Field of Science

Course Corrections

I've been teaching a course for the last 15+ years. I love this course because I conceived it and brought it to fruition. Since its inception, it has been modified a lot, primarily through interactions with the students who take the course. Initially it was a 'lecture' course, but from its inception it involved plenty of reading the scientific literature, discussion of said readings, and writing. 

One of the first major changes to the course was to make it writing intensive. In practice this did not change the course significantly, but did add an overt writing instruction component that was there but less explicit. It was about this time that I was much more active in writing to a general audience and actively engaged in science communication. These are still critically important to me, but my communication to a general audience have moved to the periphery as other commitments and responsibilities have taken over much more of my time. Regardless, my direct involvement in science communication impacted the changes occurring concomitant with the change to making the course writing intensive.

Adaptation - Education in Action

From here

While every year the course changes due to which scientific papers we use and to student interests/involvement, the fundamental structure has remained intact. This summer I am making some relatively significant changes to the course, at least in how it is delivered. The course is structured around a weekly schedule, where Monday is a didactic lecture in the organism we are discussing and relevant background related to the papers we are reading. Wednesday involves short student presentations on two primary research papers the entire class reads (the students address five specific questions related to the paper, but do not present the entire paper). Friday is a discussion related to specific aspects of the organism, papers from Wednesday, and student input from online responses.These discussion are completely open and are hard to prepare for as the discussions can go in many different directions. Regardless, the following Monday we move on to a different organism and set of papers.

Based on student feedback, I am making some significant changes. First, I am changing the M/W.F schedule to  a F/M/W schedule. Because students are reading two primary research papers for presentation/discussion, they have asked for the extra time the weekend provides to read and digest the material, as opposed to the Monday to Wednesday turn around time. This makes a lot of sense to me, so I am making this change for next semester, although it requires me to make some substantial changes to the course schedule. Second, students overwhelmingly indicate that the discussions occurring on Wednesday post-paper presentation and Friday facilitated their learning and engagement with the material. However they also noted it was difficult to see the link among organisms and topics. To be fair, there is no obvious link between these organisms/topics, other than all eukaryotes living today descended from a universal ancestral population. However, this is important and while I highlight similarities between what we were discussing in week 1 versus week 4, it occurs in passing during lecture or the discussions. So to more directly show the linkage, however disparate among organisms/topics, I am developing weekly worksheets for students to fill out asking questions like how does paper X discussed this week relate to topic Y from two weeks ago. Instead of trying to convince students of how analyses in one area can inform a distinct area, I am going to ask them to do that work in a directed way. In some cases there may be no clear links, but these higher level thinking exercises can be extremely informative to the students during discussion, but also to me (the instructor) to observe student perspectives/understanding. Third, I am developing at least one new type of writing assignment or at least making it overt that a writing assignment is distinct in style/approach than other assignments. Currently, students submit four essays that fall under the umbrella of 'essay exam'. Although these essays are completely distinct (one involves assessing a specific scientific paper, another a compare-contrast essay addressing a biological question in two distinct organisms), it appears (based on student feedback) that the distinction is not apparent. This coming semester, I am going to grade several distinct writing assignments that are completely other words do not fall under an umbrella of 'essay exams'. We already have another writing assignment, a blog post, that students do not report the same concerns with the 'essay exam' assignments even though grade associated with the blog post is slightly more than the individual 'essay exams'.

Basically, I want to facilitate student learning and embracement of, at least, some of the writing assignments. Why do I want do to this? There is much literature noting that writing facilitates learning (this is my personal experience as well).I'm not sure much more is needed to justify these approaches. However, science communication is sorely needed in society, especially societies where a significant population is more than willing to embrace non-scientific modes of thinking to justify policy decisions.

Will these changes improve student learning? I think so, but will need to make the adjustments and see how it works. The good things are these changes built on a solid foundation and are easy to alter if they do not appear to be working.

Kicking Off a New Semester

It seems like yesterday I was knee deep in determining final grades, but Wednesday I am back in the   thick of it. Luckily, my teaching is much less in the spring, two classes that meet once a week. One is a three hours lecture/lab on the Biology of Beer and the other is a writing instruction course for students writing up their research. Since I have done both a number of times, the time commitment is not onerous (I've already paid the up front costs). Of course things can always be improved so there is always some time investment improving the course(s) and keeping things fresh, but this is nothing compared to doing it for the first time.

