The Cold North Shore; What If Its Not Cold?

Lake Superior

Back from an official, albeit short, vacation. The only work related thing I did was check to see how things were going in the lab via an email. Have a paper review to complete and could have worked on it there (didn't). Lots of emails to reply to, they didn't go anywhere and I can deal with them tomorrow. Almost always when I take time off, I end up working at some level (revising a manuscript, working on a grant, etc). This is not a good thing. This time I did it right.

Spent almost an entire day, it was overcast, reading and went on a short walk to stretch my legs. Finished the vast majority of Stephen King's Holly, an Xmas present (I have since completed it). It was a great way to reset from the busy end of the fall semester that moved directly into holiday events, which while nice are also taxing. Felt more relaxed than I had in a long time. The following day was spent exploring the city of Grand Marais, bought a new book (support local booksellers), and enjoyed a beer at Voyager brewery. 

Very little animal life in evidence up there, a few crows and that was about it. Did see a deer on the drive up. You might think this is not surprising, because we are deep in winter, but usually there is plenty of evidence of animal activity especially via tracks in the snow. Can identify squirrels, rabbits, deer, mice, etc pretty easily. However, this year there is still essentially no snow on the ground and the temps have been well above normal. Walking the dog in a sweatshirt, outdoor slippers, and a hat! Usually its a heavy winter coat, boots, mittens, and boots for the dog. This led to a thought, does the increased temperature affect the hibernation patterns of animals like bears, which do wake up occasionally? I realize there are other cues that control hibernation, otherwise animals would come out of hibernation when we have an almost yearly late January warm up, which is followed by another month long drop in temps in February. Animals that wake up too early, may not be able to find food. Many plants do this as well. When to germinate? When to start budding new leaves? Much of this is controlled primarily by day light length (but temperature plays a role too). This is good, because if temperature was primarily in charge, an early warm spell could be disasterous. But what about hibernating animals? They are not out in the open so day length shouldn't be much of a factor. Guess I'll spend some time on google later today.

New Beginnings and Resolutions

Its been too long letting this site sit in limbo, maybe purgatory. I have a couple of goals this year and one thing I think will help accomplish them is to write about things I enjoy and/or want to write about more frequently. So I am planning to put something here, usually (hopefully) science related three times a week. This particular post is not science related, but damnit, I'm counting it.

Obviously the fact this is coinciding with the New Year brings up the idea of New Year's resolutions. I like the idea of New Year's resolutions, but why decide to start something on a particular date, such as January 1? I think it is pretty well agreed upon that these date-specific resolutions tend to die untimely deaths usually before the end of February, which is ironic since its the shortest month. For me, using this date as opposed to October 15th, is that this is a good transition time. I am done with my teaching heavy semester, which is why I didn't attempt to start this October 15th, because I knew it was unlikely to be successful. Also the holidays are done, so there was essentially chaos for two weeks and now it's time to establish a new routine for the upcoming semester. Writing, for fun, is one way I can ease back into a routine.

Things I'm looking forward to this upcoming semester:

• Being able to attend more seminars in person. In the fall, basically the big ones for me occur either when I'm teaching or end about five minutes before I need to start teaching. I love the option of attending online, so I can listen and see the slides but can leave early without being disruptive.
• Reading more science. Time limitations in the fall kept me focused on those papers to help with teaching, manuscript prep, and a grant submission. Now I'll have more time to read things that just look interesting (another resolution is to read a paper a day unrelated to my research interests, which I'm starting after my vacation which starts soonish).
• Read more for fun. I never stop reading but have much less time for it in the fall, usually just before bed. Now I have more time to read for enjoyment. I already started that but will emphasize it in my vacation and continue on....probably until next fall semester.
• Time to brew! I have a bourbon barrel porter aging in a bourbon barrel (an Xmas gift) right now, but that's it. :(

So some science things I'm thinking about and have been for quite awhile. Why does sexual reproduction exist? What control species barriers? How do endosymbionts become plastids/mitochondria? What should my next science tat be (I already have this one figure out, just need to get it.)?

