Field of Science

Monday Journal Club

This week our microbiology journal club discussed the paper "The cidA murein hydrolase regulator contributes to DNA release and biofilm development in Staphylococcus aureus." by Rice KC, Mann EE, Endres JL, Weiss EC, Cassat JE, Smeltzer MS, Bayles KW. published Proc Natl Acad Sci U S A. 2007 May 8;104(19):8113-8.

The main point of this paper was that CidA, a bacterial holin protein, promotes cell death which releases genomic DNA into the environment which is required for biofilm formation. I want to hit on a couple of big picture points without going into to too much detail and then focus on one aspect of the paper for teaching purposes.

First, the field of biofilm formation is, in my opinion, much like a biofilm itself.....a diffuse poorly defined thing. OK, this is not really true, but many scientists use the term so loosely as to make it meaningless. A biofilm is commonly referred to as a collection of microbes encased within an extracellular polymer. Biofilms are important medically as microbes within a biofilm are often insensitive to antibiotics and microbial biofilms can grow on catheters and artificial valves and serve as sites of continual infection/dissemination. Because the cells within the biofilm are not all uniform like what would be observed during logarithmic planktonic grown, there is heterogeneity within this structure. In fact, a biofilm could be considered analogous to a microbial tissue.

Second, programmed cell death in unicellular microbes is an interesting phenomenon/idea. However, researchers in the area of microbial programmed cell death try too hard to make it directly comparable to multi-cellular organism programmed cell death. The idea of some organisms in a population sacrificing themselves for the rest of the population is well documented and makes some sense intellectually. The idea that bacteria do it the same way as the cells in your primordial hand do it is weak to wishful thinking in my opinion.

Alright, that said, the paper. First, the authors show that wild-type cells release a cytoplasmic enzyme into the environment once they enter stationary phase (basically when they stop growing). However, cells containing a null mutation in the cidA gene do not. This demonstrates a role for CidA in cell lysis, but says nothing about biofilm formation. The authors then show several assays that demonstrate that the cidA mutant does not form a robust biofilm like wild-type cells and the authors show that extracellular DNA (presumably from lysed cells) is required for proper biofilm formation in wild-type cells. (Since cidA mutants fail to lyse there is little DNA released to help form the biofilm.) Overall this is a nice analysis that provides some insights into the role of cell lysis and DNA in biofilm formation and this analysis explains the requirement for CidA in biofilm formation.

HOWEVER, this is a simple genetic analysis paper. These type of studies are done all the time by thousands of researchers working on thousands of genes in hundreds of organisms. The authors of this study break one of the rules commandmants of molecular genetic analysis. VI. And when thoust does construct thy mutant and discover thyself an interesting phenotype, thou must proceed to carry out a complementation test or thou shalt be smiteth (Look it up, that's what the commandment says.) Now the authors know this (at least a reviewer did) and they give us this,

"Previously, we were unable to complement the antibiotic tolerance and murein hydrolase phenotypes of KB1050 (24), which was also the case in the present study, as the biofilm-defective phenotype was not complemented by supplying cidA on a plasmid (data not shown). However, this mutant phenotype is unlikely caused by a secondary site mutation because similar cidA mutations in different S. aureus genetic backgrounds also decreased their ability to form adherent biofilm (SI Fig. 7). This phenotype was also not caused by a polar effect on the downstream cid genes, because isogenic cidBC and cidC mutants grown under the same conditions produced biofilm comparable to that of UAMS-1 (data not shown)."

Let me break this down a little. When you make a genomic mutation, regardless of how you do it, there is a chance something else happened to the genomic DNA beyond what you were doing (life is a bitch). So you discover an outstanding phenotype in your mutant background...WOOHOO, contact Science, have them hold the presses.....Hold on cowboy, how do you know your mutation causes the phenotype and not some other horseshit that occurred when you made your mutant? In other words, how can you be sure the mutation and phenotype are linked? One quick and easy way, is to re-introduce a wild-type copy of the gene you mutated. The prediction (I love science) is that if the mutation causes the phenotype, putting a wild-type copy back in should rescue/restore/reverse the phenotype. If horseshit causes the phenotype, putting a wild-type copy back in will not rescue/restore/reverse the phenotype.

So, back to the authors and Im paraphrasing: our complementation tests failed for other phenotypes, and they failed for the phenotypes we present here (A, see below). We know it looks bad, but we are sure the phenotypes are not due to horseshit because when we make the mutant a bunch of times we see the same rescue (B) and other downstream genes are not required for the phenotype (C).