In the fall, I am 98% working on teaching, 10% on research, 5%grant writing, 10% manuscript preparation, and like 20% on admin things. Basically the fall sucks. So now that teaching is more like a hard 10%, how do I  maximize productivity on the research? I have a manuscript to revise, so that gets top priority, but also have two manuscripts that are basically done research-wise, so they are strong seconds....BUT grants need to be written, BUT papers need to be out there to support the grants. My life is Ouroboros, but with less rebirth.

Ouroboros tat from here

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.


How the Coronavirus and Flu Are Not the Same

There has been much attention, too much in my opinion, comparing SARS-CoV-2 with Influenza B. SARS-CoV-2 and Influenza B are the specific names for the viruses in question when we generally short hand Coronavirus and Flu, there are many types of coronaviruses, including SARS, MERS, and some versions of the common cold (although most colds are caused by rhinoviruses). There are also multiple types of flu, including influenza type A, B, and C, although A and B are the most common. From here on out, I'll use Coronavirus and Flu as this is how most people and the media discuss them, but realize this is short-hand. (COVID-19 is the disease caused by Sara-CoV-2 and is not a pseudonym, much like AIDS is a disease caused by HIV.)

Both viruses are RNA viruses, their genetic material is RNA and this is converted into DNA after infection into a host cell. These viruses force the host cell to use this DNA copy to make all the proteins required to make new virus and to make complete RNA copies which will then be packaged into new viral particles before killing the host cell and infecting other cells and/or hosts.

Both Coronavirus and Flu cause significant respiratory illness. Indeed, SARS is an acronym for Severe Acute Respiratory Syndrome. These infections make breathing more difficult, in large part due to immune responses trying to keep you alive, but they also make a patient more prone to getting pneumonia, which can also kill you. These aspects of infection help explain why the elderly, immunosuppressed, and young are high risk groups (It appears that Coronavirus is not particularly lethal in the young, however data is still limited in my opinion.)

At first glance it looks like Coronavirus and Flu are similar. This could lead some, like an orange baboon, to directly compare them. If we do compare them directly, its easy to conclude that Flu is much much worse and its a plot by the universe to be concerned about Coronavirus. In the US, Flu infects 10s of millions, leading to hundreds of thousands of hospitalizations, and 10s of thousand deaths! Every year!!! To date world-wide, Coronavirus has infected over 100,000 people and caused about 4000 deaths. For non-viral comparison sake, car crashes kill about 40 thousand people in the US, comparable to the flu virus. Gin deaths are similar in the US.
Your basic Orange Baboon. From here, although I realize the image on the left is an infant orangutang and the image on the right is an actual orange baboon.
Since we don't shut down schools, concerts, etc for the flu and don't seem to care that much about vehicular deaths and definitely aren't willing to do anything about gun deaths, what is the concern about Coronavirus all about?

It's because because these comparisons are, at best, inadequate but more likely abysmal.

First, we need to consider what happens when someone gets sick with either virus. Maybe nothing both viruses cause symptomatic infections, although these patients can readily pass the viruses on to others who may not be so lucky. Next possibility is you get sick but not so severely that you go to the hospital. Hopefully you stay home and recover, but this being America, many people will have to go to work or are otherwise unable to rest because social safety nets are for commies, you know like every other developed country on the planet. More severe cases lead to hospitalization and of those a subset will leave the hospital in a casket. Here's one of the first places where Coronavirus and Flu differ. Roughly 2-3% of infected individuals will die of Coronavirus, aka leave in a casket, this number will likely change as more information is obtained (in other areas of the world because the US is wasting time and energy NOT testing even likely infected patients). However, the Flu leads to death in roughly 0.1% of patients.

Second, lets consider some other critical differences.

1. There's a Flu vaccine! That's right there's a vaccine against influenza, but somewhere between jack and shit for SARS-CoV-2, to be fair it's closer to shit than jack shit. Regardless of what orange baboons say, it will be a long time, at the earliest before, there's a vaccine. In fact, it may take many years before there's a vaccine. We still do not have anything close to a vaccine to HIV and we've been working on it since the 80s. The flu vaccine isn't perfect because it has to be developed before flu season begins so some years its more effective than others (if it were developed afterwards, it would be too late to be useful....hmmmm). To be clear, even when the vaccine doesn't match well, it still provides some protection and reduces mortality and severity, shortens length of illness, and reduces chance of infection. Also evolution matters and flu, much like other RNA viruses, I'm looking at you SARS-CoV-2, evolves quickly. This is why you should get a flu vaccine every year. By the time a Coronavirus vaccine is developed, in the best case scenario, most of the planet will already have been exposed.

