Field of Science

On Screwing Over a Generation of Biomedical Researchers

We, the biomedical community in the United States, live in interesting times. Below is the funding dollars for NIH over the last couple of decades. I completed my Ph.D in 1998 about the time the historical trend line and actual funding line separate. This separation marks the 'doubling,' when Congress passed legislation to double NIH's budget over the course of 5 years. I completed my post-doctoral training and obtained an academic position at a top research university in the midst of the doubling. This was a time of great expansion and much hiring by universities and research institutes across the country. Along with the hiring came investment in new facilities to house and recruit the increased numbers of scientists. This was not an instantaneous process at all institutions, but those who did not expand missed out on this additional ~38 billion dollars of new resources. It was shortly after the doubling was completed that I obtained my first NIH R01 grant.
From Here
Since the doubling was completed, you'll notice there has been a steady decrease in funding every year through 2013. In fact, 2008 represents the year when the 'doubling' was essentially undone. As of 2008, NIH is funded less well than if it had simply not been doubled and kept on it's annual growth rate of 3.3%.

Remember all those universities and research institutions that hired and expanded in the early 2000s? Well now what do you think is happening to those researchers? Maybe we shouldn't care, I mean those institutions didn't have to expand. But this is a lousy argument in my opinion. Congress let it be known that they and by association the country cared about biomedical research (FYI: this was under a republican president). Of course the government also cares about the troops, at least when it comes to sending them overseas to fight. Once research institutions expanded and hired more scientists to make use of this additional funding, Congress changed its mind about caring. Kind of like support dries up when the troops come home. So we hired more scientists who also trained more researchers to help conduct the research. These trainees obtained PhD's and actually wanted jobs too (go figure). And the cycle continued over the short term. If you look at the number of PhD's awarded over time in the biomedical sciences, which is primarily funded by NIH, you see a large increase in the number awarded beginning around 2003. This is 5 years after the 'doubling' began, which is the average time to completion for a biomedical PhD.

The problem as you might have realized is that with the lag between the initiation of the doubling and the graduation time of PhD's, as the first round of PhD's arising from the increased funding during the doubling entered the workforce, the downturn began. Of course there was already 5 more years of researchers in the midst of their training. So we see a huge increase in the number of PhD's being conferred between 2003 and 2008, when ~8000 biomedical PhD's were conferred (remember there are ~24,000 more PhD students in years 1 - 4 still being trained).

So concomitant with reductions in funding, we were still churning out PhD's. Armchair quarterbacks will state the biomedical community should have planned for a decade plus contraction that reversed the NIH doubling and put us in a position where biomedical funding is comparatively worse than at any time in my life time. (I am not arguing absolute dollars are less, they are not, but for the number of scientists that were trained and put to work under this system, we are much much worse.) Of course if we could have predicted that, we could all fund our research programs by visiting Las Vegas every year. This would reduce a ton of paperwork.

At this point when I talk to undergraduates interested in graduate school in biomedical fields, I tell them about the problems and encourage them to think about what they want to be doing in 10 -15 years. If it's running their own labs or being in a science leadership position, then I ask if they would consider moving to a different country. They might have a chance elsewhere.

Birthday wishes

Alright, so today is my birthday. YAY me, I managed to survive another trip around the sun (despite what many Americans think). Not really a big accomplishment considering ~20,000,000 other people are alive world-wide that were born on this day at some point during the last 115 years. Similarly,  ~880,000 other people in the US were born on this day. Hell, I share a birthday with ~150 people in Greenland (Inuuinni Pilluarit! fellow birthdayers). The disconcerting thing to me is that tomorrow is the first anniversary of a set of major seizures I had, which basically destroyed all memory of last year's birthday and most of the surrounding few months. While there is no reason to consider tomorrow especially concerning, it does give me a reason to think about that event more than I have over the last few months. While this year has been an interesting one (with all the baggage associated with 'interesting'), it has also been an amazing one. First, I didn't die. Second, I have mostly recovered from the seizures (I think), although there are some issues associated with the medications I'm on or the psychological impact of knowing there's a potential bomb in my brain. Third, I met an amazing person who I thoroughly enjoy being with. Fourth, watching my son grow up. He's currently 12 with a standard deviation of ± 6 years, depending on the day. Fifth, I am actually generating some data, although given the current funding climate may be a waste of time. Regardless, I love learning new things about the world in which I live. Sixth, I am enjoying making beer and can brew some decent ones (although a solid blueberry ale has still escaped me). Seventh, I enjoy writing and am able to it again (broken hand), but hate that I have not done more with this blog since my brain blowing up. So this is a simple way to dip my toes back in the water. Hope to get a couple more papers out the door this year as well as some grant applications (waste of fucking time probably) and post some items at least a couple of times a month.

