Field of 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.

The Changing Climate of Science in the USA (not a post on climate change)

UPDATE: If you are coming from please substitute the letter o for all letter u's to avoid 'the vapors'. Also, substitute Darwinius masillae anytime you see the word ENCODE so you won't miss the fucking point (to make things easy, you'll only have to make this substitution once).

One of my heroes: from here
I have seen a shift in the way science is being conducted in the United States. This shift still reflects of minority of the science being done, but it also represents the majority of the science being reported or disseminated to the public. In short, it appears to me that the pendulum has swung from favoring rigorous science to favoring and rewarding what I will call 'splash' science. To be clear this struggle between rigorous and splash science is not new nor different than in previous generations. Nor is all rigorous science not splash and vice versa. However, I think in the US the pendulum has swung dramatically to the splash at the expense of the rigorous. This change in trajectory is not surprising as funding has constricted immediately following a massive expansion. There are too many mouths at the trough and they are competing for those few morsels of grain.

More and more, scientific research is being sold on its revolutionary impact and not on its scientific merit. Of course 'impact' sounds much more important than 'merit'. Hell, important and impact both begin with the letter 'i' so there must be something to that. It seems much more science is being sold as 'paradigm shifting,' 'completely unexpected,' 'novel' (the only one that is true, but only in the trivial sense), or 'needing to rewrite the textbooks.' In these cases, it's also 99.99999999% bullshit (e.g. ENCODE).

2nd edition, 2011
Now admittedly and importantly, there are many studies that reveal unexpected results that lead to interesting and a variety of unexpected questions, which can themselves lead to new insights. For example, I sat in the audience at an American Society of Microbiology conference on Candida and Candidiasis where the phenomenon of white-opaque switching (a well known but poorly understood phenotype of certain Candida albicans strains) was directly and elegantly linked to mating (a process that, at the time, had recently been described but the biology nor the relevance was not understood). This was one of those 'HOLY SHIT!' moments that was amazingly cool, but also neither paradigm shifting nor required the rewriting of textbooks. In almost every single case these types of studies will not shift a paradigm nor require the revision of any textbooks. The results may be unexpected, but at most they will lead to the addition or significant revision of chapters in specialized topic books, such as the Candida and Candidiasis book from ASM.

It could be argued that inflating the importance of a study does not undercut the underlying data. But this argument is generally wrong at several levels. First, in order to emphasize the ephemeral, the actual suffers. In order to emphasize the ability to grow in high levels of arsenic, Wolfe-Simon focused on the bacteria using As in place of P in DNA and other macromolecules. The ability of the isolated bacterium to grow in such high concentrations of arsenic is interesting, but this was ignored to focus on the rewriting of textbooks on the structure of nucleic acids, which was wrong. Second, to push your paradigm shifting results, you have to actively ignore or overlook the contradictory data, even that data contained within your own work. Third, you have to discount and/or disregard the data, usually mountains of data, that led to the current paradigm in the first place.

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! We do not identify the next great anti-cancer therapeutic target, we identify a protein that is required for uncontrolled cellular replication in a certain cell line under certain growth conditions in the lab.

If we as scientists, have truly identified a paradigm shifting result or established that the textbooks need to be rewritten, this will come out in the end. If we hoist ourselves by our own petard, then we have a problem. Think about this, when we push these boundaries of science as I see happening too often in publications and manuscripts I review, are we any different than the snake oil salesmen of yesteryear, or the person at the other end of the psychic hotline, or the politician that assess every problem to some simplistic social issue we already agree with.

We're scientists. We're better than this.

Response to poorly argued opinion on student evaluations

This week the campus paper published an opinion piece by Harlan Hansen, professor emeritus, College of Education and Human Development entitled 'The missing factor of course evaluation discussion' with the subtitle 'The University should use its best faculty to teach and improve others.' I have commented previously on the issue of student evaluations and release of information to prospective students. Despite a previous attempt to have student evaluations released, which failed by a large margin, the proposal will not go away. Basically, I think the administration and associated faculty who want the information released should simply mandate that the information be released and send a big 'and fuck you too' to the 90% of faculty who do not want student evaluation information released. Otherwise, it seems like we will just keep discussing and voting on it until the vote comes out the right way.

Regardless, I want to rant about this opinion piece for several reasons.

First: the first paragraph or as I like to call it, holywhatthefuck!