Ok, I have accomplished day 1 of writing for my personal benefit. No need to go on and on and on and on.

Daily routine

7:00 am coffeeeeeeeeeee
8:00 am more coffeeeeee
9:00 am more coffee maybe shower, maybe already showered. Regardless let's assume already showered

10:00 get to work/lab If I car pool this means getting dropped off at the St. Paul campus and taking the shuttle bus to near where I work, if I don't car pool this means parking next to my building and kicking the fuck out of the card reader until it decides I can get into my building.

10:05 open some doors and walk up several flights of stairs. Go to my office and unlock the door and drop my shit off.

10:10 go back through all the doors and down the stairs to get some more coffee. This requires going through key carded doors that don't require kicking the shit out of. In fact if I get near them with my card they work (Fuck you one outside door that is a total fuckstain!).

10:15 drop off coffee in the office and go to bathroom to wash hands. Yes I'm thinking about the shuttle bus handles and chairs as well as the door knobs I've touched getting to and from my office as well as getting my third coffee. Yes I use soap and get the paper towels ready ahead of time. Yes I use soap and use the paper towels to turn off the water. Yes I get more paper towels, which is ok my hands are still wet, to finish drying my hands and open the door. I use my foot to prop the door while I took the paper towels and exit the bathroom.

12:00 I don't know if this is the correct time, but I wash my hands because I've been in the lab doing science. (If I haven't been doing science in the lab, I wash my hands anyway because its time, and I want lunch.)

1:00 Go into the bathroom and wash my hands, I might use the facilities too as I've had 3+ cups of coffee.

3:00 Leave lab or office and wash hands, because its time and whether I realize it or not I've almost certainly done some things regrind door handles, stairs, countertops, or something lots of hands have touched.

5:00 At gym, use sanitizer. After running laps on track use sanitizer. Do some weight lifting with pulleys. Mucho sanitizer.

5:45 Don't touch face, you don't know what you've been in contact with.

7:00 Arrive home and wash hands well with soap and water. Make dinner, assume I'm safe. Wash hands and dishes, partner will appreciate (at least the dishes part) and I'll feel good about a full day, complete with active knowledge of where my hands have been.

9:00 get ready for bed, wash hands anyway, because as confident as you are, you're probably off by a bunch.

#Flattenthecurve

Manifestation of Prof Stress

The Spring semester has ended, which means something from a teaching perspective but not from a research perspective. At least that's true for me. I know others can vary in their teaching/research mileage. For me, teaching is basically a fall/spring semester concern. I do teach a couple of weeks during the summer, but this requires little prep work so I don't count it. Research is a year long venture, but does suffer during the fall/spring, especially the fall, because of my teaching duties. A couple of weeks ago on consecutive nights, I woke up around 2 am from bad dreams. These dreams, I won't say nightmares because they were stress inducing but not terrifying, related to these two big areas of my professional life.

The first night it was a research related dream and the focus was on grants, big surprise to people in the field I expect. The dream actually started out on a good note as I was just awarded an R21 grant from NIH! The happiness and relief of having some money to conduct the research I want to do, quickly transitioned to stress as I began thinking about how quickly I could get someone hired and trained to do the research successfully. I became increasingly stressed because the R21 is only a two year grant. If it takes 6 months to hire and get someone well trained (a stretch in my opinion), I basically have 6 more months before we need to be generating most of the data in order to write a larger grant. For those not in the know, it takes a few months to write a proposal (for me at least) and then ~ 9 months before funding decisions are made. Thus, in order to maintain constant funding from the onset of the R21, I basically have 12 months to get most of the work done with an untrained person. I woke up a mix of happiness combined with a whirlwind of stress. I was up about 2 hours before going back to sleep.