A. Not being able to complement one phenotype is bad, but not being able to complement a subsequent phenotype is not supportive evidence that things are working well.
B. Making the mutation a bunch of times independently does indeed tell you that the phenotype is not due to unlinked horseshit, but it could still be linked horseshit.
C. This is a little trickier. Generally bacterial genes required for a given process are found in operons, which are essentially chains of linked open reading frames (protein coding units). One or two transcriptional start sites exist to make mRNA which is then used to translate all the proteins in the operon. This allows for an efficient way to regulate all the components in a process simultaneously. So, the fact the cidB and cidC can be mutated without having an effect on biofilm formation tells us they aren't required for the phenotype. What the authors are considering is that the cidA mutation affects expression of cidB and/or cidC and that these are the true genes required for biofilm formation, not cidA. This would explain the lack of complementation because the authors add back cidA on a plasmid not in the chromosome (the authors did it right if you ask me), so if the cidA mutation disrupts cidB expression, putting the cidA gene back into the cell wouldn't help, because you still wouldn't get cidB expression.

OK, lets give the authors credit, they addressed some possible issues of horseshit. Here's one not addressed, what if the gene next to cidA (opposite cidB and cidC) is screwed up because of the cidA mutation. Let's say the mutation destroys the promoter of this hypothetical gene. You could make the cidA mutant over and over again and you would get the same phenotype that could not be complemented with cidA because this other gene would always be fucked. You could delete cidB and cidC with any affect on the phenotype. See my model fits all their data, actually mine is better because it fits all their data including the inability to complement the mutation. The authors never actually propose a model to explain this, they simply consider two possibilities and sweep the issue under the rug.

Now that being said, I still think the authors main conclusions are correct. There are many reasons to explain why you may not get complementation, although the authors failed to provide evidence for one of the reasons. However, and I think this is important, if you cannot complement your mutation, the bar is much higher to justify your conclusions. My problem is that the authors didn't consider a trivial explanation (the one I proposed) and based on my reading I expect the authors only mentioned anything regarding complementation and the lack therein in response to a reviewer. Again based on what the CidA protein does, the authors are likely correct. However, I think this paper allows us to highlight the importance of complementation testing in a rigorous molecular genetic study.

Edited for a couple of grammatical errors and to make a couple of points more clear.

pH: it actually matters outside of chemistry lab

You know there are many things that you are exposed to during your life that you think "I can't wait until this is over, I'm never dealing with this again." In science I have found that I said "I will never work on this" or "I will never take this approach or use this methodology." only to find myself working on that using that approach and methodology. CRAP. It has gotten to the point where I find myself not verbalizing such things as it may curse me into doing things I initially find dull or tedious. I will say that when I have been working in an area or using a method I had previously considered anathema, it is with excitement or a certain amount of passion, because I came into it to learn something new about a problem I had been studying. pH is one of those things.

pH is better known as how acidic or basic something is. Acid has a low pH and base has a high pH. pH is really a mathematical term meaning -log[H+] or -log of the concentration of hydrogen ions. pH is something you learn about in general chemistry in high school and college. You find yourself doing some math problems and using acids and bases to bring some solution to a given pH or adding acid and bases to a solution and taking a plethora of measurements to determine the buffering capacity. (This latter procedure involves opening the spigot on the acid/base solution and trying to hit the pH you're looking for as quickly as possible, usually you overshoot, have to add the opposite acid/base, and repeat). So why do we care?

In biology, pH is one of those issues all cells have to deal with. Well, they could die instead. My work is focused, in large part, in understanding how Candida albicans, a fungal pathogen, responds to pH. The reasons are historical....I identified the pathway that senses pH and allows Candida to respond appropriately to changes in environmental pH. I identified the pathway first, then figured out what it did...so my interest is in the pathway and pH turned out to be an acquired interest. Over time my appreciation for pH has grown dramatically, not from a chemistry perspective that's always been what it is, but from the biological implications. First, most organisms can live in a relatively small range of pH. Normally we think of pH in the range of 2-14 although extremely acidic solutions can have a pH of ~ -5! This range may seem small, but remember pH is measured on a log scale, so the difference between pH 2 and pH 14 is the same as the difference between 100 and 10,000,000,000,000. Most organisms can grow over a small range of pH (2-3 pH units) and survive over a slightly greater range (4-5 pH units). Our body fluids are maintained at a pH ~7.4, however conditions such as acidiosis occur with an arterial blood pH <7.3 and alkalosis occurs with an arterial blood pH >7.5. C. albicans can be grown in the lab from pH 2-10. The range may be greater, but this is the limit that we analyzed. All solutions have a pH and all organisms grow in or are contained in fluids (yes even us). What is interesting is that the process of being alive generates chemicals that make solutions more acidic and more basic. So, a living organism can and will change the pH of the environment it finds itself in. Our bodies are well buffered, in other words we contain mechanisms to keep the pH of fluids such as blood at 7.4 in response to these chemicals. Remember these are chemicals (metabolites) we generate ourselves, this isn't some pollutant from the environment. Finally, I should point out pH matters to a cell. Most proteins a cell makes has a pH optima around 7, however there are many exceptions. For example, cells in that grow in an acidic environment secrete proteins that function best in an acidic environment (but even these cells maintain an internal pH of ~7, so the internal proteins work best at pH ~7). Helicobacter pylori, which lives in your stomach is a good example. Also, some digestive enzymes in your spit work best at acidic pH so are not very functional until you swallow. Suffice it to say that environmental pH is an important stress that all cells must deal with (or as said previously die). Further, cells can change the pH of the surrounding environment. So cells must be able to adapt quickly to environmental pH or suffer the consequences.