Birthday cake (hopefully cream cheese frosting)
If I get a cake with candles, my birthday wish for this year is to not almost fucking die again (included in the previous statements is to not successfully die either).

What I read (2014)

(Grade A-F, no E's) Title-Author Additional thoughts

B+      The Hunger Games by Suzanne Collins. Good story, can see why it was wildly popular. Not a fan of the ending though, Collins sets up issues with the system government and rebellion, but then ignores it at the end. I realize there are sequels, but it seemed to me to be an obvious missing piece.

D      Doomed by Chuck Palahniuk. Bleh. Not clear this is a sequel (to Damned) and sadly it seemed like the first needed to read to understand what the hell was happening in this story. Characters were all horrible and no reason to care about them.

C      Raising Steam by Terry Pratchett. Some amusing scenes, but not as fun a romp as many of Pratchett's other books. Also lacked the social commentary found in many of the Disc World novels. Or maybe I just don't like trains that much. 

B      It by Stephen King. A good story working back and forth in time with great character development. While the monster is horrific, the bullies are worse (like in real life).

C+      Sleeping Late on Judgement Day by Tad Williams. The last of the three part Bobby Dollar story. (Though probably not the last incarnation of Bobby Dollar or his world.) This book gets a boost from the first two, which I enjoyed more. Much gets sorted out, although not all, but it requires a "from right field" plot twist that I found a bit of a stretch. Maybe with more development I would have more readily flowed with it, but it was abrupt IMO. 

B-      The Fifth Elephant by Terry Pratchett. Pretty good read, hits on issues of rapid communication (clacks) and the intrinsic antagonism between fundamentalism and reform.

D+      Best Served Cold by Joe Abercrombie. Meh, unlike the Garrett PI, this was not a fun read. Good idea on a revenge story, but weak in execution in my opinion.

A      A People's History of the Supreme Court by Peter Irons. Excellent brief history of the US Supreme Court, focusing on important decisions both good and bad and important.

B      The Fell Sword by Miles Cameron. Does not live up to the first book, TheRed Knight, but still a good read. A few too many characters that prevents depth. Strongly recommend the series.

A      The New Jim Crow by Michelle Alexander. Excellent book! A must read. Extensive references that support the positions taken. Thoroughly engaging and damning.

B+    V for Vendetta by Alan Moore and David Llyod. Because 1984 could never be rewritten as a graphic novel.

F     Memories of Ice by Steven Erikson. What the hell was I thinking? Oh wait, I was just recovering from a life altering seizure. Will take another seizure before I read the next installment.

B      The Road by Cormac McCarthy. Loved the movie, which does the book justice. In fact, I would argue the movie is better because it establishes more of the back story with the mother.

B+   Religion and Science by Bertrand Russell. I know it is only recently that atheists have become militant and clearly articulated the endemic problems with religion. Of course that viewpoint requires ignoring Bertrand Russell's 19XXX book.

A     Spillover by David Quammen. Outstanding book, reminiscent of Laurie Garret's 'The Coming Plague.'

B+   Introducing Garrett PI by Glen Cook. Funny, a blast of a read.

B     Sandman: Preludes and Noctures by Neil Gaiman. Great rewriting of the god of sleep.

17 books this year, worst outing ever, but considering I was mostly dead for the spring and part of summer I'm not too surprised. Probably my son read as many books as I did if not more (including the Hunger Games, Divergent, and Maze Runner series). Of the 17 books: 13 were fiction for fun (and 2 were Graphic Novels, which some people may not count but they should),  2 were US history/sociology, 1 was philosophy/religion, and 1 was science.

Rape Culture and Parenting

Enough with the rape threats already.