Ok, the savvy among you are already thinking, if there's a vaccine but still a shit ton of people die from Flu, why should I care about Coronavirus? Well, most people are not vaccinated for the Flu, maybe 50%, which is well below what is needed for 'herd immunity'. However, health care workers, doctors, nurses, EMTs, etc. are almost uniformly vaccinated against flu. Thus, they are much less likely to miss work because they have the flu, which means they are available to care for those who do get sick and require hospitalization.

2. We know the flu is coming! Look there's a reason you need a vaccine every year. As above its due to evolution. But here's the thing, for well over a hundred years we've known this is coming. Every single year. And as our medical personnel are kind of smart and know this is coming, they are prepared. Besides being vaccinated, hospitals and clinics generally have the resources available to handle the influx of respiratory illnesses that will show up during flu season. We know thousands of patients are coming in, so its factored into the medical care equation. Don't believe me, think this is some kind of plot conceived by the MSM? Ask yourself why do insurance companies, the epitome of capitalism in the US, prepare for these expenses every year? In the US, hospitals are generally revenue generating, at least for the wealthy, so why aren't they prepared for this change in hospital cases every year? The short answer is: they are prepared. They are prepared for flu, they are also prepared for other cases, like heart attacks and broken bones. However, they are NOT prepared for dealing with fundamental changes in the status quo.

Coronavirus is a change in the status quo.

3. Here's the problem if hospitals plan for X number of beds being occupied, even during flu season, what happens if more than X number of beds are occupied due to Coronavirus? What happens to any potential extra patients, like Grandpa with a heart attack? In the US, we live in a firm capitalistic society, if someone isn't making money then why bother. So hospitals don't have a bunch of excess beds for, just in case. Hospitals don't have extra doctors, nurses, or other staff sitting on the bench for, just in case.

TV medical dramas give a false sense of time frames in regards to infectious disease testing. One thing they do give reasonable service to is bed availability. If two school buses crash into each other, the local hospital cannot compensate with the increased patient load. This becomes the plot focus for episode this week. In these scenarios, patients are triaged and sent to other hospitals or patients left to wait for a team to be available to treat them. This is the drama of the episode. So what does this mean in the real world in the face of a pandemic?

4. If a small percentage of health service professionals, EMTs, nurses, doctors, get sick then everything fails. There are a finite number of nurses available to serve at a given hospital, there are only so many goalies available on game day (2 in fact). If the goalies get injured you are basically fucked. Yes there was this one game this one year that the team won, just saying. However, the reason this is notable is that most third string goalies never get in and when they do they fail.

If fewer medical professionals are available more people fail to receive adequate care, so these people get worse results. Furthermore, new cases get pushed to the back burner making the problem last longer. Also Grandpa who shows up with a heart attack is part of this queue.

5. This leads to the St Louis vs Philadelphia conundrum. (Not fair to either city.) During the flu of 1918, problematically called the Spanish Flu, Philadelphia took a Trump MAGA approach, not doing shit, and St. Louis took a more draconian approach of closing dance halls (clubs), schools, and other gathering areas. This this led to the 'flattening the curve' idea that is all over the nets.
From here
The gif is better in my opinion: Flatten the Curve

Basically the idea is that if exposure and infections are delayed, severe cases do not overwhelm the health care infrastructure. The bad part of this is infections occur over a longer period of time. The good part is that fewer people die! To be clear without flattening the curve, there's a much greater chance of people dying from Coronaviruse, but also Grandpa dying of a heart attack, because the health care system is overwhelmed. If doctors, nurses, and other staff are home sick they are not helping Grandpa out and there are not people on the zamboni who can come into the game successfuly.

We, in the US and most other places, are not prepared for pandemics. It's not our business model. However, by taking steps to mitigate the potential, and almost certain problems, we can respond adequately. To be clear people will die, people will get sick, there's no denying that. However, we can significantly reduce the number who die and get profoundly sick.

As an academic, a skeptic, and a realist I doubt we will succeed. Overall I think we are Philadelphia, not St. Louis.

Prove me wrong.

What I read 2019

A      The Shining by Stephen King. Excellent book! Saw the great movie of the same name. They're different, I'll leave it at that.

C-      Sherlock Holmes vs Cthulhu: The Adventures of the Deadly Dimensions by Lois H. Gresh. If you want to combine two distinct universe into one and spend a few hours on the beach reading about it, this one's for you. If you're looking for depth, look elsewhere.

A      The Institute by Stephen King. Great story, probably my favorite of King's recent works. Maybe a prequel/sequel to Firestarter, never read it, but saw the movie many years ago. Deals with many themes, not the least of which are reminiscent of locking kids in cages for political purposes.