You might ask, how can cells change the pH of the environment? Well there are many ways, but the simplest and most widely known is through glucose metabolism. Glucose is the sugar of choice for most organisms on the planet, it is a great source of carbon, which we need for virtually every molecule within our cells, it is also a great source of energy. A cell converts glucose into a bunch of ATP, which is then used to allow most other cell processes to happen, such making proteins, moving things in and out of the cell, etc. ATP is the currency the cell uses to get things done. When cells use glucose they generate a molecule called NADH from NAD. Unfortunately there is a finite supply of NAD, so when it is all converted to NADH, then cell cannot use anymore glucose. Thus, no more carbon and no more energy. However, cells can recycle NADH back to NAD in two general ways. One is fermentation (Yes that fermentation). The process of fermentation allows NAD to be recycled without the use of oxygen. To recycle NADH back to NAD, electrons (damnit not physics!) are taken from NADH and given to another molecule making it into something different. Often it is pyruvate, which conveniently enough is the last thing made when glucose is broken down for energy. So the cells can recycle NADH and use the end-product of glucose metabolism to do it. Life is sweet. When pyruvate picks up these electrons, recycling NAD to be used for more glucose metabolism, it is changed into something else. If we are lucky (and currently I am enjoying some luck) it is converted to ethanol, this is how beer and wine come about. If we are unlucky it is converted to lactic acid, this is why are muscles burn after prolonged exercise. Lactic acid is acidic, DUH, which our bodies/muscles do not like so much. So we make a lot of acid in our bodies, which is dealt with, but some pain ensues temporarily. The same thing happens to microbes, they can make lots of acid, such as lactic acid, although other microbes make other things (and this is important, which Ill try to blog about another time). In effect, microbes by secreting acid into the environment can make the environment more acidic. If they could not respond to this appropriately, they would kill themselves, and who wants that?

So you see, pH matters in biology. Not just to make sure your reagents are correct so your experiments work but because life causes changes in pH, which life responds to, which changes the pH, which life responds to, which......repeat until your head explodes.

Interesting philosophy quiz - Battleground God

Battle ground God quiz

How I did...

Battleground Analysis

Congratulations!

You have been awarded the TPM medal of distinction! This is our second highest award for outstanding service on the intellectual battleground.

The fact that you progressed through this activity without being hit and biting only one bullet suggests that your beliefs about God are internally consistent and well thought out.

A direct hit would have occurred had you answered in a way that implied a logical contradiction. The bitten bullet occurred because you responded in a way that required that you held a view that most people would have found strange, incredible or unpalatable. However, because you bit only one bullet and avoided direct hits completely you still qualify for our second highest award. A good achievement!

Bitten Bullet 1

You answered "True" to questions 6 and 13.

These answers generated the following response:

You stated earlier that evolutionary theory is essentially true. However, you have now claimed that it is foolish to believe in God without certain, irrevocable proof that she exists. The problem is that there is no certain proof that evolutionary theory is true - even though there is overwhelming evidence that it is true. So it seems that you require certain, irrevocable proof for God's existence, but accept evolutionary theory without certain proof. So you've got a choice: (a) Bite a bullet and claim that a higher standard of proof is required for belief in God than for belief in evolution. (b) Take a hit, conceding that there is a contradiction in your responses.

You chose to bite the bullet.


The questions...
Question 6. Evolutionary theory maybe false in some matters of detail, but it is essentially true.
Question 13. It is foolish to believe in God without certain, irrevocable proof that God exists.

I bit the bullet but think these questions are loaded. If there was any evidence to support the existence of god, then things might be different.

Hat Tip: Sandwalk

Minnesota needs scientists

The state of Minnesota Department of Education is accepting applications for people to serve on the Science Standards Revision Committee. (see MN Science Standards). There is a healthy time commitment from the March 2008 - February 2009, however I strongly recommend that if you are truly interested in maintaining/improving science education in the state to apply. The application is painless some quick questions to find out who you are and a place for any relevant comments. Before applying read the Science Standards Revision: Assumptions.

I wonder about this assumption: (emphasis mine)
"7. Science Standards will reflect the scientific facts, laws, and theories of the natural and engineered world and will not include supernatural, occult or religious ideas. In addition, the following benchmark from the 2004 standards will be included in the revised standards for grades 9-12:
The student will be able to explain how scientific and technological innovations as well as new evidence can challenge portions of or entire accepted theories and models including but not limited to cell theory, atomic theory, theory of evolution, plate tectonic theory, germ theory of disease and big bang theory."

The first is well done in my opinion. That latter part has been used to suggest that Minnesota allows criticism of evolution. (Technically this is true and fine, however we all know that when the IDiots discuss criticism of evolution, they really mine substituting Bullshit for science.)