As the father of a pre-teen I have concerns about the internet and online trolling/cyber-bullying. Well those birds have finally come home to roost. Today I get a report from the school that in an online chat room (associated with an extracurricular activity my kid is involved in) the following chat was sent to my son:
fuck you racist bitch you rape your fucken mom.
There were associated smileys, which I omitted. Unfortunately I first had to deal with my son's responses to CatiousHair and had to discuss online etiquette. This was not the first time, some of these issues (of online etiquette) have come up, but now I had tangible data to use. After that was dealt with and several hours and dinner had passed, we were able to once again discuss the chat room discussion from the standpoint of rape. Because there's nothing I wanted to do more than talk about rape, what rape is, what it means, how rape affects people, the commonality of 'rape' in online trolling. We got to talk about what it means to be in a community, how hard it is to avoid the online rape culture, how easy it is to exclude entire swarths of humanity based on your behavior.


Not an easy discussion when the protagonist is prepubescent and knows about the parts and how they are supposed to work, but little else. But we had the discussion. Sadly, I know we will have to have this discussion many more times over the next few years. Thanks humans and while you're at it, fuck off.

Women in Science: an Example of Roadblocks

It's exciting times in our Medical School. We recently completed a Strategic Plan entitled Strategic Vision 2025 and we hired a new Dean. There are numerous problems at the university medical school, but these are off-set (in part) by the many strengths of the medical school.
Our new dean has embraced the Strategic Plan and had a Town Hall meeting this last summer to outline in broad terms 6 goals to be addressed in the next year (some are of course longer term goals, but can be started sooner rather than later). These goals line up well with those outlined in the Strategic Plan, although the Dean has put them in a context he finds most compelling.

The 6 goals are to:

  1. Increase scholarship
  2. Increase NIH ranking
  3. Improve diversity
  4. Merge the diverse health systems
  5. Reduce medical student debt
  6. Increase financial resources
In the format of a town hall, there was little time to get into specifics of how each goal will be reached. However, the two approaches to improve diversity were striking to me in their focus. First the issue of diversity is readily backed up with data, this can not be ignored as simply an issue of 'political correctness.' As a percentage of the state population, minorities are underrepresented in the medical school faculty as are women. Half the state population is female and, not surprisingly, half of the assistant professors in the medical school are women. However, there is a precipitous drop in the percentage of women being promoted to associate and full professor such that 30% of associate professors are women and 10% of full professors are women. 

This begs the standard question, why is there a discrepancy?

Two general answers to this question come to mind. 1, there is a problem with the women that are hired such that they are unable to be successfully promoted; 2. there is a problem with the administration that, at least subconsciously, fails to promote women.

During said town hall meeting two ideas were presented to improve diversity within the medical school faculty. First, we need to have more mentoring to improve the success of our female faculty. Second, we need to have workshops to facilitate female involvement in various collegiate activities.

These two ideas suggested one thing to me: the administration believes the reason women are not being promoted is because of the women.

I am a huge supporter of mentoring, for everyone, at all levels, but I wonder why mentoring is specifically pointed out here. Are women not being mentored, but men are? If so, then this is an administration problem not a women problem. Are the women we hire in special need of mentoring that the men do not need? If so, then this is an administration problem not a women problem, because we are clearly not hiring high quality well trained women. The same arguments can be made for the workshops. Maybe the men are getting this extra information in the locker room or over cocktails after work when the women are not around. Regardless, this is an administration issue and not a women issue.

What struck me at this town hall was the focus was on 'fixing' the women so they could be promoted, not 'fixing' the administration such that women were not overlooked and ignored.

I couldn't help but wonder what the women faculty in the audience of that town hall thought. Not growing up in an environment where I was implicitly considered lesser based on my gonads, I couldn't help but think they would be insulted. But maybe they are used to it.

'How It Works' via xkcd

First Class in the Books

The state fair is over indicating the end of summer and the beginning of a new semester. I taught my first class today, which of course means I basically met the students and introduced them to the course. In other words, we went over the syllabus…kind of. The course I am talking about is Eukaryotic Microbiology, an upper division course that focuses/uses the primary literature to teach students about eukaryotic microbes, scientific thinking, argument, etc.