When I arrived as a faculty member of the University of Minnesota in 1968 I remember a publication that rated course instructors. A few years later, I believe, it suddenly ceased publication because of faculty requests, I assume. Forty-three years later, the request for that information by students is still a nagging question.
Can you find all the logical fallacies? So in 1968 there was a publication that ranked course instructors. I will accept this position at face value, but I have some questions: was this information disseminated to the student body and if so how? Was this information disseminated to the faculty as a whole and if so how? Was this information used by students to help decide which classes to take? How were course instructors rated? Did this information rate every course and every instructor, including non-faculty instructors (I'm assuming some courses/labs were taught by graduate students in 1968, though this may not be the case.)? I'm not sure if Dr. Hansen realizes this or not, but technology and dissemination of information is fundamentally different in 2014 than it was in 1968.

Then we get to the second sentence, which includes both 'I believe' and 'I assume'. I cannot help but wonder what kind of academician Dr. Hansen was. Let's accept that this publication existed and ceased publication in the early 70s. Why should we assume that it ceased suddenly (did you hear the ominous music just then?) because of faculty requests? Dr. Hansen simply assumes it. Here are several other possibilities: maybe no one went to the library to obtain this voluminous publication to help choose courses or for any other reason, maybe it was out-of-date by the time this information was published (remember this was before computers were collating all the information via scantron forms and then imported into excel spreadsheets for rapid organization), maybe the costs associated with the publication were not off-set by the usefulness of the publication. See there are three other possible reasons without even trying. Your assumption carries no weight.

Finally, we get to the last sentence, which has little to no linkage to the previous sentences. Have students been requesting this information for 43 years? Is it really still a nagging question? In 1983 there was an outcry for instructor rating information, even though that information wasn't actually collected and therefore didn't exist? A student who turned in  a paragraph like that in my classes would not fare well. But alright, let's assume an editor took out all the cohesion in the introductory paragraph setting up the issue to be addressed.

Second: unsubstantiated claims or as I like to call it, pullingshitoutofmyass, I assume.

Consider the following points made by Dr. Hansen:

"students say they want information that will lead them to more interesting and effective professors. Second, faculty who were quoted in the news minimized the students’ requests as wanting easy courses with high grades by instructors who tell good jokes."
I'm sorry but isn't an instructor who tells good jokes generally considered more interesting? Regardless, I have to concur that many, not all, students would rather have an easier course on a topic than a more difficult course on that topic. I could be wrong, but a slightly earlier opinion piece published in the campus paper seems to support my position.
"relative to my years of experience at the University, ratings of faculty instruction do not change over the years." 
I would not be surprised about this, but data please. Also, how the hell does he know? Didn't this bible of instructor ratings stop being published in the early 70s? Maybe he was department head and saw the student evaluations (when we actually had them), which would raise the question, why didn't he provide training for his ineffective faculty?
"“A” and “B” instructors have no problem sharing their ratings
Again data please. Hell, I'll even provide a data point, on my student evaluations using a 6 point scale (6 being being the top score), I fall well above 5 in almost every category every year. In those remaining categories I still fall above 5 every year. So, does this make me an 'A' or 'B' instructor? It seems like it should, and if so count me as an instructor who has a problem sharing my ratings.

Third: problem solving. 

By establishing the problem using holywhathtefuck and pullingshitoutofmyass approaches, Dr. Hansen then proceeds to assign blame. See it's not just the ineffective instructors, it's an administration problem. (Again I want to stress we have never defined effectiveness or established criteria to quantify effectiveness other than student evaluations, which are best correlated with students' expected grade.) And now we get to the solution:
"The president of the University should charge deans and department heads to put in place programs that can help all instructors improve over time."
Personally, I think these programs are useful and important. However, I wonder where the resources are going to come from for deans and department heads to do this. Programs do not come from the vault of readily available no expense resources. This solution also raises the question, why don't faculty development programs exist already? The answer is that they do, I have attended several. I wonder when Dr. Hansen retired such that he is unaware of them. Admittedly, these programs are voluntary, but they do exist.

Of course Dr. Hansen does have a remedy to this apparent lack of teaching development:
"The key factor is assigning current colleagues who have demonstrated quality teaching skills to share and demonstrate with those in need. While this may appear threatening to individuals, it establishes a community of scholars within each unit where, eventually, everyone can share positive techniques with each other."
Yes. because nothing rewards successful teaching like getting more work and responsibilities to train and manage the ineffective instructors. Don't forget, these are the same ineffective instructors who really don't want to get better as Dr. Hansen noted above when he states that faculty instruction does not change over time.
My opinion of the opinion: from here.

