Field of Science

What I Read (2015)

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

B     The Bazaar of Bad Dreams by Stephen King. Some good, some less good, but mostly good collection of short stories.


D     Bleak House by Charles Dickens. Took me longer to read than it took Dickens to write I expect. Kind of got interesting ~80% of the way through, wrapped up a little too neatly.


    The Sandman Vol. 4: Season of Mists by Neil Gaiman. One of my favorite collection of stories so far in this series. What happens when Lucifer gives up control of Hell?


    Gotham Central Book 4: Corrigan by Greg Rucka, Ed Brubaker, Kano. Good analysis of a corrupt police officer and the effect it has on several other members of the squad.


B+    Gotham Central Book 3: On the Freak Beat by Greg Rucka, Ed Brubaker, et al. Good integration of the police dealing with supervillians and problems associated therein. Didn't like the introduction of a superpower to a police officer (psych ability), which defeats the purposes of stories.


    The Fifth Season by N.K. Jemisin. A new world with a new culture. Not sure where this series is going, but Jemisin sets up an intriguing world.


C+     Symbiont by Mira Grant. Not as good as the first part of this trilogy. Felt a lot like filler, main plot really didn't move much.


B-     Gotham Central Book 2: Jokers and Madmen by Ed Brubaker, Jim Starlin, Michael Lark. A good follow-up. What happens when a normal police have to deal with The Joker. Ultimately Batman saves (most of) the day, so it didn't work out as well as I would have liked.


B      Deathpunch'd by Jeremy Spencer. Humorous and scary, discussing drug addiction and life in a upcoming band. Got a bit repetitive though.


A-     Doctor Sleep by Stephen King. One of my favorite recent King books since I read 11/22/63 or It. The kid from The Shining all grown up.


B-     The Alienist by Caleb Carr. I realize this came first, but I liked The Angel of Darkness much more.


    A King's Ransom by Sharon Kay Penman. Historical fiction is interesting. Taking known events and people and trying to write the story of how things unfolded is an interesting genre.


    Informal Logic by Douglas Walton. A good synopsis on many aspects of argumentation. Pretty much stuff I already knew, but presented in a more formalized manner.


    Revival by Stephen King. I enjoyed it when I read it, but frankly can't remember what happens at the end. That kind of tells me something.


    The Defenders of Shannara: The Darkling Child by Terry Brooks. A good follow up to The High Druid's Blade, but suffers from a 'more of the same' vibe.


B+     Nemesis Game by James S.A. Corey. Unlike Cibola Burns, Nemesis Game returns to some of the original plot themes of the earlier books, conflict between earthers, martians, and belters. Overall an engrossing story.


    Gotham Central Book 1: In the Line of Duty by Greg Rucka, Ed Brubaker, Michael Lark. A police procedural in a world of super-heroes and super-villians. Interesting take and perspective. Decent characters, look forward to the others in this series.


    Wastelands 2 edited by John Joseph Adams. Again some good, some less good. Mostly good though. I thought the first volume of Wastelands was much better overall.


B+    The Golden Son by Pierce Brown. I like this world, but it is not new now. Still the story moves along well and ends in dramatic fashion. Looking forward to the last in this series...in a good way.


    Inferno by Dan Brown. I liked it better the first time I read it when it was called the Da Vinci code.


B     Neuromancer by William Gibson. I liked this book, but not sure why it is considered such a great story. Probably it's a contest thing. Stories in this genre are more common than when Neuromancer was written.

    The Belgariad vol 2 by David Eddings. Read this many many years ago too. Also, a fun read but it wraps up a little too neatly.


B+    The Belgariad vol 1 by David Eddings. Read this many many years ago. A fun read, though there may be some sentimental value associated with my score. 


     How the Mind Works by Steven Pinker. Outstanding book on the brain and the work that has gone on into understanding how it works...or doesn't. Particularly interesting for me after the seizures of 2014 and thinking about the recovery process.