The third slide in this lecture is the following (from here with slight modification)
This slide gets used throughout the course but I use it in the Introduction lecture to highlight how little almost all students are familiarized with the diversity in the eukarya. Basically students are familiar with green plants at 12:05, fungi (except for the microsporidia) at 3:15, and the animals, including sponges, at 4:00. Other than the Opisthokonts (in blue) and a minor fraction of Archeaoplastids (in green), the vast vast diversity of the eukaryotic lineages are basically ignored in biology courses. Admittedly there is lip service played to Plasmodium falciparum (the primary agent of malaria) over in the Alveolates. But just look at how little is brought up! Of the eight major eukaryotic lineages, only two are routinely discussed, think of all the biology out there we know so little about! This, in my opinion, is incredibly exciting.

Aspects of this problem were recently brought up by Larry Moran and PZ Myers (by way of   Jeffrey Ross-Ibarra). Again all that diversity noted above falls into the choice C.

Now that I hopefully have instilled some small sense of awe or at least lighted a candle of interest in my students, we deal with the syllabus and some course specific issues. I do want to point out this course is writing intensive, which means a bunch of things but basically we do a fair amount of writing (surprising huh?).

There are two things we did today I want to mention. First, I asked them what their goals are in relation to the course. (Other than getting an A.) So I had them spend a couple of minutes writing down their thoughts and then we discussed them. This represents one easy way to get the students talking in a relatively stress free environment. Open discussions are an integral part of the course and the sooner I get students comfortable speaking up the better. My goals were: 1, to give the students a broad sense of that importance of eukaryotic microbiology; 2, to increase their fluency with the scientific literature; 3, to hone their critical thinking skills. I won't divulge the students' goals.

Second, we discussed plagiarism as it is a writing intensive course. I have found that students know what plagiarism is, but if you ask 20 students for a definition, you'll get 12 - 15 different variants. I also have the students write down what they think the consequence for plagiarism should be. This leads to yet another relatively stress free discussion and serves develop a sense of student ownership for the course. Once the discussion is complete, we agree to a definition and consequences that is posted onto the course website. This year we came up with:
The 4161W class of 2014 has agreed to define plagiarism as not giving credit for others' work, including words and ideas, that is not common knowledge.
and the penalty:
Students who are found to have plagiarized will receive an F on the assignment and be reported to the Office for Student Conduct and Academic Integrity for the 1st offense. A subsequent offense will result in an F for the course and another report to the Office for Student Conduct and Academic Integrity.
As normal for the first lecture, I did not get through everything. Luckily Friday allows time to finish up going over the course and to discuss our first paper. This discussion allows me to demonstrate what I expect of the students when they do presentations and gets the students started reading papers. The paper we discuss on Friday is:
Complementary adhesin function in C. albicans biofilm formation. Nobile CJ, Schneider HA, Nett JE, Sheppard DC, Filler SG, Andes DR, Mitchell AP.Curr Biol. 2008 Jul 22;18(14):1017-24. doi: 10.1016/j.cub.2008.06.034.

Uncommondescent Unfockinghappy Unfockingfortunately

Uncommondescent makes Jesus facepalm
About a week or so ago, I noticed a spike in traffic to a post I wrote. The post was about how I see science being written and disseminated more and more from a PR standpoint. It's more about selling your work as totes-magotes awesomeness, about claiming no one ever once could have possibly grasped the revolutionary new paradigm you figured out, about how your one result is changing how we think about cell biology, cancer, the world, nay the fucking universe. That kind of crap.

Apparently this is how 'science' is done in the intelligent design creationism community, so the people at uncommondescent took offense. I utterly love the title:
Precious: American atheist finds ENCODE to be bullshot science
My post was many things, but I didn't consider it to be precious. Regardless, thanks!

I am American and my post was specifically how I see science changing in the USA (you can tell from my title, where I use the acronym USA), so it seems relevant that uncommondescent would note my nationality.