The second night it was a teaching related dream. In real life I had just completed final grades for my Spring semester course and was breathing a sigh of relief to have ~3 months to focus on experiments and writing (papers and grants). In my dream, I felt like I was in the same place and at work setting up experiments when I realized my Fall semester classes were starting in a couple hours and I hadn't set up the course website, planned any lectures, etc. I was running around trying to get together some slides for the introduction and to print off some worksheets for the students but couldn't find a printer. To make things worse I couldn't find out where my class was meeting and time was ticking down to the point where I was figuring out how late I would be. Basically this was my adult version of the 'just realizing you have a final in a class you didn't know you were enrolled in all semester' nightmare. Again up for a couple of hours without being able to sleep.

Haven't had anymore repeats of the stressmares™, but apparently my sleep schedule basically requires waking up at 2 am. I do get some reading done I guess, but would rather get a straight 7-8 hours of sleep. Stupid brain.

On the 2016 AmericanBrexit

I planned to write an after-election post on what I thought about the election. I assumed a Clinton win and wanted to write about the divisiveness that exists in this country. I wanted to write about the racism, sexism, xenophobia, and homophobia that was normalized during this election. I wanted to write about the normalization of violence in politics. I wanted to write about how none of this goes away simply because Clinton won and that we needed to work hard to offset the divisiveness.

I wanted to write about those things...

and then Clinton lost the electoral vote...

So what do I write now? What is there to say?

We have not only normalized racism, sexism, xenophobia, and homophobia. We have made it the official position of the country. Are all Trump supporters racist? sexist? homophobic? No. Maybe many are, maybe most aren't, I don't know. But when the KKK backs your candidate, when other white supremacist groups are working to get your candidate elected, you have to own that. When your candidate rates women on a scale of 1-10, talks about the size of his penis, you have to own that.  When your candidate's choice of vice president advocates electro-shock therapy to 'treat' homosexuality, you have to own that. You don't get to say, but I'm not homophobic, I like those people, and get a pat on the back.

I learned some things that were articulated by Secretary Clinton, we are a much more divided country than I would have guessed. It's probably because I matured and live in a setting of higher education where I am exposed to amazing and talented people from all walks of life regardless of gender, color, religion, country of origin, etc. I'm not terrified of the 'other' like many people in this country. 'Home of the brave'? I think not.

I no longer think most of the people who voted for Trump are racists, sexists, xenophobes, and homophobes. This leads me to question why these people voted for him. There is the anti-establishment crowd with whom I can commiserate. Neither party has done much for them, although one party is outstanding at allocating blame at the 'other' for all the suffering they feel. The allocation of blame can lead to racist, sexist, xenophobic, and/or homophobic ideologies. But here's my problem, if you really feel the establishment is fucking you over, why vote for one of the parties? Why not vote for third, fourth, etc parties? Why not get things done at the local and state level to build up alternative solutions? That's a long term solution, but how long did African Americans live in bondage or the effects of bondage (which Michelle Alexander eloquently argues is rampant today), when did white women finally get the right to vote? Some people work hard over a long period of time to get their intrinsic rights, but apparently lower middle class and lower class white people can't wait.

Maybe you think Clinton is the most corrupt politician ever. Trump has a fraud case this month and a rape case next month, Clinton emails no court dates. Trump foundation is a farce that he doesn't donate to and uses to pay off personal debts. Clinton foundation only put out 88% of proceeds and used the other 12% for overhead. Millions of dollars spent thousands of hours used and nothing on Clinton. Republicans have controlled Congress for the most recent 6 years and nothing. Are the republicans that incompetent? If yes, why did you vote for them? if no, why do you continue to call Clinton the most corrupt politician?

You are upset with the system, you just gave a party the White House and Congress. Trump gets to fill Scalia's seat (because the party you voted for refused to do their job) as well as probably another judge. For the next generation (not 4 years, an entire fucking generation) you have supported the party that wants Citizen United to remain the law of the land. You can kiss having government be interested in your needs goodbye when companies and billionaires can donate millions of dollars without oversight. On the plus side women's reproductive rights will be set back 50 years, but fuck them. (Not literally because they'll have to keep their legs closed to hold up that aspirin.)