If you can not serve on this committee, you can still comment on the current standards, which were developed and approved in 2003.

Course evaluations IIIb

More follow up on the evaluation questions I asked my students in an effort to improve the course. See Course Evaluations Part III for the initial premise and first couple of questions.

3. Currently the discussions are informal yet generally good. However, WebCT is not uniformly used. Make postings mandatory: I am hesitant to do this as I think it will overall diminish the quality of the postings since some students may be posting to cross off a requirement. Leave it as is: This is my leaning but I am happy to consider other ideas.

As I have outlined in previous posts, the course is set up in a module format, each module represents an introductory lecture given by me, paper presentations and brief discussion given by two students and myself, and a discussion session based on questions regarding the topic/papers/etc generated from questions posed by the students to a class website. Certain students are assigned to post questions must be posted before the second session, although any person can post at anytime. Further, students or myself can respond to the original post resulting in a "discussion" prior to the discussion. Throughout the course there was some fairly deep discussions on the website with students cogently responding to each other, finding new information, or posting things they had found that they thought would be of general interest to the class. I thought the website discussion board worked beautifully. However, it was a few students that drove the discussions (not surprising), with a fair number at least reading the discussions and occasionally posting, and a few that did not contribute. So, my question here was essentially do I make posting a requirement? The limitation being, I know that if I do, more students will post because they have to, not because they are intellectually motivated. Will a large number of "required" posts diminish the more rigorous and curiosity driven posts?

The students respond (paraphrased by me):

-I say leave it as for the reason you said. Sometimes I didn't have any worthwhile questions to add. Although postings include responding to others thoughts/questions/ideas.
-I agree. A discussion board filled with clutter would annoy everyone and would happen when people are merely asking questions for points. On the other hand, I wish there was some way to encourage everybody to post - I've learned so much from other students this way. This harkens back to a note I made in the previous post, students wanted more participation from their colleagues because they feel they are missing out on other insights. I would also say one of the best ways to learn is to ask a question, propose an idea, etc. and then find out what was wrong with your question/idea/etc. This format is good for that, because unlike an exam you don't lose points for making an error.
-I liked the mandatory questions for certain people every week. I think you should leave it as it is but maybe be take more participation points from those who never post or read the discussions. Students get 1/3 of their grade from participation, which includes speaking in class, doing the presentations/posting questions when assigned, and contributing to the website discussions. I left it open for students to participate in any way they chose. I may put more restrictions in how they get their points next year. BTW: These aren't gimme points, well they are, but you have to get them. The participation grades had a spread similar to that seen with the test.
-I say leave it as it is. Mandatory posts actually helped me a lot. This one confuses me, it seems contradictory as there are only 2-3 mandatory posts throughout the semester.
-Leave it as is is the best option. However, more thread for each module may encourage people to post. These threads could include further organism background, recent articles on organism, and something more specific to the problem being analyzed. This is a great idea, I will definitely implement it in some way next year.
-I like a hybrid approach: a number of mandatory posts, plus some voluntary posts.
-I say leave it as is for the reasons mentioned above.
-Can we post anonymously in case someone had a potentially 'stupid' question? Is it feasible? Would it lead to abuse? Yes feasible, trivial in fact, I simply click the box allowing anonymous posts. It could lead to abuse, but doubt that it would. I don't like this idea because we all make mistakes. I have made some doozies. In fact, I gave my best answer to a question in class, which I learned afterwards was completely wrong. I had told the students I was unsure and the reasons why I favored my answer. So I took a few minutes in the next class, refreshed their memories on the question pointed where I was wrong and why. I am dealing with soon to be graduates who are entering the workforce, although most are planning to go on to professional school. It's my opinion they should suck it up and open their mouths, a huge gaff may get made, but I guarantee that the school paper won't have a full page spread on it. Finally, its helpful during the discussions to call on a person to explain a comment or idea that may not have been clear on the board, an anonymous post makes this impossible.
-Mandatory posts are going to create useless questions that people throw out there "because they have to". I'd make it completely optional, that way the people on the forum would be really interested to interact.
-I think the current system is the best course of action. Mandatory postings would create redundant and/or useless questions, although increasing the number of assigned posters each week could be advantageous.

So it seems the vast majority favoring keeping the website as is, although there are a couple of suggestions for modification that could improve usage.

4. Some changes I am considering: Make each module be on one organism AND one topic. Currently, most modules cover one organism and two topics. Make each module be on one organism AND one methodology. For example, one week is fluorescence microscopy, another week is mutant construction.

This is a topic getting at the heart of this course. The idea is to use euakryotic microbes to introduce the students into actual cutting edge research being done. Learn something about these organisms, often as a way to learn about ourselves, learn how questions are asked and how these questions are addressed. Currently, there are generally two topics for each organism that way the students are presenting distinct papers. However, for some of the modules during the discussion session, we spent the entire time discussing how you localize a protein and the advantages/disadvantages of different approaches (referring to the papers during this discussion). Personally I prefer the current system, with slight modification.