I am an atheist, and proud to state that. How that relates to my post on how I perceive science is being sold seems irrelevant. I also have black hair, albeit with some gray, why not title the post: Precious: Graying American finds ENCODE to be bullshot science. I am a parent so maybe: Precious: American dad finds ENCODE to be bullshot science. I'm also a scientist, which seems relevant. It's more relevant to my post than my views on god, my hair color, or parental status. But you know what, me being a scientist is not relevant to uncommondescent's post. In fact, I'ld argue it undercuts the strength of their post. Pointing out I think their god is hooey, is essentially poisoning the well so that their readers, conservative christians, will not bother reading my post or thinking. (I was going to write more after 'or thinking,' but realized I didn't need to.)

Also, I used the word bullshit, not bullshot. Bullshot makes no sense. What the fuck is bullshot science? Unless you're an 8 year old and think jesome crow or freaking or shoot or darn does not mean exactly what everyone knows it means. As an adult I will say Jesus fucking Christ shit damn. Not all the time, but when I think it is appropriate. If someone writes something I want to comment on or acknowledge, I will not change their word because I am too delicate to deal with it.

Here is their beef with my post:
Not exactly the way he pronounced it, but read it  here. Readers will remember that ENCODE found that, contrary to Darwinian (Christian or otherwise) hopes, there was very little human “junk DNA” — and those people have been having a fit about it ever since:
Note, they link to my post (thanks), but won't someone think of the children! I used adult language in my post and they just willy nilly put in a link to it without considering the ramifications of a reader seeing words like bullshit! But let's get to the meat of their argument: ENCODE found that little human DNA is junk and that this finding is contrary to evolutionary science. Two questions:

1. Did ENCODE find that little of the human genome is junk? No. The ENCODE authors changed the definition of 'function' as it is generally used in genome biology and then used their definition to claim that most of the human genome does something. It's true that all of the genome does something, every last base does something, 100% of the genome does something. Each base is bound by DNA polymerase and used as a template to make a copy of the cognate strand. This stuff was suggested by Watson and Crick in 1953 and demonstrated shortly thereafter. But this is 'trivial' function and not what 99.9999% of scientists mean when they discuss genome function, at least until ENCODE. Regardless, the issue is not how we use the word function, it is whether having a function promotes a piece of DNA from junk to non-junk status. In my car I have some old receipts for gas on the floor. It's there, I can show it does something, like absorb water from my wet boots when I get in the car. As far as the car is concerned, it's still fucking junk.

2. Is junk DNA a prediction of evolutionary biology? No. In fact, we've known about the E. coli genome for almost two decades and understood much about it before we had the entire sequence. Know what? It almost all does something, there is very little junk in there. I would love to see some publications that support the idea that junk DNA is required in evolutionary theory. And please for fuck's sake don't use the term Darwinian evolution when discussing junk DNA. DNA was not even known to be the genetic material when Darwinian evolution was developed. Avery, McCarty, and MacCloud published the definitive work in 1944 (Origin of Species came out in 1859). Hell, the Modern Synthesis had been well established by the time DNA was linked to heredity.

Now I'll admit there may very well be papers out there suggesting that junk DNA is required for evolutionary theory to be tenable. The point is not only to find support for your position, but to deal with the contradictory evidence and ideas as well. This was part of the point of my original post.
These issues are what concern me most. This is not how I was trained as a scientist and is philosophically opposed to my understanding of the scientific process. In science, at least at the core, we try to prove ourselves wrong. We do not try to prove that X causes Y, we try to prove that X does not cause Y. When we obtain data that undercuts a paradigm, we do not write a fucking press release, we first consider how we fucked up the damn experiment! 
I mean unless you work for ENCODE, then fuck it.
Notice, he chooses ENCODE (“if ENCODE is right, then Evolution is wrong” to rant about).
Upon reading the above sentence from uncommondescent, does anyone think it suggests I wrote 'if ENCODE is right, then Evolution is wrong'? Because that line comes another intelligent design creationist (who also has issues with big kid words).

What amazes me is that I used ENCODE as an example of what I perceive is the problem exactly one time (in a 778 word post). I also mentioned the paradigm shifting rewriting the textbook work on arsenic bacteria. I was also going to use the Darwinius masillae fossil with it's joint publication-TV special clusterfuck but I couldn't remember the name off the top of my head when I wrote the post. None of this shows up in their response. In fact, the entire point of my post was ignored, it's almost like they had an agenda and simply jammed my post into their framework. If it makes you feel better uncommondescenters, I put an update in my original post just for you.