    Jingo by Terry Pratchett. Witty and good satire, but does not hold up as well to other Pratchett stories.


    The Defenders of Shannara: The High Druid's Blade by Terry Brooks. I enjoy Brooks a lot, again probably some sentimental effect here. But I have found much of his recent work to be somewhat predictable, different characters, different settings (within the Shannara world) but ultimately the same arcs occurring with the same pacing. The focus on a Leah descendant and the entwined story of Arcannen mixed things up enough that this book was a pleasant surprise.


     Parasite by Mira Grant. Great take on the zombie genre!


     Red Rising by Pierce Brown. Interesting Sci-Fi story dealing with class and revolution. Part one of ?.


A      Crossed Blades by Kelly McCullough. Introduction of Jax and greater development of the universe McCullough is creating. Look forward the remainder of the series, though I needed to read some other books. Characters are flawed yet heroic.

B-     Devil in the White City by Erik Larson. Two good historical stories that I liked but did not think wove together well.


     Cibola Burn by James S. A. Corey. I enjoy The Expanse series immensely, though I usually do not enjoy space related sci-fi. Great story that deviates from the previous three in plot.


    Bared Blade by Kelly McCullough. Another good read of Aral and Triss (Aral's shadow familiar). Further development of the McCullough's world.


    Broken Blade by Kelly McCullough. This world reminds me much of the Thieves' World universe. Although there is more diversity of culture, much of the story takes place in a Sanctuary-like city of Tien. (At least as how I recall Sanctuary after 25+ years.) Fun story, great character in Aral.


    I Killed Pink Floyd's Pig by Beau Phillips. Humorous stories of many of my favorite bands. Enough diversity in the types of things from drunken hotel room destruction to the title of the book that is stays fresh throughout.


34 books this year, although some will consider the 5 graphic novels as not counting but fuck 'em. Of the 34 books: 29 were fiction for fun,  2 were on the music industry/biography, 1 was philosophy, 1 was history (although not academic), and 1 was science.

New Student Posts en route

As Thanksgiving is over and another semester winds down, a time of great celebration is soon to be upon us. By which I mean student blog posts from my Eukaryotic Microbiology course! As I await the submission of the final drafts to roll in, I discovered some older posts in a folder that never made it onto Traveling Small with a Nucleus. So look through some of the older ones or check those that were not previously posted until now. Feel free to leave a comment or two for the students!

Eukaryotic Microbiology Intro Readings

My advanced microbiology course, Eukaryotic Microbiology, is up and running. At least the website is. I have assigned several introductory papers for the course as a primer for the students. The papers include:

    I've used the Cavalier-Smith and Koonin papers in the past to introduce the basic ideas surrounding where eukaryotic cells come from (I think the Koonin paper is more clear here) and what is a eukaryotic cell (Cavalier-Smith wins here).

    This year I've introduced the other three papers to provide additional perspective on the origin issues. The McInerney paper does a good job summarizing the four basic hypotheses for the origin of the eukaryotic cell (see the figure) and I think it is good to come after the first two papers as they deal more directly with the science behind the origin of eukaryotic cells.

    I particularly like the last two papers by Williams and Forterre as they basically argue different things. This allows me to introduce ambiguity into the course from the beginning, which I think is important. One of my goals is to teach students to think critically about the science they read. This is quite difficult as I think the students have been taught that if it's written in a textbook or scientific paper, it must be correct. Here, I am giving the students two papers, written the same year, that argue two different points of view. Logically they cannot both be correct. It will be interesting to see if this helps students get over the hurdle of being able to question authority or not. 


    How to Study: One Approach: Repetition is good

    With the onset of a new semester and a new crop of students having arrived or shortly arriving at college, here are some words of advice from someone who had to learn to study the hard way...

    Here is an advice column for students looking for some techniques to improve their study habits. I am not an expert in learning, but I am an expert in being a college student with no fucking idea how to study and had to figure it out over the course of a year or two. I was one of those students who didn't have to do much to maintain an A/B average in high school. Although I was exposed to study skills and habits while in high school, none of it stuck because I really didn't need to study to do reasonably well. So here is what I learned that worked for me. If you have your own successful techniques, please feel free to add them in the comments.

