Field of Science

I am Lazarus

Image result for wash me
So dusty

Look I haven't blogged in ~forever but now is as good a time as any to post something. As a PI trying to run a lab, teach effectively, raise a young adult, be a partner, have my own time not necessarily in this order, this has been a stressful few years. (#thankgodfortenure).

Regardless, its time to reset and recharge while in the midst of my heavy teaching load and just receiving news that not 1, but 2, fucking grants were 'not discussed'. But first I'll enjoy a couple of tasty malt beverages and then get back into the thick of it.

My goal now is to use this space for brief updates to ensure I keep writing.

What I Read (2018)

B High Deryni by Katherine Kurtz. Final of the trilogy. I like the antagonism between some leaders of the major religion (Christianity) and Deryni magic (I read as a proxy for science). Ending was abrupt, I didn't have a good reason to believe the war would actually be averted that easily.

F War and Peace by Leo Tolstoy. Basically the Kardashians for the media and audience of the late 1800s. Most of the book is essentially a 'lifestyles of the rich and famous' expose. I care little about the turmoil of the extremely well-to-do, which all stories from this period seem to revolve around. Battles were well described and the conditions of war better dealt with than many other attempts. The ending and a couple of chapters in the latter has were philosophical reflections on history, which were interesting albeit wordy.

C Red Dragon by Thomas Harris. Much like Lee Childs Jack Reacher stories, this was an easy fast read, good for relaxing.

B- Deryni Checkmate by Katherine Kurtz. Decent follow up to Deryni Rising although this is not a stand alone story rather a part I of II.

B+ Deryni Rising by Katherine Kurtz. I first read this book several decades ago, probably late middle school/early high school, and remember enjoying it a lot. Spent a fair bit of time trying to remember the titles or the author recently with no success, I knew they were written by a woman and happened to the three original books (of which Dernyi Rising is the first) on a shelf at a used book store. I snapped them up no question. A short novel introducing the world and main characters and telling a good story. One aspect I forgot is that the story basically occurs over a couple of days, reminding me that a good fantasy story does not have to be an epic quest covering months to years.

B+ The Rise and Fall of D.O.D.O. by Neil Stephenson and Nicole Galland. I tried reading Quicksilver but got bogged down, it wasn't 'quick', and gave up. This story kept me engrossed. A solid story, encompassing reality (as I understand it), magic, and time travel. Reminiscent of Stoker's Dracula in that the narrative is driven by letters, journal entries, emails, etc. Took a long time to embrace the plot, but the world building was compelling and worth it. Ending wide open, which I enjoy, but not saying I need a sequel (would likely read if there is one).

A Fascism: A Warning by Madeleine Albright. Excellent part-biography part warning call. While you can fell the presence of Trump throughout the book, he doesn't really make an appearance until the last chapter. Makes an important point that Trump is a symptom not the actual disease. Might be my book of the year, but The Three Body Problem still wins.

C+ Alice by Christina Henry. Alice and an asylum, what's not to like. Much of this book actually. An interesting take on a classic story. It builds a new universe, but there isn't enough there there to really understand the rules in my opinion. Doesn't quite reach American McGee in its craziness but seems to try. The ending was a surprise.

B The Shadow of What Was Lost by James Islington. I enjoyed this book when I read it, but much of it didn't stick with me. The ending was a whirlwind of action and gripping. The world building dragged a bit for me, but I say this in hindsight at the time I was right there. I have the second volume of the series but when I got it, I had to refresh my mind on the previous volume. Could be a personal issue, regardless I enjoyed this at the time and when I reminded myself what is was about.

B+ The Skaar Invasion by Terry Brooks. Good book, dialing up the Empire Strike Back vibe to 11. Pretty much the standard second installment of a Terry Brooks trilogy. However, there were enough differences and surprises (no spoilers) to bump this up. Brooks is one of my favorite fantasy writers and I admit much of this might be nostalgia, but I enjoyed this iteration of book 2 of 3 much more than probably any in the past two decades.

A Persepolis Rising by James S.A. Corey. Another enjoyable ride through the solar system and 'proximity' via stable 'worm holes'. The story is wrapping up with this and the next two books making Persepolis Rising the first in a classic trilogy. This book is distinct from the other books, which is something the duo writing under James S.A. Corey have done exceedingly well in previous iterations of the series. Raises the stakes and tension to eleven (Realize that this is the same series that basically destroyed the Earth a couple of books ago so that's saying something!).

