Field of Science

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!
    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

    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 that's not! 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.

    We Need to Work Much Much Harder

    I recently spent some time with family very dear to me that I had not seen in many years (contradictory yes, reality sucks). It was wonderful to catch up, meet new cousins, and have them meet my son. It was also socially educational as many members of my family and I lie on different spots of the political spectrum, with me lying solidly in the progressive liberal side of spectrum well to the left of the democrats and them lying much further to the right somewhere between the republican and tea party depending on specific issue.

    Actually that's not completely true, through a number of discussions we had, mostly not initiated by me, I think we have much more in common than not regarding specific issues. This includes even the more contentious issues. However, their viewpoint clearly originates and is framed by a right wing perspective, much like mine originates and is framed from a left wing perspective.

    That being said I was glad to be able to talk to and hear what people, whom I care about, think about a number of issues important to them and to me. These discussion lacked any real debate and both sides were cognizant, I think, of each others feelings and strived to communicate clearly without being aggressive. Based on these albeit too brief interactions, I have a few posts I am planning that address some of these interactions, although I will not necessarily mention my family in them but try to introduce thoughts I heard more subtly.

    Here, I simply want to bring up one thought that was mentioned in passing that I think reflects a tremendous problem scientists and science enthusiasts need to start dealing with yesterday.

    "Some scientists are just trying to disprove god."
    (Not an actual quote, a paraphrase.)

    This one thought, which was simply stated in passing, concerns me greatly. First, the fact that it was easily stated in passing suggests to me that the idea is so entrenched and obvious (to the stater) that it doesn't justify defending or supporting. Second, science is fundamentally misunderstood. Third, what scientists do is not at all clear to people at large.

    I want to be clear here, I am concerned about the scientists, the science enthusiasts, and anyone remotely interested in determining the truth and I am concerned with what we should be doing. I am not concerned with the general public, they are a victim of FOX propaganda and a massive misinformation campaign that is easily available on the internet.

    From that one statement (above in blue), which almost caused another bout of seizures, it became painstakingly obvious how much work we need to do. This thought came from a caring hard working family man who I think represents almost (no one is perfect) everything good about humanity. So I am going to go out on a limb and say that this idea is not some odd minority opinion, but a reasonable representative of a vast majority of Americans. I feel comfortable in this conclusion based on the number of Americans who attest to believing in a ~6,000 year old creation plus those who believe in a slightly more refined, older, creationism.

    So here are my responses to the three concerns I raised above.
    1st, the fact that this was stated so easily without concern for a justification or defense. We need to do more! Anyone interested in science or approaches to define reality need to do more! We need to directly and forcibly call out supporters of pseudoscience and those who are wrong. If it is a public figure, this needs to be done loudly strongly and without remorse. If this is a friend or family member, this needs to be done with more sensitivity, but it still needs to be done. I think the forces opposing good science get a free pass by publicly calling into question climate change and at the same time requiring a measured response. This is gaming the system (FYI Fuck you Scott Walker!).

    2nd, science is fundamentally misunderstood. Science is about understanding the universe, it's about understanding ourselves. Hell, it's even about understanding our place in the universe. What science is not is showing that specific religious tenets are wrong. The problem lies in that all religions make specific claims about the reality of the universe and sometimes science clearly demonstrates that these claims are wrong. It is not that scientists set out to show these claims are wrong, but that their work ended up showing these claims are wrong. (I will allow that there may be some scientists who have an underlying agenda to clearly demonstrate that Islam, or other religion, is wrong but this is not what science is. When your religion makes definitive statements about the universe, it was created 6000 years ago, it was created yesterday, the world is flat, the world is a dodecahedron, humans are not animals, humans are not related to animals, then you are subject to having science show you are wrong. That may be unfortunate, but that's the fault of your religion making statements about the reality of the universe, not the fault of science.

    3rd, it's not clear what scientists do. I will speak for all scientists here, someone can correct me if I'm wrong (I'm not). Scientists do not care if your religious tenets are right or wrong. The problem is that as we ask questions about the universe, like why do people get sick and die, we learn things that contradict certain religious doctrines. While things might have been different in the 1600's, no scientist is going to get the resources to show that the earth is not 6000 years old. You might get resources to address specific aspects of science that lead to the understanding that the earth is 4.7 billion years old, but if your goal is to show that the earth is 6000 years old you'll probably fail. Kind of like if you want to get money to show that π is actually equal to 3, you won't get funding (because things like mortars only work if π=3.14.... regardless of personal interpretations of the bible).

    So the short response to issue #3 is that scientists are trying to learn more about the universe, whether that is how planets form, how microbes cause disease, how economics affected German policies leading to WWII, etc. We don't have time nor the interest in showing that your personal belief in the afterlife may or may not be true. Surprisingly (to me) this is something we have to fix, unfortunately this is something we need now, since we didn't fix it in 1974.

    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.