    Learning is an active process, it requires energy. It may not be as physically taxing as a 45 minute work out, but then again you may not be doing it right. What I discovered is that I learn when I do things, when I engage the material, when I'm an active participant. If it's a couple of days before the big exam and you're wondering to yourself 'What's the best way I can study? I know, I'll take some time to search online and get some tips.' Well, if this is you, you're fucked or at least I don't have anything for you. Come back after your upcoming exam, my advice might help you for the next exam. Right now, you are in cram mode, so you better start cramming and not wasting your time reading blogs. I will admit that cramming works, to a degree. Cramming is a short term solution, getting enough material under you belt to survive or even succeed at the exam. But it's a long-term problem. Are you really in college to survive exams and classes? That was really high school wasn't it? Cramming is problematic because the material is never actually learned, it may come up again on the final, it will likely be important next semester or the semester after that in your more advanced classes. Learning and cramming both take energy, but the former is far less stressful and provides both short-term and long-term gains.

    Step 1. Find an environment to study in. Ultimately this became at my desk in the bedroom of my apartment. I also kept my stereo close by set at police notification level. I learned quickly that I could ignore the music, but sounds from the street, from the kitchen/dining/living room area, or from anywhere outside my room were distracting. To this day, when I'm working on grants or papers and do not want to be disturbed, I  close my office door and crank up some music. Although I am a chaotic person by nature, my desk was neat and organized. I needed a place to work comfortably and that was it. My textbooks and notebooks were stacked in/on some milk crates I used for shelves. (These of course were the store bought kind of 'milk crates' not the easily available sturdy and inexpensive milk crates available behind 7/11s, like the one across the street of my apartment. Although if they were the illicit version, which they weren't, they would have been returned when I moved to go to graduate school.)

    $0.69 for 3 in 1989
    Step 2. Get a bunch of notebooks. I used spiral bound notebooks available for next to nothing at drug stores. Of course these notebooks will have absurd cover designs or pictures you would never in a million years gravitate towards (see picture of my Molecular Biology notebook). That's not the point. The point is what's inside the notebook, and that will be gold. I mixed up the designs on the notebooks I bought so I could easily identify which one I wanted. The alternative is to be flipping through them wondering if this is the black notebook Im looking for. Get one notebook for every class you take (except maybe for the golf/tennis/etc classes). Any class that has a lecture has its own notebook. No cheating by getting a three-subject notebook. Also, get a couple of additional notebooks.

    These things are evidence of evil
    Since you're at the drug store all ready, get some pens and pencils. I love pens, but despise cheap ass ball point pens. You'll be using these a lot, so get pens/pencils you are comfortable with. Make sure you get a variety of colors. I survived with black, blue, and red, but there is a veritable palate of colored inks now. Get what you love or at least can tolerate. I prefer mechanical pencils, but if you get classic ones, you better kick in for a decent pencil sharpener or two. Also grab some highlighters also in assorted colors.

    Step 3. Do the readings strategically. Chapter 3 is covered Wednesday? Read it through by Tuesday night. That isn't very strategic is it? The strategy is to skim read the text. Get a sense of what's in there and what will be the likely topics and points for the upcoming lecture. You don't need to be more than familiar with the material. (In the case of labs, this is not true. You must be intimately aware of the material, because you will be using that information in the lab. Hell, there may even be a quiz on the lab manual!)

    Step 4. Go to class. Although you probably couldn't pass a quiz on the readings material, the vocabulary is familiar. Now you already know a bit about the upcoming lecture. Gather up your pens and pencils and one of the extra notebooks. Leave your textbooks at home, along with the highlighters, and other notebooks. You don't need much.