D John Constantine, Hellblazer Vol 2: The Devil You Know by Jamie Delano and David Lloyd. Kind of a mix of stories with an overarching narrative in the latter part.

C  Giant of the Senate by Al Franken. Always solid in political satire or more aptly sarcasm, Franken does a solid job with this book. It is a pity he stepped down, but several chapters in the early middle, did not do much to help his case and were by no means humorous to read in light of his behavior.

A+  The Three Body Problem by Liu Cixin. This is one of the best science fiction books I've read in forever. At the time I read it, it was my choice for must read book of the year. Great narrative through time. The fact that it is written by an author from a different culture, Chinese, and translated into English and it's brilliant! Leaves an open ending that I think is the perfect way to end the book. Bought the sequel, but deep down I  wish there wasn't one.

C  Drawn Blades by Kelly McCullough. I like this series a lot, but this installment lacked some of the world and character building I enjoyed. Seemed more as an action adventure place holder in the ongoing story of Aral.

C  The Sandman, vol 8. Worlds' End by Neil Gaiman. I like the Sandman stories overall. This is a collection of short stories based on characters trapped/stuck in an otherworldly inn to wait out a storm. The characters tell stories to each other to pass the time. Sadly, I recall little of the actual stories at the time of this writing even though I enjoyed them when I read them, which means something....hence the C.

B+  How Not to Be Wrong: The Power of Mathematical Thinking by Jordan Ellenberg. Highly recommend this book to get a sense of mathematics with some history and personalities thrown in. Many parts are readily approachable, but there are numerous places where some solid math foundations are needed to follow the arguments.


C    Running Blind by Lee Child. If you have a few hours to kill and nothing better to do, this will get you through it. Extremely fast paced, which is good because you don't want to have a moment to think about the characters or logic.

B    The Sandman vol 7, Brief Lives by Neil Gaiman. A good story overall touching on aspects of life and death (although Death herself only makes minor appearances).

C+  On Writing Well by William Zinger. The first part was great, lots to incorporate into my writing and my classes. The second part was meh overall. The third part was a mix of the first and second parts.

A-   The Witchwood Crown by Tad Williams. Happy for a new installment of this series. Think the length of time between writing this book compared to the original series makes the writing fresh. Characters are wonderful, though I dislike the grandchildren and wonder if this is intentional on Williams part. There are suggestions throughout the book that something is afoot regarding the children.

21 books read this year. Worst number since my seizures knocked me down for a few months. Of these 21 11 were sci-fi/fantasy 2 were other fiction 3 were graphic novels 1 was a classics 4 were non-fiction.

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.

What I Read (2017)