I am still surprised by the whole student evaluation movement. We have no good data suggesting that student evaluations gauge effective instruction, some studies do suggest this but many others do not. I have heard from colleagues that students simply want more information about a course and god forbid they go to some commercial site like rate my professor. Well I am all in favor for more information as long as that information is valid for what you are attempting to learn/show. Student evaluations do not, I repeat not, seem to correlate with effective or quality teaching, so what information are the students receiving about a specific course/instructor? The student evaluation is being changed to ask the following questions, which are relatively minor changes in wording compared to the current evaluation:
1. The instructor was well prepared for class.
2. The instructor presented the subject matter clearly.
3. The instructor provided feedback intended to improve my course performance.
4. The instructor treated me with respect.
5. I would recommend this instructor to other students.
6. I have a deeper understanding of the subject matter as a result of this course.
7. My interest in the subject matter was stimulated by this course.
8. Instructional technology employed in this course was effective.
9. The grading standards for this course were clear.
10. I would recommend this course to other students.
11. Approximately how many hours per week do you spend working on homework, readings, and projects for this course?
   • 0-2 hours per week
   • 3-5 hours per week
   • 6-9 hours per week
   • 10-14 hours per week
   • 15 or more hours per week
Of these questions, only those in blue are proposed for release to the students. Questions 7 and 10 seems to provide useful information on whether the student liked the course or not.  Question 8 is irrelevant to the discussion of instructor rating for the most part. Questions 6 and 9 may provide insight into the instructor's effectiveness and fairness. Question 11 is the great equalizer. If two sections of the same class are different here, which do you think a student would gravitate towards? This is not minimizing student concerns, I would rather take a course that required less work too other things being equal. 

You may be asking, 'Why the hell aren't questions 2, 3, and 5 being released?' Good question, as these seem key regarding a student's ability to decide which courses they want to take. Courses do not exist in a vacuum, without an instructor we might as well attend google university and write papers on vaccines and autism. Those questions are not being released because they may reflect specifically on an instructor. (Duh!)

Of course we must consider what ever will a student do without online released student evaluations? I mean what has happened over the last 43 years! If only there were some way one student could relate information to another student about a course. Some form of communication, I don't know, like texting, or tweeting, or posting to any number of social media sites, fuck maybe they could simple open their mouths and have words come out in the direction of another student's ear. If only. Sadly, I doubt our students are even aware of these modes of communication.

Life and Lemons: Follow-up on 'the' conversation

I told you we would get back to Dr. Ego Tistical

This isn't really about Dr. Tistical specifically, but the medical doctor (as opposed to nurses, EMTs, etc.) profession in general. Based on my experience I expect that a majority of medical doctors care deeply about titles and I wonder why. My issue isn't so much with the focus on titles, it's the implicit disrespect of others that comes with their use of titles. The conversation between myself, the Dr. Tistical, and the medical technician John, is one I have seen played out many times. The doctor goes by Dr., I have a Ph.D. so I am introduced as Dr., and the non-professionally degreed individual is referred to by their first name. (Of course if the doctor is unaware that I have a Ph.D., then I am also introduced by my first name.)
Establishing positive relationships, from here
Herein lies my issue, if you are going to introduce yourself as Dr. Tistical, your colleague is not John, it's Mr. Getoveryourself. By promoting your lofty accomplishments, but not granting your colleague, and dare I say fucking partner in the whole patient care-testing process, the same level of respect, you are a douchebag. In this specific conversation, Dr. Tistical always called me Angry, and I always called her Ego, until we were in the presence of John, then I was Dr. Choice. I am ok being introduced as Dr. Choice or Mr. Choice as I think we could do with certain level of formality in professional settings. When I introduce my son to new adult friends/colleagues, I almost always introduce them as Ms. or Dr. Lastnamehere. My issue is that I was introduced as Dr. Choice and John was introduced as John. Why not Mr. Getoveryourself or why not introduce me as Angry?

This is not an isolated case. I have met with many doctors over the last two months. They are uniformly introduced as Dr. Soandso. It's a toss-up on whether I am introduced or referred to as Angry or Dr. Choice. I have also met with many nurses, technicians, and other hospital staff. They are uniformly introduced by their first name. I am introduced or referred to almost always as Dr. Choice. Why? 

