyone agrees.

Citations matter.

One problem (out of many) with the "Supplementary Materials", that are now very close to required at some journals and heavily encouraged at others, is that they are ignored by the ISI's Web of Science indexing and, so far as I can tell, Google Scholar.

So, by engaging in this perverted system by which journals are themselves competing with each other, you* are robbing your colleagues of their proper due.

Nat observed that you might actually do this intentionally, if you are a jerk.

So now, not only can supplementary info be used as a dumping ground for your inconclusive or crappy data, but you can also stick references to your competitors in there and shaft them their citations.

Try not to be a jerk. Resist this Supplementary Materials nonsense. Science will be the better for it.

__
*yes, this includes me. I just checked some Supplementary citations that we've published to see if either ISI or Google Scholar indexes them- they do not.

25 responses so far

Older posts »