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

C+     The Man in the High Castle by Philip K. Dick. An alternate history where the axis wins WWII and life in the US under oppression. Many story lines that were linked, but he connections seemed weak. Still not sure about the importance of the man in the high castle (although he moved) other than to imply the strange twist at the end. I guess that keeps the story in the sci-fi genre.
      Lost Gods by Gerald Brom. Didn't know what to expect, but I liked the cover. Fun story merging horror and fantasy. 
C       Island in the Sea of Time by S.M. Stirling. I enjoyed the premise of this story and it got better in the final two acts. There were many clunky technical details in the beginning that did not fit in with the narrative well. Seemed like the Stirling learned a lot about schooner ships for research and tried to jam it in.
C       Wytches vol 1 by Scott Snyder. Meh, but not as Meh as God Country.
B       And Then There Were None by Agatha Christie. Ok this was fun. Glad Christie included an epilogue how the hell everything happened.
D      God Country by Donny Cates & Geoff Shaw. Meh. American Gods is a great book and would make a great graphic novel. This was not American Gods.
B+    The Stone Sky by N.K. Jemisin. I did not enjoy the second story in this series, by the final entry is a winner. The story came to a solid conclusion tying up many loose ends.
B       The Walking Dead Compendium Two by Robert Kirkman et. al. A good follow up to the first one. The survivors discover a idyllic community only to have everything go the shit. People suck.
B      Breakfast of Champions by Kurt Vonnegut. I understood this book better than Slaughterhouse V and thus enjoyed it more. Satirical book touches on many aspects of life in the US. Author drawings throughout the book is interesting.
B      The Black Elfstone by Terry Brooks. The first Shannara story I read was Elfstones, shortly after it came out. I've had a fondness for this world for decades and while some stories have felt repetitive, this one is starting out on familiar territory but is introducing some new complexities and territory. A solid beginning for a new quadrilogy (and a change from the trilogy form Brooks has generally used).
C      Grave Peril by Jim Butcher. See Fool Moon below.
A      It Can't Happen Here by Sinclair Lewis. A timely book, incredibly timely. How a populist can come to power in the US and quickly devolve into fascism. Although written in 1935 the populist plank could be written (and much of it has) by today's tea party. This is my required reading book choice for the year.
C      Fool Moon by Jim Butcher. Another easy read to pass some time. Didn't add much to the Harry Dresden's character which was something I was looking for.
B      Storm Front by Jim Butcher. Recommended to me by a prince of assholes, a fun read before bed. Look forward to reading more about Harry Dresden. Wish there was more character development in the book, but a good first story.
A     To Green Angel Tower part 2 by Tad Williams. Rereading this series in preparation for the Witchwood Crown, originally read this series during graduate school when I took some time off to mentally relax after writing the initial draft of my thesis.
B+   To Green Angel Tower part 1 by Tad Williams. Rereading this series in preparation for the Witchwood Crown, originally read this series during graduate school when I took some time off to mentally relax after writing the initial draft of my thesis.
A        Coraline by Neil Gaiman. A story of a not very nice mother, the other mother. Not really a children's book although I would have read this to my son when he was younger anyway. The world's not all kittens and puppies.
B+     The Stone of Farewell by Tad Williams. Rereading this series in preparation for the Witchwood Crown, originally read this series during graduate school when I took some time off to mentally relax after writing the initial draft of my thesis.
A       The Dragonbone Chair by Tad Williams. Rereading this series in preparation for the Witchwood Crown, originally read this series during graduate school when I took some time off to mentally relax after writing the initial draft of my thesis.
A       End of Watch by Stephen King. A great ending to the series. Intertwines with the first story well, but each of the trilogy is a stand alone story.
B       Weaponized Lies by Daniel J. Levity. Good book, but covers some ground I'm quite familiar with.
C       Blade Reforged by Kelly McCullough. I enjoy this series and the flawed protagonist but this story was entertaining yet fleeting. It provided more backstory for Aral and the war amongst the gods in this world.
 B      Tripwire by Lee Child. An easy fun read. f the three books I've read so far, the villain in this story is the most developed and interesting and all around evil.
B-     Injustice: Gods Among Us Year 2 The Complete Collection by Tom Baylor, Bruno Redondo, and Mike S. Miller. A decent follow up on the initial story. Lags because the first collection established the world and key problem of Superman becoming an authoritarian. This is developed further and the two sides more fleshed out.
B      Paycheck and Other Classic Stories by Philip K. Dick. Has any short story sci-fi author had as many movies made out of their work? I doubt it. Some of the stories in this anthology I enjoyed, others were just so-so, but thats to be expected.
A      The Walking Dead: Compendium One by Robert Kirkman et. al. Great first compilation of the graphic novels. It's hard to read these stories and not give up on humanity. Basically a reasonable analysis of the human condition.

26 books read this year. Below average by a few books, not going to count the 4 rereads against myself since it was a good 20 years since I read before. 
Of the 26 books: 5 were graphic novels, 1 was philosophy, 4 were older books.

Eukaryotic Microbiology: The Blogs Are Coming

Despite my desire to keep updating the blog with course information, which has been an abject failure in regards to updates, I still want to post when I can. To be fair, I'm behind on grading, so I can't in good conscience be blogging about the course when assignments need to be graded.

However, I'll take a minute to make this brief post. It's getting to my favorite time of year: Student Blog Posts at Traveling Small with a Nucleus! I know for many students this is a writing assignment they truly enjoy. (Of course I'm sure some students do not like this assignment, but I have yet to hear from them.)
S0, I invite you to check out some previous students posts in the interim. The majority are quite good and there are some real gems in there. It's possible TSw/aN may be invaded with some organisms lacking a nucleus too. I'll keep you posted. 