There are many ways a doctor could introduce themselves. For example, one could introduce themselves thusly: 
Hi I'm Ego, I'm your neurology doctor. How are you feeling today Angry?
This is the form the nurses and staff used to introduce themselves to me.

I want to stress that the interactions I had during my life and lemons episode with the doctors, nurses, and staff were wonderful. And my issues with introductions and titles were  mild. I did not get the sense that my doctors were being elitist snobs and I actually believe this is a training issue. When students are in the clinic they see the Dr./staff and Dr./patient interaction modeled. However, this culture can foster a cesspool of elitism where douchebaggery can thrive if not flourish. This is my reason for writing this post. For example, one weekend my ex-wife and I were in the elevator going to her lab when a guy wearing a lab coat got on. My ex introduced me to Paul (name not changed because he is a waste of space).
"Paul, Angry. Angry, Paul." 
"It's Dr. Imanarrogantfuck" immediately responded Imanarrogantfuck. 
Wow just fucking wow, was my only thought."Dr. Choice, Dept. of kissmyass" was my reply.
Paul looked somewhat abashed, maybe professionals don't ever wear jeans with holes in them like I had on or maybe MDs and/or PhDs in Paul's world do not marry non-MD and/or PhDs or maybe they don't allow their spouses to work. I don't know or care, from that instant on, Paul was and always will be a waste of a sperm and an egg. (Aside: Paul is a small man, literally and figuratively.)
A possible result of unreciprocated titles, from here

Life and Lemons: Testing and Results

When we last met I told that I was recovering from a seizure(s) and detailed a bit about how my short memory was fried or at least seared. After a few more weeks of recovery and numerous doctor visits and tests, I know a bit more about what happened and what didn't happen. The important thing is that mentally I am back to normal or back to the same level of abnormality I was at pre-seizure (I think).

I also know that I have to accept the fact that there are important aspects of the 'medical incident,' as one colleague described it, that will never be known. However like any scientific study, we have hypotheses that are best supported by the available data. But this is a story for another time. 

Today I want to discuss the neuropsychological testing I had done and the outcomes of those tests. (Aside: Anyone think I would be writing these posts before the ACA and changes in insurance regulations preventing being kicked off the roles for a preexisting condition or massive increases in rates?) Several weeks after the birthday gift from god, I went in for a scheduled four hours of testing. At this point, my short term memory seemed to be working reasonably well, I had mostly recovered from an angiogram (the recovery was from having my femoral artery perforated as part of the procedure), and was back at work part-time. In short, I was feeling confident and not too concerned with the upcoming tests. 

Then I got to the hospital. I found the check-in office easily, despite the fact the hospital is actually four or five distinct buildings connected by walkways. The buildings are color coded and signs directing you to each building by color are frequent. Basically finding your building and the elevators within each building is trivial. After check-in, I was brought through a number of doors and down a few corridors to a new area to wait. My doctor, Dr. Ego Tistical more about her later, said she needed a few minutes and asked if I needed anything. I asked for directions to a cafeteria for some food and coffee, mostly I wanted coffee. She gave me directions to another building that used a different set of elevators. Getting there was no problem, the directions were great. Getting back, not so much. I was able to get back to the elevators easily and to the floor I needed, but then I was in the tangled web of similar corridors and doors. I made a couple of correct decisions/guesses and was about to go the wrong way, when the doctor waved to me from her office door.
'Was that the first test?' I asked
"No, but it would be a good one.' was her reply.
We sat down and talked about my recovery, how I thought I was doing, etc. I tried to be as honest as possible, not embellish or over-estimate how I was doing. In response to my mental functions, I said I thought I was back to normal although I tired out faster. I thought back to 90% of pre-seizure function was a conservative estimate. We talked about the seizure and events surrounding it, wasn't sure why though. Maybe it was to see  if I remembered anymore details, see if I had any questions (I did, and still do). After going over the results of the testing, I think a major reason for this discussion was to have a discussion. The topic was probably irrelevant, but it allowed her to get an idea on my verbal and language skills. She talked about the testing that would be done and answered my questions about what the tests assess and how they do it.

Then we began the testing.

Actually we went to a different room, where I was introduced to John. (All names changed to protect the innocent and not so innocent.)

"John, this is Dr. Choice. Dr. Choice, this is John, he will be administering the tests."
I extended my hand, "Nice to meet you, please call me Angry."
"Nice to meet you too, do you need anything before we begin?" asked John
"Well I'll let you get started and will talk with you again after the exams are completed." Dr. Tistical told me.
"I'm good John, thanks," I noted, coffee in hand, "Thanks Ego, see you then."
(See subsequent post for some thoughts on this conversation.) 
So now we begin the testing.