    Get to class on time and get a good seat. In large classes, I recommend a seat near to the front and in the middle where the professor can actually see you. Why? Psychology that's why. Take two students doing equally well, one student the professor recognizes, even if there is no name associated with the face, and one student the professor has barely, if ever, seen. If both come to discuss an issue regarding an examination or writing assignment, which one will have at least a sub-conscious advantage?

    Open your notebook to page 1 get out a couple of writing implements and get ready. If the professor has handouts or, god forbid, print outs of the slides, then definitely pick them up, but DONT use them during the lecture (with rare exception). Your job is to take a shit ton of notes. Don't worry about neatness and perfection, just get the stuff written down. Write down the points on the slides, the drawings, incorporate what the professor is saying. The very act of writing things down is helping you learn the material! 'But we have the slide print outs, so why write stuff down?' you ask. In my more youthful days I would have responded with 'Because we didn't have the material presented to us, so stop being so fucking needy.' But in my dotage I think an example is better. What is another name for a television? Did 'idiot box' spring to mind? There's a reason for that. Some people watch tons of TV, these are not inherently the most educated people in the world. My mother loved to watch soap operas during the 70s, hours of soap operas. She was not an expert in social interactions because of this nor was she an expert story teller, she just watched a lot of soap operas. This is one of the biggest impediments to learning, fucking handouts. Remember I said learning was an active process. Lectures are not television. You should be doing something not just watching. The problem with handouts is that it facilitates the TV watching mentality. There are reasons to hand out the notes, which is why you are collecting them, but wait until later to use them. For now, take a shit ton of notes.  Do not be tempted to put notes in the margin of the print outs, you bought the cheap ass notebook, so use it. (Plus you'll want a pristine copy of those hand outs for later.) So, you were in class sitting in a strategic location, you took a shit ton of notes, now what? Go to your next class and repeat using the same notebook.

    Notes on chromosomal
    melting temps.
    Step 5. THE MOST IMPORTANT STEP: The next day. So you went to all your classes, even the ones you think are boring, and you took a bunch of notes, even on things you think you know already. Now what? Hang out with friends, watch TV, play some Xbox, then go to bed and the next day go to all your other classes. At some point on this second day, you need to carve out some studying time. When depends on your schedule. I did this in the mid-late-afternoon, because I was generally done with classes then. Go to your studying environment, get out your notes from yesterday, one of the fresh notebooks that will be specific for a specific class, any handouts, and your textbook. Now you will rewrite your notes in a more organized and legible manner. As you rewrite, you will refer to the text for additional points, and in your class-specific notebook you can either incorporate the textbook material or simple refer to the page numbers/figure numbers. Either redraw or cut out the handout figures you need and add them to your notebook. This could take as long as the original lecture, but probably won't. Regardless, you are now learning some serious material. The act of rewriting helps embed the information into your memory, by organizing the material in a manner that works for you (which is probably like it was presented) you are thinking about the material in total not simply one fact after another. You are also reading the text in a more in depth way, which is easier because you already skimmed it and went to the lecture. Do this for those boring easy classes too. It helps maintain good study habits and instead of simply learning the material, you'll own it. Another benefit is that if you do this, you will know before the next lecture what material you may not understand. This gives you a ton of time to meet with your colleagues, TAs, professor to get things straight.

    Step 6. When you finish going through the crappy notes, rip out the page(s) and throw them away. You don't need them anymore because they are rewritten and you'll feel good about the progress you made.

    I won't guarantee these steps will improve your grade, but I do guarantee that they will improve your understanding and knowledge of the material.

    Additional thoughts:

    A. Write in your textbooks, at least highlight important information. I used different colored highlighters for different purposes. Red was for definitions, blue was for what I thought were key concepts, green was for things referring to my class notebook. Will writing in your textbook reduce its value when you resell it? Well hopefully you will not resell it. Having that chemistry textbook could come in handy when you need to revisit something you forgot in your molecular biology class. If you absolutely do not want the book, why buy it in the first place? Probably you could borrow one from a colleague or use the library.