Wonder what the students thought:

-I like the one organism/one topic approach for next year. When there was more than one topic, we didn't cover it as deeply which made it hard to remember come test day.
-Ditto. One organism and one procedural topic would be easier to consume and to recall.
-I agree. I feel like I would really understand the methodology and be more able to remember it for test day.
-I like the organism/methodology approach, however you might want to make it two methodologies, or a class of similar procedures. While I suggested this approach, I do not like it because it constrains the organisms that can be discussed significantly and there is more to science than methods. However, there are specific modules that would benefit from having a methodological discussion. So, Im thinking of making a specific methodology a major point of the website each week (to coincide with the papers/topic/organism) and maybe take a few minutes in every discussion session to discuss the highlights of the website discussion.
-I prefer one organism/one methodology. Students could do a presentation on both a paper and a methodology.
-The topic number can be dependent on the organism and if more than one topic can facilitate learning a methodology or class of methodologies. Prefers the one organism/one methodology approach I infer
-I like the new idea. It is much easier to follow and learn when the topic is focused. Instead of a paper on something deep within a cell, then a paper on the organisms in the large scale. The papers are too long and complicated to understand both topics fully. Maybe consider one paper on one topic on the second day of the module then one paper on another topic on the third day and eliminate the discussion sessions. I dont find the discussion days helpful because I dont have enough time to dig as deeply into the papers as the discussions require. This class would be extremely successful if I were only taking 13 credits and didnt have to work or anything. It seems like this class (as it is) has more work than a 3 credit class should. Couple of issues here. First the idea of breaking things up isn't a bad one. I could have a paper mini-discussion on the second and third days of the module, but that would also eliminate the usefulness of the discussion board. I did want to point out that the class, by all estimates I have seen, was extremely successful and was not dependent on the student's other commitments. Clearly, I think the idea here is that the student would have been more successful if yadda yadda yadda. I mean, come on. Ill let the commenter handle this and move on.
-I prefer the current setup. I like that this format demonstrates the multi-faceted research occurring in (nearly) every one of the species discussed.
-Yes, I like the current setup.

Alright, so the consensus is to reduce the number of topics per module. This is useful information for me. Doesn't mean I am changing it though. A couple of issues, first the topic number appears to generally be an issue at test time. I try to diversify the topics one on molecular biology one on ecology or one on host interaction and one some basic molecular biology. I am most comfortable with the molecular genetic side of things, so you can guess which topic would get booted. One thing I try to do is provide a broad range of topics to appeal to everyone's personal interest (you know not everyone wants to go to med-school, and of those that do, many should be ready with a back up plan). Getting back to tests, there are two a mid-term and a final. I am considering adding an exam, which would reduce the number of topics/exam and/or adding a significant written assignment and reducing the weight of the exams. Also, while the students may have struggled leading into the exams, they did well so I am confident the tests were not over-the-top. So clearly, some things to think about deeply over the next few months. Regardless, I reiterate my contention that these self-generated course evaluation questions are better for me in assessing my course, and eliciting an intelligent and personal response from the students. But wait, there's more to come....only one more post regarding these evaluation questions and my course. Afterwards I compare/contrast my current course with my old course and then will take on ratemyprofessors.com

Interesting science - conclusion overstated

In the November 2nd, 3007 issue of Science, there is an article Disentangling Genetic Variation for Resistance and Tolerance to Infectious Diseases in Animals Science 318:5851 p. 812-814.

In plants, there are two ways, evolutionarily speaking, in which a host can respond to a pathogen: resistance and tolerance. In the "normal" case, a pathogen infects a plant grows to a certain level and causes a certain level of disease (which can be death). The thing to note here is that growth and virulence are partially independent. For example, we have ~100,000,000,000 E. coli cells/gram of feces in our gut (lovely isnt it?), so high growth/low virulence. However EHEC (Enterohaemorrhagic E. coli) can get in you and cause a bloody diarrhea and potentially death. The infectious dose of EHEC seems to be in the ballpark of 100,000,000 cells, which we will assume can grow at least a little, so high growth/high virulence. And of course there are examples of low growth/high virulence, and low growth/low virulence. Using that simplistic model what does resistance and tolerance mean. Resistance is essentially preventing a high growth/high virulence organism from growing. If growth is inhibited virulence will be reduced/eliminated. Tolerance, on the other hand, is essentially preventing a high growth/high virulence organism from being virulent without inhibiting growth.