D      Origin by Dan Brown. Pretty much every other Dan Brown book, except in Spain. Fast paced easy entertaining read, but I already read this story when it was called The DaVinci Code.

C      The Dread Wyrm by Miles Cameron. A good book to pass some time but meh. Good prose regarding troop movements and ideas of warfare, but I could use more, much more, on character development.

C+   Except the Dying by Maureen Jennings. Only read this book because I started binge watching Murdoch Mysteries on Hulu, which are based on the characters in the books this one starts. The characters in the book are profoundly different from those in the TV series, but its a fun read. I am looking forward to reading the next one by the fire this winter at Lake Itasca.

A     The Rage of Dragons by Evan Winter. A great world built by Winter. Definitely ephansizes the difference between the 'haves' and the 'have nots'. In this day and age, it is good to see the unaccountable powerful get knocked down a peg or two. Reminds me of Pierce Brown's Red Rising books in this way. 

B-    Nest by Terry Goodkind. Not sure how to define this book. Kind of suspense/thriller, but kind of sci-fi, if you count psionic powers (I do). Interesting premise, but as is Goodkind's want, it becomes a heavy handed political hammer in the latter portion.

B+   Empire of Grass by Tad Williams. Really did not like some of characters in the first book, which I expect was part of Williams story arc. Maybe I'll like root for them by the end of the trilogy. Could also be having a teenager, makes reading about teenage angst hit too close to home rather than being a fun escape.

B     The Stiehl Assassin by Terry Brooks. Been reading Brooks since I was a teenager, it's weird knowing this world is coming to end with the next book. Regardless, this quadrilogy is some of the best Shannara work since Elfstones and Wishsong.

A-    The Colorado Kid by Stephen King. I enjoy King's forays into different genres and styles, like the installments of The Green Mile and this pulp mystery short story. Really the mystery is a mechanism to describe how an outsider becomes accepted into a small community.
A     The Priory of the Orange Tree by Samantha Shannon. Did not see this coming! Sometimes its great to have a Barnes & Noble 20% coupon to take a chance on a book. Another new world, but this seems to be inspired, at least in part, by East Asian mythos.

B+   Pet Sematary by Stephen King. Book is so much better than the first movie or the more recent version. Particularly the ending.

C     The Dark Forest by Cixin Lui. The Three Body Problem did not need a sequel, it was a great read in and of itself. Regardless, The Dark Forest takes us into dealing with the future arrival of an alien fleet and how to survive. Seemed a little clunkier than The Three Body Problem, but that could be an issue of translation from the original Chinese. 

A     She Has Her Mother's Laugh by Carl Zimmer. This is probably the best science book I have read over the last decade. Should be required reading for anyone into the biological sciences. This is my book of the year!

B     The Haunting of Hill House by Shirley Jackson. A great horror story/decent into madness story. Leans more towards the horror side. Reminded a little of Stephen King's Rose Red miniseries, where a group of strangers are brought to an ostensibly haunted house. Just googled it, and Rose Red is a degree of separation from Jackson's work.

B+   Sand by Hugh Howey. A different world built by Howey, from the Wool trilogy. A post-apocalyptic story where the world, at least what we see of it, is basically buried in desert. Looking forward to the next follow up, if there is one, to see where this goes.

A     The Handmaid's Tale by Margaret Atwood. Horrific book that captures what I think many male Evangelicals would like the country to look like. Albeit they would miss out on the fact they would not be the elite with wives and broodmares.

B+   Outsider by Stephen King. A continuation of the Mr. Mercedes universe, but since (spoiler alert) Hodges is dead how does it continue? This story focuses on a new police officer and Holly, the introverted colleague of Hodges from the early stories. Like the earlier books, its a mystery crossed with sic-fi horror.

C     Echo Burning by Lee Child. Jack Reacher being Jack Reacher. To be read at the beach with a beer or two.

B     An Echo of Things to Come by James Islington. A solid second novel in the Licanius Series. After establishing a strong world in the first book, absent much historical information, we begin to fill in those gaps. This makes the second book more than simply a lever to help get us to the third book. 

D     Night flyers and Other Stories by George R.R. Martin. A collection of good short stories by GRRM. All, if I recall correctly, are sci-fi and not fantasy which is distinct from his more popular Game of Thrones books.

22 books read this year. Slightly better than last year. Of these, 21 were fiction, 10 were sci-fi/fantasy, 5 were by Stephen King, and 1 was a classic. Only 1 non-fiction book and it was biology.