First, as I recall was the repeat the number game. John says 1, 2, 3. I say 1, 2, 3. We start with three digits all 1 - 9, then four digits, five digits, six digits, etc. We do a bunch of each group before we move up to the next group getting progressively harder. This easy to more difficult is a recurring theme throughout. Not sure how many digits we ultimately got to, I think it was eight but maybe ten. It's fairly easy to repeat back a single set of six digits, but try it after doing 5 - 10 sets of three digits, 5 - 10 sets of four digit numbers, 5 - 10 sets of five digit numbers, then do the six digit numbers. Maybe it will be easy for you, but it started getting difficult for me.

After doing digits forward, we repeated the process, but I had to repeat the numbers in reverse order. This was much easier than the forward process, probably because it was easy to memorize the first couple of digits, then the last couple of digits were fresh in my mind. So this reversing the digits was much easier. Except it wasn't. This was actually turned out to be my worst performance, but I felt good about it at the time (Kruger-Dunning?).

Finally, I had to repeat the digits back in numerical order: 4, 6, 2, 4 was repeated 2, 4, 4, 6. I also found this one easy because I could simply bin the numbers or remember that there were sequential runs of numbers like 3, 4, 5, 6 became 3 - 6. Apparently I actually did well on this exam, like I thought I did.

Now we move on to different tests. There was the see a picture like the one below:

The picture goes away and now I have to redraw it. Then the next picture comes up and as above they get progressively more complicated and have multiple objects. After completing this test, I am told that in a few minutes I would have to draw the pictures again from memory. Wish I known that at the beginning, but of course that is part of the test. Surprisingly, I was able to nail all these pictures. First time through and more importantly the second time through.

Next test was to be read a story and repeat it back as close to verbatim as possible. These were fairly long passages that were heavily detailed oriented. Not sure how I did, but it was frustrating trying to remember all the specific details. After the first pass and my attempt at repeating the story, John reread the story and I repeated it again. This time I was able to include more details or correct those I got wrong the first time through. We then repeated this process with a different heavily detailed oriented story. FYI the first story was about a woman, Mary, who cleaned offices and was robbed on 12th Ave. while going home on 8th St. This was problematic because she didn't have money for food for her kids or the rent. Luckily, the police officers took up a collection and gave her some amount of money $50 and change. (Probably the details are incorrect, except 8th St. but these are the kind of details included and only represent a tiny minority of the details included.) No idea what the second story was about, but I bet if you started it, I would recall the major details. After this activity was concluded, John then went back and read a number (20/story?) of statements me to which I had to give true-false responses. 'Mary worked as a secretary.' 'Mary was robbed on 8th St.' those kind of statements. Often upon hearing the factoid in the statement, I realized the error I made in my retelling. I have no idea how I scored, but it felt painful.

There were dexterity tests. Using just your left or just your right hand, pick up these pegs and insert them into the holes as fast as possible. Repeat using the other hand. I'm left handed so of course my fastest hand was my right. There was also keep your hand flat on the table and use your index finger to press a counter as fast as possible for 10 seconds. Repeat a couple times. That sucked, but I think I did ok from years of cell counting. Actually I didn't do as hot as I thought. I realized at the time my left hand was not as good as my right hand in these tests. This was surprising to me because I am left hand dominant, and it isn't even close. Of course, it turns out I have an issue with the right hemisphere of my brain (topic for another post), which correlates well with brain lateralization and handedness.

There were trivia tests. 'Who is associated most closely with the theory of relativity?' and language tests 'What does those who live in glass houses should not throw stones mean?' These latter tests also included John showing me a written word and asking me to say the word and define it. Again they got progressively harder, but were all simple for me. Until we got to the penultimate word, John unfortunately flipped to the final word, which I saw, before flipping back to the second-to-last word. I said and defined it, then as John was going to the final word, I said the word (as I think it was pronounced) and said I didn't have a clue what it meant. He asked if I wanted to take a stab at it, to which I replied 'No.'

There were three more tests I want to mention, although there more tests taken. The first was a move the block test, referred to as the Tower of London test. Basically, you start with the blocks arranged on the posts as shown on the left and John has another set arranged differently, like that shown on the right. The goal is to move one block at a time among the posts to make the image on the right. 