Eukaryotic Micro: Week 3 the last of the fungi

So this week (actually last week) we covered what is probably the last unit concerning fungi: Cryptococcus neoformans. The first two weeks covered two ascomycetes, Candida albicans and Fusaruim species, and now we move over to the basidiomycetes, otherwise known as 'if I asked you to draw a fungus this is what you would draw'.

The primary research papers were:
This is an interesting point in the semester. Upon completion of this week, we are ~25% of the way through the semester and exactly 25% of the way through the 12 modules. This is the point where students have completed the short writing assignment four times now, so hopefully they are comfortable with what I am looking for. I lay out the guidelines on day 1, and then model what I expect. There are two difficulties. 1: Getting students to explain a dataset of their choosing such that someone would walk away knowing what was done, what it showed, and most importantly be able to ask informed questions about the data set. Students are reasonably good at explaining the data after a week or two, but struggle to give enough experimental information such that you would know how the data was obtained. 2: Identifying limitations with the data set. This is in fact difficult, but it is an important skill to foster if we really want people who are critical thinkers. I ask them that their limitation answers the question 'how does this affect the authors' conclusions or interpretations?' This latter issue usually takes a couple more weeks to get better at for most of the class.
It's also interesting because Cryptococcus follows up the ascomycetes we already discussed extremely well. Like Candida albicans, C. neoformans is a budding yeast, which is distinct from Fusarium, which although more closely related to C. albicans, is a filamentous fungus. However, like Fusarium, C. neoformans forms dikaryotic filaments during sexual reproduction and grows in a filamentous form during asexual spore production. 

I like these two papers (this is the first year I've used the Gerstein paper) because they deal with different aspects of development/differentiation in different ways.  The Gerstein paper is focused on a role titan cells play using primarily genomic approaches; the Huang paper is focused on spore formation and development using classical genetic approaches.

Gerstein et al ties in conceptually with the Selmecki and Ma papers from the Candida and fusarium modules respectively. All are centered on the acquisition of additional genetic information and the outcomes of this. I'm certain creationists always talk about the inability for an organism to acquire new 'information'. Well here are three independent examples.

Huang et al ties in, slightly, with the Lui paper from the Fusarium module by dealing with cellular differentiation and development. This is something we will come back to in the future frequently and is a biological concept I think is often underappreciated in microbes.  

Eukaryotic Microbiology: Two Weeks In

Have the second week of Eukaryotic Microbiology in the books (except for some residual grading to complete). So far we've covered Candida albicans and two Fusarium spp. Last week was C. albicans and we discussed two papers. (I'm not including the review articles students read at the beginning of each week.):
And this week was Fusarium and we discussed:

While I planned to discuss each week individually, these end up going well together, plus this is a difficult time of the semester for me guaranteeing I can't write as frequently as I would like.

So we stay within the ascomycota for the first two weeks. Some things that I wanted to emphasize in class and that came from the students:
  • What does it mean to be 'wild-type'? This came up with regards to a 'wild-type' genomic sequence. Is the CFTR mutation (the allele that causes cystic fibrosis when homozygous) a mutant genotype? Does the fact that in the caucasian population a cystic fibrosis causing mutation in the CFTR gene occurs with a frequency of 0.025 make a difference? What about the allele that causes sickle cell anemia when homozygous? People who have a 'mutant' allele and a 'normal' allele are more resistant to malaria, so this mutation is potentially beneficial.
  • How is phenotypic diversity generated in asexual organisms? This is an important question because sexual reproduction is promotes phenotypic diversity in many eukaryotes. However, there are significant issues associated with sexual reproduction that prevents using it as a simple explanation for phenotypic diversity.
  • How do organisms adapt to their environment and is a pathogen really any different from any other organism (short answer is 'no')?
  • How do duplicated genes evolve? This (Lui paper) goes hand-in-hand with the Candida Selmecki et al paper and the Fusarium Ma paper.
We'll be revisiting many of these issues throughout the semester. We spend a fair amount of time dealing with specific aspects of the papers, but I try to highlight some of these broader issues. This week we tackle Cryptococcus neoformans and will highlight at least one of the above issues again.