In this paper, the authors start from the premise that genetic variation in plants promotes both resistance and tolerance (true), whereas genetic variation in animals promotes resistance (true). An effect on tolerance by genetic variation has not been analyzed extensively in animals (maybe true/maybe false). Regardless, the authors look to see if they can find evidence of genetic variation promoting tolerance. The authors use a mouse model of malaria as the host-pathogen system. This is a good one, because mice get malaria (as do most, if not all, mammals in areas with Plasmodium species and biting insects. Note: there are unique Plasmodium species (the causative agent of malaria) for each host and unique vectors (the biting insects). Further, there are distinct strains of mice that are like breeds of dogs, and thus have gene sets (alleles) that are different from each other (this is why people from different geographic areas look different, they have different frequencies of certain alleles). The authors then infect these strains of mice with Plasmodium and look to see what happens. Basically what they find is that Plasmodium infection causes a greater reduction in red blood cells (RBCs) in some strains of mice compared to others. Similar results were obtained by analyzing mouse weight loss. Since Plasmodium infects and kills RBCs, causing anemia, leading to weight loss these assays effectively measure virulence. So, some strains get more disease than others, not surprising similar results have been observed for many pathogens in mouse strains (without being published in a journal of Science's caliber). What was interesting is what happens in a given strain if the dose of pathogen varies. If tolerance is an issue adding more or less pathogen (Plasmodium) should have little effect, in other words the effect in RBC reduction should not change much. In a resistant strain, dose is critical, adding more or less pathogen (Plasmodium) will have greater effects. This is what the authors found. A resistant strain C57 (a common mouse background used for making mouse mutants) showed significantly more weight loss at higher doses than lower doses, ok all the strains showed more weight loss at higher doses than lower doses, the important issue is the "rate" of change. The C57 strain weight loss changed faster as dose varied compared to the other strains. (I realize it is hard to explain without the graphs, but check the reference to see for yourself. I focused on weight loss here, because the effect on RBC reduction was less pronounced.)

Anyway I found this to be an interesting paper, although I had an issue with one part of their conclusions. The authors note that host resistance leads to an evolutionary war with the pathogen, the "resistance" has a negative impact on the pathogen, in other words the pathogen can not grow as well. Thus, there is strong negative selective pressure, any pathogen cell that overcomes that resistance will take over very quickly (it will leave more descendants since it grows better). This effectively removes resistance, so the host is under strong negative selection to find new resistance mechanisms (and the circle of life continues). However, tolerance avoids this negative selective pressure, at least in the authors estimate. I find this to be extremely short-sighted. In the tolerant host there is still negative selection. The host may not be doing something specifically to prevent the pathogen's growth. However, there are finite resources. There are x number of RBC's the more one genotype of pathogen infects the more of that genotype that is passed on. So there is negative selection, by way of competition with your cousins (for one simple example). So now you have a host full of pathogens that are being "tolerated" but which are themselves evolving. Nothing spells accident waiting to happen in my mind than carrying around a lot of a pathogen all the while selecting for variants that may grow faster better stronger etc. So while I agree with the authors' assertion that the resistance counter-resistance cycle is ripe for continual selection for more pathogenic organisms (and resistant hosts I would add). The authors implicitly suggest that this isn't true in a tolerant model.

I wonder if this analogy is any good....I live in Minnesota and nature doesnt want me outside, thus it is currently butt ass cold. I resist that by putting on a jacket and hat when I go outside (suck it nature). Nature is less fit because Im out there stepping on it and being a nuisance, so over time it evolves to become 100°F hotter (-10°F to 90°F happens all the time, well every year). I am now much less fit, so I take off my jacket and mittens and put on shorts and a tank top (take that nature and people with discriminating tastes). And the cycle repeats. However, in my house nature is tolerant of me because Im not stepping on it and I walk around all year long in sweat pants (be happy Im wearing pants), I dont need a jacket or a tank top. Of course the furnace may break or the AC, there may (will) be a power outage, electric bills are too high so I cut back on heat and AC...crap where's that jacket/tank top. Damnit I had to evolve....well the hell with you nature, Im coming back outside and Im bringing my mountain bike!

Course evaluations III

Alright the plan was to compare my current course with my old course but that will have to wait. Instead I want to talk about my current course some more. My blog, my rules.

First off I think the "official" evaluations are a necessary evil although not that specifically useful to me. How do the generic and vacuous questions asked directly help me improve the course (See Course Evaluations Part II for the official questions.)? Obviously I think they don't. I have a course website that I use to post the papers used in class and for the course discussions. At the end of the semester I posted a set of questions to get some specific feedback from students that I thought would provide information to help me improve the course. I also asked for any additional comments/suggestions that the students had to help make the course better.

So here are my questions, thoughts about those questions, and my synopsis of the student's responses

1. Would having more scientists come in to talk about their research and answer questions be a good idea? I am thinking in the manner of our one guest lecturer this semester. Some pluses: The one guest lecturer was overwhelmingly looked at favorably, guest lecturers break up having to hear from me incessantly, which I think keeps the course more interesting, and it is a good way to talk with active scientists and hear how they approach their research. Some minuses: I have no control over how good or bad a guest will be, and everyone will be different which can make for difficult transitions/expectations.