83% of Americans identify as Christian. Tell me what aspect of Trump's rhetoric over the last 18 months you find Christian? Is it 'grabbing them by the pussy'? Is it mocking a disabled reporter? Is it egging on supporters to commit violence? Is it the overt racism (birther movement, etc)? Would Clinton get the pass Trump got if she was on stage with her 5 children by 3 different husbands? But there's a war on Christmas.

My point is, many Trump supporters for whatever reason do not care about all the other things. The female racists don't care about the sexism, the financially concerned don't care about the racism. The list goes on and on and on and on. People are upset, that's their justification for ignoring the hate. This is the mentality the causes some people to think I'm pissed, so I'm going to crash into this car that I think cut me off. This is the mentality the causes some people to think I get to use public lands to feed my cattle for free, and gun toting douche bags support them. This is the mentality that gets women raped because of how they dress.

There are major divides in this country. This election uncovered the extent of that division. Now let me ask you, how does electing Trump solve these problems?

Here's my pessimistic view. Trump has legitimized bullying and the basest of our instincts. The republican party has learned that this approach works and works better than expected. Olympia Snowe (former senator) and Susan Collins are republican senators from Maine that I disagree with on many issues but I think would not support this appeal to the worst. Cruz, McCain, Christie et al have shown that they are happy to give up values for power. So I see Congress moving farther to the right. The democrats will also move to the right to try and recruit republicans who care more about values than power. The DNC will assume more liberal voters will stay with them because anoth option is non-existent.

Young women, non-whites, Muslims (it's a religion so you can't tell based on country of origin or skin color), the LBGT community, and anyone else who could be considered 'other', I feel for you. You are in a bad place now. I sympathize with you, which at some level makes me an 'other' too. Hell I'm an elite because I have an advanced degree, so I'm already an 'other'. At least I can blend in, although I tend not to. "Others' you are in a bad place. We can, and should, work hard to get Congress out of republican hands in two years, but the long-term damage is done. The Supreme Court will be staunchly in the conservative column for the next few decades. I'll be dead before this can be rectified, but my son won't.

My son is growing up knowing that bullying is a legitimate and workable strategy. N**ger and B**ch are now terms that can be used without any real repercussion. Hate is a reasonable approach to getting what you want. I do and will continue to do my best to teach him the 'do unto others...' approach to life, but he is now at the age when friends and society have a growing influence on him. Pussy, in reference to the vagina, is now a part of his lingo. He didn't learn it from me and I'm trying to explain why words matter. My problem is the president-elect of the USA has made pussy 'normal'.

Since I can't even, here are some kittens and a puppy.

Cute kitten

Kittens with puppy

The Grant Is Dead, Long Live the Grant

Alas poor R21, I knew it well.  There comes a time in every person's life when you have to face reality. For me, one of those times came yesterday. My R21 grant, a two-year exploratory proposal, was assigned to a study section. The study section is the group of scientists who will evaluate your proposal and decide if it warrants funding.

Of the last 14 grants I have submitted, 12 went to this study section (11 of the more involved R01 type of proposal and 1 R21 ). Of these, 0 were discussed. 0/12 (o.00%). Basically, these proposals were considered by three reviewers to not be competitive (on average), so they were not discussed in front of the study section panel. In a study section, of the proposals discussed a fraction, roughly 10-20% actually get funded. So I took the time to write 12 proposals of which 0 were considered to be in the top ~30% (i.e. those discussed). Maybe I suck at writing grants.

The problem is that the 2 grants (both R01s) that did not go to this study section (each went to a separate study section), both were scored and discussed in front of the whole panel. 2/2 (100%). So maybe I don't necessarily suck at grant writing.