Starting position, from here
Goal position, also from here

The other point is you need to do this in the least number of moves and also in the fastest amount of time. I was never told which factor was more important, move number or time. In one trial, I made a couple of moves quickly and realized I screwed myself. Instead of trying to figure a way out, I simply reversed the moves back to start and did it the right way.

The next test I want to mention was the last test I took and one John had never given before. It was a pattern recognition test, kind of like the Wisconsin Card Sorting test. I was shown a picture and asked if it was represented by the number 1, 2, 3, or 4. The practice trial was the only one where I could guess more than once. The key thing here is that the picture was the first of many in a series that all followed the same rule. For example, the practice picture was:
 My first guess was 2, for two things, a white square on a black background. 'Wrong' John said. Then I guessed 4, for the four-sided object. 'Wrong' John repeated. Since there was no way 3 made any sense, except by way of exclusion, I went with 1, thinking one object. 'Right' John stated. The rule was in fact # of objects on the background. Once I had this card correct, John went to the next card and the next and the next, all of which I got correct because I had determined the correct rule. Now remember, this was the practice trial. For the real trials, I got one attempt on the first card. Right or Wrong, we went to the next card in the series. So in a real trial, it would have taken me three cards of trying to get the correct rule and the remaining cards correct. You should also realize that the cards varied in number of objects, shapes of the objects, colors, etc. So in the above example the next card could be 2 black triangles on a white background and now the correct response would be 2. Once the real trials began, if you guessed/deduced the correct rule in the first couple of cards, you breezed through them. If you did not things got more complicated, because you had to remember the previous cards, your guesses, and the hypotheses (rules) you already tried. You get to card 4 after incorrect guesses on the previous 3 cards and think of a new rule. Now you think back, does this new rule work for the previous cards and do I actually get different answers using this new rule for those cards? I was told this tests for 'executive function' but in many ways I think it tested for frustration coping mechanisms.

Finally, there was the memorize, in about 2 seconds, this person's face, now this person's face, now this person's face, etc. There were many faces, I guessed 30, but was told during the results phase that there were 48! Once we went through the 48 faces, John got out another stack of pictures and I was simply asked whether a face he showed me from this new stack was in the original stack or not. Some of these were easy to pick out, there was angry guy, happy guy, high guy, Ego (looked a bit like the Dr.). There were many others I remembered or could eliminate due to some particular hair style, facial feature, etc. and many I could not recall one way or the other. We know eye witness testimony sucks, but remember I was asked to specifically remember these faces and that I would be asked to recognize them or not afterwards. I found much of this test extremely difficult and think it reinforces those studies raising concerns about eye witness testimony. Of course, about 20 minutes later after taking some other tests, John pulled out a stack of pictures and asked if the faces were in the original deck or not. Now I am trying to parse whether a given face was in the first deck or one I remembered from the second deck. This test sucked.

Four hours of testing completed in two and a half, this was off-set by the fact I didn't take any breaks and also that I did not have any significant impairment (I was not aware of this at the time.). Regardless, when I left I did not feel good about myself and how I did. The confidence I had going into the testing had fled. After two weeks, I met with Dr. Tistical to go over my results. The good news, as mentioned a second ago, is that I have no loss of mental function. I scored extremely well overall, and ended up on the right hand side of the curve. Even those tests I did poorly in, I was still well to the right of the curve. Dr. Tistical told me about cognitive reserve, which I hadn't heard about before, and apparently I had enough of it to recover from the seizures. Here's hoping I do not have another, as there is no guarantee that I will be so fortunate in the future.  
From here, I ended up in the 3σ area

Life and lemons: The Memory Addition

About two weeks ago I opened my eyes realized I was in a strange room laying in a strange bed. I saw my ex-wife sitting off to the side. Other people were around. I thought to myself 'oh shit! wtf happened?!' I then immediately passed out.
What you see  ~1nsec before 'WTF?!'' leaves your lips.
At least I think that's what happened. The last thing I remember, in real time, was attending a talk given by a colleague on a Friday afternoon. But since that time, I have learned a lot about human memory using an experiential approach. At some point after the talk, probably the next day, I had a number of seizures that seem to have been fairly significant. I was then unconscious and kept alive via a ventilator for a couple of days. Not sure what drugs, besides anti-seizure medication, I was given but they behaved more powerfully than aspirin. Of course, I'm also not sure how much residual burn-out there was from the massive neuronal firing that took place in my brain.
From here: I was probably the brain in the lower right UPDATE: lower left
So as I slowly recuperate (not actually that slow considering), I figure I will document some things I learn by going through this process. I should probably point out that nothing like this has ever happened to me before. I did knock myself out once, for a minute or two, in graduate school playing wallyball, which sent me to the hospital with a concussion. I also smacked my head pretty good as an undergraduate, which did not send me to the hospital, but may have caused a concussion. Otherwise, I have never had seizures nor had many head injuries. At least not that I remember.