Based on the schedule this year, I had one slot for a guest lecturer. The format being the lecturer provide a relevant review or two (to provide any background) and one or two primary research papers for discussion. All the students then read the papers and post questions to the web site. Students can respond to each other and the lecturer gets to peruse those questions ahead of time. During the class, it was essentially a conversation between the lecturer and the students about those questions or additional issues. The feedback from the students was outstanding following the class. They enjoyed getting a perspective a little different than my own and talking to the actual person who did the studies and getting deeper insights into the decisions that when into a given scientific approach.

The student responses (paraphrased to protect the innocent):

-We should have had more scientists discuss their work.
-One student noted that there were ample opportunities to here researchers talk, but the class was more conducive to interaction.
-I enjoyed learning what the guest lecturer's thought process was when she was writing the papers.
-During our regular class discussions we make assumptions about what the author was thinking, so it was nice to hear it directly from the author. I think the pros overrule the cons on this one.
-I enjoyed this part, you really get a chance to figure out what they were thinking.
At this point the student's raised a new issue.
-I like the idea of having more speakers and going to seminars, its more interesting than just reading a paper. You could require seeing 6 seminars per semester or something, or have the seminar speaker come to class. A student suggest I require more outside work! I advertised when seminars were being held on topics relevant to the class and am happy to say several students attended
-I, also, think students could be required to attend one or more formal seminars/lectures on any eukaryotic microbiology topic being presented and then write up a one or two page summary from it.
-I agree, it would be a good idea to require students to attend one or more formal lectures. I also think it is good to have a couple of guest lecturers because it is always valuable to hear the thinking process they went through when designing experiments, what directions to take after they obtain their results, and changes requested by the editor. Sometimes I wonder why the authors took a particular approach to a problem and having the author come in is the only way to really clear this up.

For me, this is extremely useful information. Students appreciate the intellectual benefits of guest speakers and valued actual seminars. Further, they suggested a writing component. Both of these are issues I have been considering in some form or another (reminder: this was the second year this course existed and the first year I had it solo, so changes were not plentiful this year). Students value the type of guest lecture I had and would like at least one more despite the risks. Formal seminars are useful in the context of this course and could warrant being included as a requirement. Much better than "Instructor's rapport with you as a student. Mean 6.3 SD 1.0 Median 6.7"

2. Currently, I have you turn in a written set of answers to your presentations. This is strictly a mechanism to help you prepare. Potential changes: This could be a more significant assignment that then is graded as part of your presentation.
I could include an additional significant writing assignment that is graded. Taking some of the points from the examinations/presentations.


Student's give a short presentation on an assigned paper 10-15 minutes. I ask the students to address 5 questions. What is the problem the paper addresses, what are the main conclusions, which conclusion do you think is most important/interesting and why, what data best supports this conclusion and explain it in detail noting the limitations, and why is this conclusion important. I also require that the students turn in a written response to these questions as a way to ensure the presenters have prepared. However, this course could truly benefit, I think, from a significant writing assignment such as a critique of a paper or report on a topic etc. What did the students think?

-I actually think that would be a good change. Not that i think there should always be more homework, but this class was interesting but easy to forget information since it was not again until the test.
-I agree. Some students are great "test takers" while others may be better at read/write/research-type activities. This would give everyone a better chance at success.
-I think that writing assignments would help to learn the material better. I would definitely have them next year.
-I would like it if we found a paper we were interested in (not any that was assigned for the modules) and critiqued it. This could also give you ideas of papers for the year after that. see, here is an example of the "evaluation" getting valid student participation. I think that from my approach with these questions, the students understand that they are helping to improve the course. Because they enjoyed it, I think they have a vested interest in the course's progression. Maybe its me, but I think that is really cool!

-This might just be me, but I do enough writing in other classes, although it might be ok if this course were made writing intensive. Our biological science students have to take several "writing intensive" courses, however we are moving away from this to have some writing in all courses (about time), so this latter point will likely not be an issue in the near future.
-The presenters could provide a significant summary of the paper they are presenting greater than currently being done.
-I dont think adding significant writing assignments would be good unless the course is "writing intensive". Although turning in summaries to the papers weekly would be ok, as it forces you to read and outline the papers. favoring more smaller writings than one or two larger writing assignments. This also brought up a theme that came from this message board and a class discussion, ensuring all the students were actively participating. I don't think there is a good way to do this without hampering the course, but it was interesting to me that some of the student's were not thrilled that their colleagues were less involved. Im a cynic, but I think the motivation of those with the concern is that they were missing out from not having additional perspectives from their colleagues.
-Have each student pick 3-4 of the organisms and find a paper on current research on that organism and summarize it. This would expose them to the scientific databases through PubMed or Medline, a benefit to those who are not familiar with it.
-Adding an extra exam or a writing assignment would take some of the pressure off. Writing assignments take longer but also require organizing thoughts and a lot of research. Usually, I remember more after writing on something specific. Also, thank you for considering our ideas.
-Having a formal writing assignment on one or more of the organisms would be a good idea since some people are much better at writing their thoughts although you should then make the course "writing intensive". I don't necessarily think it would be a good idea to require a more formal writing assignment for the paper you present. The goal of the presentation is presenting and writing should be saved for a different time. Here is where the "conversation" is apparent, this is in response to a previous post to simply increase the significance of the current writing format. Again, the student's care enough to take the time to disagree with each other.


