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.

FUCK!

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.
Exactly!

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 uncommondescent.com 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