Not that I remember. This is what I have experienced since waking up. I have been amazed at the specificity of what I have forgotten, the extent that my memory has lapsed, the rapidity with which I think I can effectively think again, yet the areas where I still have difficulties.

Again, I remember going to my colleague's talk. I think I remember the general topic discussed, however I am generally familiar with what my colleagues do, so maybe this reflects more long-term memory and not actual memory of the talk. I remember transforming a yeast species Friday morning (sadly that experiment was lost over the intervening week and a half and was needed for an R21 resubmission due in a week (some of that preliminary data they can't ask for)). After the talk, some friends offered to take me to a local bar for a celebratory birthday beer. I didn't mention this started on or around my birthday? Oh well, happy birthday to me. I had one beer and then went home. All this other stuff, I had to be told by others. I have no recollection of even discussing going out afterwards. The only reason we know I made it home is that that is where the police found me just before getting an ambulance the next day. My memory really stops at ~5PM on Friday and again no injury occurred at this time. It is a viable hypothesis that my friends promised to take me out this week instead and are using my memory loss to their advantage.

On Saturday, I was expected at the airport to pick up my family and at some point I sent a text message letting them know I saw the flight was on time. Again, no record of any of this exists in my brain. No record of anything from Saturday exists.

I did not arrive at the airport, which was met with surprise. I consider myself dependable and generally succeed at arriving early for things like this. Further surprise occurred when I did not answer a phone. At this point or not too long thereafter (sorry but I was unconscious), my family called some friends for a ride. They also called the police. Things got a bit weird here, initially the Minneapolis police department was contacted, I'm guessing because 911 was dialed as people drove through Minneapolis. The Minneapolis police department told them to call back in 24 hours. I probably would have been dead, so thanks for those birthday wishes. After my son was taken care of and situated my ex and a friend called my hometown police, who decided to check out the house. They even exited their vehicle and looked in the windows where I was observed seizing. Deciding that 24 hours might be a bit long to wait, they simply kicked in a door and started keeping me alive. I was already in the back of the ambulance getting ready to hit a hospital by the time my friends and ex arrived to the scene. (Full disclosure, I heard these details several times, but I was still on the foggy-side, so it's possible a detail or two is not exactly correct.

So ventilator for a couple of days, then awake. (This is definitely one place an exclamation point would never be appropriate.) I think it was two days before I actually began to sense that the fog was lifting. I was walking, initially with a walker but by Thursday on my own. I could actually read, at least my brain seemed to be able to concentrate and focus well enough to read. I read about 20 pages of a book I was 3/4 of the way through. I currently remember those 20 pages, but there are several hundred pages I've lost. I've gone back to reread hoping to spur some memory, but nothing. I remember looking forward to finishing the book and being done with it, I don't think it's worth going back to near the beginning and rereading knowing how I feel throughout the rest of the book. The interesting thing to me is that these 100s of pages were read weeks before the seizure. Yet they are gone.

Once I could type reasonably well (I'm still getting better at it), I contacted my undergraduates to let them know what happened and have them contact me. One of them, who was continuing a project from the fall, had to remind me the specific experiments being done that week, but I knew the goals of the project. However, for the other students I had no clue. I couldn't have given you a reasonable guess. The thing was I could have listed all the things I wanted done in the lab and the projects I wanted to move forward. I simply could not look at one list and tell you who was working on what parts.

I know my son and I went to see the Lego Movie. I know Chris Pratt played the lead character. Otherwise, nothing. Can't tell you the plot, other than it was lego-centric, but duh!

I've looked at my calendar and I will see something out of the ordinary and haven't the slightest idea what it's for. I was planning to submit a fungal white paper next week, I guess. No idea what it was for. Doesn't even matter, spending the last two weeks either in the hospital (week 1) or slowly getting my shit back together (week 2), there's no way I can complete it in time. I know how to cook, I know how to get around on roads (although I am not allowed to drive for 3 months). I know how to do laundry. I remember how to play my flute and can still figure out music fairly well by ear. I can type, email, etc. although these higher level motor skills take a bit longer than they used too. Still every day is better.