    B. Scheduling. You need to prepare ahead of time when things are getting done. If you don't, you will almost certainly get behind or not have enough time. If you want to go to that party or game, you may need to start rewriting your notes earlier than normal to make sure you have enough time to finish before going out. Also, there will be several big assignments due for other classes throughout the semester, you'll need to be prepared for catching up on those notes you couldn't rewrite the day after class. (Don't get more than a class or two behind or you'll defeat the purpose of rewriting.)

    C. Turn off your phone. You can survive an hour or two without reading all those awesome texts and tweets coming in. A 30 second distraction actually amounts to much longer, because it takes time to get back to where you were before you were distracted. Every time you break focus, you are back to a more superficial level of learning and it takes some time to get back to that deeper level.

    D. When it's test time, you'll find it much easier to study. The material is already there in your mind because you've been through it at least twice already. You may have to pull an occasional all-nighter, but it will be different than the cramming you did previously.

    Notes for a recently submitted grant
    from a relevant paper.
    E. For the record, I still use these techniques to prepare grants and papers (see photo). I do a lot of background reading and have notebooks dedicated to taking notes on the papers, complete with different colored pens. This allows me to make connections and think about the material in a much deeper way than I would be able to otherwise. Same for seminars I attend, I bring a notebook.


    With those words of advice,
    Good luck and have a great semester!

    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.

    The last few days before a grant deadline

    FML
    Why does it always seem that when the grant deadline is imminent, all the work I've done is basically irrelevant and I have 100 times more to do than I already have done? No really, why?


    Too Easy, but What the Hell

    I 'belong' to a 'Creation Evolution Debate' group on Facebook. I joined this group, not because I think there is a debate, there isn't, but because I wanted to see what Creationists thought was debatable. Was kind of hoping to see some thoughtful discussion or potential misconceptions that could be cleared up. Basically all I see is the same old arguments from ignorance that have been dealt with time and time and time again. For example, this little gem showed up awhile ago complete with a geocities approach to web design.



    1. How did nothing turn into something? It didn't. I'm assuming this question is referring to Big Bang Theory, which has nothing to do with evolution and is a problem of physics. I recommend Stephen Hawkings' A Brief History of Time: From the Big Bang to Black Holes for an answer. I like the sub-heading though, as discussing evolution is banned. 

    2. How did life come from non-life? I don't know. One place you could start to address this question is Freeman Dyson's Origin of Life. (Full disclosure, I haven't read it but have read papers on the topic.) Of course the origin of life is not the same as evolution, but what the hell. Regarding the sub-heading, what is the first law of science? Is it conservation of mass? The 1st law of thermodynamics? Neither are relevant here.

    3. How did millions of life forms evolve with absolutely no evidence of major change? What? I mean really, what? Let's see I do not look like my cat nor a mushroom, not a bacterial colony. Isn't that evidence of major change? We have these things called fommits...no that's not right...mossels...no...OH! Fossils!!!! Right. A good place to start reading about this would be Richard Dawkins' The Ancestors Tale or Neil Shubin's Your Inner Fish.

    4. How can a watch come into existence without a watchmaker? It can't. Also, don't mention DNA, because it's so complex it's beyond the complexity of all computers on earth. That's probably why DNA is used to control computer synthesis machines. Wait that's not right, computers control DNA synthesis machines. I'll go with another Richard Dawkins' book, The Blind Watchmaker.

    5. How did thought come from non-thought? I don't know, but I do not think thought is as super special as our geocities web host. I recommend Steven Pinker's How the Mind Works as an excellent starting point. Sub-heading is true, the first thought, if there is such a thing, did not come from an evolutionary biologist since the major tenets of relatively modern evolutionary thinking is only a couple hundred years old.

    So I answered all 5 questions! Probably the author is not happy with those answers, but I answered them, so the point of that geocities abomination is shown to be wrong! Oh wait, I'm not an evolutionist (whatever that means), so I guess the red and blue vomit of words still stands.