Now you may be asking why I sent my grant to the former study section and not a different one. Well, in my cover letter I suggested 2 study sections I thought were appropriate that were not the 0/12 study section. The administrators at NIH disagreed with me and sent it to the elephant graveyard of study sections. I no longer consider this recent submission to have any hope of funding or even discussion.

It's kind of the name of the game, but consider this. Consider the number of hours I spent reading the literature, writing, revising, and working on this proposal. Multiply that by 12 (not entirely accurate because there are resubmissions included in that cohort, which require less time) and you have an approximate amount of time wasted on grant writing. Now multiply that by all the people at my institution doing the same if not more and multiply that by all the institutions doing similar things. That represents the amount of completely wasted unproductive time. Compare this to teaching, where students learn something or writing reviews or papers where there is a tangible product at the end of your struggles. Fuck, playing Diablo III on my playstation at least provides some enjoyment and I get to level up!

FML

When I started my career, the valid argument was that the time spent working and reworking a grant put you in kind of a zen state of understanding and thought regarding that area of biological research. I agree with this thought. Now however, we are cranking out grant after grant after grant that are basically different aspects of the same thing. After that initial submission, the zen of understanding is lost to the trials of trying to get funding. Admittedly if your ideas suck it doesn't matter how many times you submit a shit idea, you won't get funded. However, from my reviews (from the 3 reviewers) suggest it is not a shit idea problem, but a great idea, but there were some others we liked better. (And by others, I mean other researchers we know who we like better.) So I am stuck resubmitting grants hoping these other groups do not have proposals in at the same time and that my proposals are good enough to compete with all the others in the same boat I'm in.

Maybe I'm just bitter, but when my proposals go to other study sections, they are suddenly competitive (n=2). I don't know what the message is here other than I believe my recently submitted proposal is already DOA and I highly discourage anyone in the US from entering into the field of biomedical research.

And on a more important and happy note:

But a massive YAY to the 5 supreme court justices with whom I agree and more importantly to the multitude of US citizens who are slightly more legal than they were before.

On Screwing Over a Generation of Biomedical Researchers

We, the biomedical community in the United States, live in interesting times. Below is the funding dollars for NIH over the last couple of decades. I completed my Ph.D in 1998 about the time the historical trend line and actual funding line separate. This separation marks the 'doubling,' when Congress passed legislation to double NIH's budget over the course of 5 years. I completed my post-doctoral training and obtained an academic position at a top research university in the midst of the doubling. This was a time of great expansion and much hiring by universities and research institutes across the country. Along with the hiring came investment in new facilities to house and recruit the increased numbers of scientists. This was not an instantaneous process at all institutions, but those who did not expand missed out on this additional ~38 billion dollars of new resources. It was shortly after the doubling was completed that I obtained my first NIH R01 grant.

From Here

Since the doubling was completed, you'll notice there has been a steady decrease in funding every year through 2013. In fact, 2008 represents the year when the 'doubling' was essentially undone. As of 2008, NIH is funded less well than if it had simply not been doubled and kept on it's annual growth rate of 3.3%.

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

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

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

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

Birthday wishes

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

Birthday cake (hopefully cream cheese frosting)

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

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!

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.

My Book Has Landed

I am super-excited! I won a copy of 'Species: A History of the Idea' by John S. Wilkins and it just arrived this evening (Can I get a BOOYAH)!

Of course that means I need to clear some things off my reading plate ASAP. I'm already sporadically reading Origin of Species (with 2 chapters for blog posts in the cue), Decline and Fall of the Roman Empire, and The Problems of Philosophy and I cannot take on another serious non-fiction book at the moment. Probably will whip through the rest of Russell's book in the next week or so and then I can crack the binding of 'Species.'

As an extra special bonus, my copy is signed by Dr. Wilkins, which I was not expecting and reflects my total awesomeness I'm sure.

Finally I want to plug 'Evolving Thoughts' as an excellent site to gain insights into the history of biological thought, biological philosophy, and definitely check out the basic concepts posts for primers on various important scientific topics.