I can read science papers, albeit slowly. I can focus on seminars and can identify areas to question, however it is more difficult vocalizing that question. That may have as much to do with the chunk from the side of my tongue I bit off as anything else.

So while I am still going to take it slow for a few weeks or at least not push myself too hard, it's good to see improvement. It's also interesting to experience the short-term memory losses associated with the seizure, not a good thing , but interesting. It's amazing how fragile memory is and really begs the question 'what is memory?' Maybe neurologists have a handle on this answer, but I am not aware of it.

An Exciting Weekend!!!!

Looking for things to do this weekend (and you do)?

Why do you need something to do, you ask? It's Valentine's Day weekend you point out. You plan on lots of dancing and romancing with your significant other, you say. So why do you need something to do?

Two reasons: 1. To prevent chafing, it's not a bad thing to take a break. 2. To embrace some science.

On Saturday:
we have the annual homeschool (creation) science fair taking place at Northwestern University in Roseville. The fair is in the Maranatha Hall lobby.
From 36 head north on Snelling Ave.
Judging is from 10:00 - 12:30, so the kids will be there then. I love talking science with kids, so I plan to be there around 11:00. Afterwards I plan on having lunch at Grumpy's (marked with a star). Even if you don't go to the fair, feel free to join me afterwards. I'll be at Grumpy's, in the bar area, sometime between 12 and 12:30. If you go to the fair because I brought it your attention, you must play nice with the kids.

On Sunday:
we have Dr. Sehoya Cotner speaking at the Southdale Library at 2:00. Her talk is "Are we still evolving?" Of course the answer is yes, but there is much interesting information and fun associated with these talks. Afterwards there may be a lunch, although I'm not sure I'll be going. I may have to brew up some beer instead.
The pin denotes Southdale Library - Duh
If you go to the talk because I brought it to your attention, feel free to be an ass. (Not responsible if Dr. Cotner kicks your ass though.)

Highly Conserved Is Relative

When discussing some aspect of biology, we often want to know how common is the gene, pathway, structure, interaction, or other phenomenon we are interested in. This can be important in two distinct manners: 1. if we find our gene, pathway, etc. is maintained in many different types of organisms, this suggests that our gene, pathway, etc. likely plays an important or fundamental role in some level of biology; 2. if we find our gene, pathway, etc. is not found in different types of organisms, this suggests our gene, pathway, etc. likely can tell us something about the unique biology of what we are studying.

To discuss this phenomenon of commonality, we say that something is conserved (or not). Of course saying a gene, pathway, etc is conserved doesn't tell us much by itself, because we need to know the level of conservation. Is the gene, pathway, etc. conserved among sister species? within a class? a phyla? a kingdom? The answer to this question tells us a lot about whether we are looking at a fundamental process or at the level of specificity of the process. In the seminars and papers I read, I generally see a short-hand approach to discuss conservation where the speaker or author uses a superlative or adverb to suggest the level of conservation.

For example, I recently heard a talk where the presenter stated that a protein was 'highly conserved, being found in both mammalian systems and yeast.' That sounds pretty impressive. But I immediately thought of eukaryotic phylogeny (mammals and yeast are both eukaryotes), and this figure I borrowed from Lab Rat a former FoS blogger who blogs at Scientific American. This is a figure my Eukaryotic Microbiology students see every week in class (the bacteria and archaea are not included in this figure).
I want to draw your attention to the Opisthokonts over at ~4:00. This is the supergroup of eukaryotes containing the metazoa (animals) and fungi. If we blow up this area of the figure, the last common ancestor of animals and fungi is indicated by the red arrow. (FYI humans, including you, are indicated by the green arrow.)
Now look at the first picture and think about all the eukaryotic diversity absent from the Opisthokont group! Is something found in both mammals and yeast highly conserved? I suppose so, since that last common ancestor lived ~1 billion years ago. But mostly I suppose not, because the vast amount of eukaryotic diversity lacks it.

A tangential point, but it's probably worth pointing out that the eukaryotic kingdoms we mostly hear about: animals, fungi, and plants represent little of eukaryotic diversity. Animals and fungi are contained within the Opisthokonts and plants are contained within the embryophytes at ~1:00. Everything else on this wheel represent non-animal, non-fungal, non-plant eukaryotes.