There is more but I'll leave this at its current length so you won't have to make another cup of coffee. I want to point out that here are valid useful comments regarding the course. Particularly focused on new ideas to improve it, but also there is (at least coming up) some discussion of what didn't work. I find this much more useful than to vague bullshit on the generic form. One last thing to consider, from the message board nothing was anonymous (and many of the comments came from after the course was completed, so there was no issue with grades). Our generic evaluations bend over backwards to make sure they are anonymous and everyone knows it, this allows students to put down some despicable and horrid comments without any concern about repercussions. Personally, I think the anonymous nature of most evaluations makes them less useful not more useful.

Democratic debate

Caught a little of of the democratic debate from New Hampshire tonight and here are my thoughts...

Clinton: Seemed angry and overly aggressive. Not sure if this is her or her advisors, but it was offputting especially when it was obvious she was trying to dominate the discussion (final word, etc.)

Obama: Seemed inclusive and big-tentish. Also tried to dominate the discussion similar to Clinton. One thing I think Obama has going for him, is that his tone is distinct but pleasant. He talks about working together, doing what's best together, etc. This is different than Bush and many of the candidates who either say or seem to say, that is they know what's best so shut the hell up and let us do what's best. Obama is the only candidate tonight who emphasized the role the people must play in a functional democratic government, the other dems seem to talk from a perspective that plays into the "welfare state" mentality of the far right. (I noted that the republicans are falling all over themselves to appease the religious right so anyone not in that camp knows they are screwed.) Based on what I heard, I think Obama stands the best chance of pulling in independent votes and the votes of republicans who are sick of the BS Bush et al have brought to us using the disguise of republican values, when in fact these are neocon- religious right-republican value themselves and none other.

Edwards: Said many excellent things, but is a bit too far in the "government must help you because you are incapable of helping yourself" camp. Obviously, Edwards does not feel this way, but it is the message I got. I think Edwards can and should play a major role in the next administration.

Richardson: Clearly the odd man out. He did not try to dominate like Clinton, Obama, or to a lesser degree Edwards so lacked there. But Bill Richardson had many good things to say and a perspective as a state governor that was lacking in the other candidates.

Interestingly, it seemed to me to be an Obama/Edwards vs Clinton fight with Richardson abstaining. Although I have to admit Clinton seemed to be the aggressor, with Obama responding and then Edwards essentially affirming Obama, even when he had policy disagreements with Obama. This made Edwards and Obama come off much better. Obama was good about redirecting attacks from Clinton towards the similarities between the dems and their stark constrast with the republicans.

Finally, I think Clinton has an extremely tough road in front of her. In fact, I believe the USA is not mature enough to elect a woman to the highest office. I have said it before, it would be difficult for a non-white citizen to be elected, but if they were male they would have a chance. Clinton (white woman) NO - Obama (black man) YES; Rice (black woman) NO - Powell (black man) YES. The racism in this country is profound, but not epidemic. The sexism in the country is not profound but is epidemic. (Clearly, if you are dealing with either racism or sexism it is profound and epidemic, my point is that more people in this country would be uncomfortable having a pair a breasts running the oval office than some additional melanin.)

Crap. As I re-read this I find myself falling into the Obama camp. I don't want to be that decided at this point.

Can I live with Obama

Congratulations to Senator Obama and his "principle of the thing" victory in Iowa. I have to admit I have been in Kucinich's camp to date and by in I mean peripherally thought he was most inline with what I think. By far my biggest concern is how these candidates view science and the role science plays in society. Thus I am automatically discounting the entire Republican slate as they all cowtow to the religious right (who have defined themselves as anti-science at least until they need some medical help or TiVo). So of the Democrats who's my top pick?

Using the following "quiz" which ranks on a variety of issues and the importance of those issues (and gives you 20-odd options to get a bazillion spam emails afterwards) Barak Obama is my winner. Kucinich was close so that's reassuring, but I was surprised to see how far back Clinton is on my list (Iraq is a bitch).

2008 President Selector http://selectsmart.com/president/2008.html Rankings:

1. Theoretical Ideal Candidate (100 %)
2. Barack Obama (82 %)
3. Christopher Dodd (withdrawn) (80 %)
4. Dennis Kucinich (79 %)
5. Alan Augustson (campaign suspended) (75 %)
6. Joseph Biden (withdrawn) (71 %)
7. Hillary Clinton (71 %)
8. Wesley Clark (not running, endorsed Clinton) (71 %)
9. Al Gore (not announced) (70 %)
10. John Edwards (69 %)
11. Mike Gravel (withdrawn) (67 %)
12. Michael Bloomberg (says he will not run) (60 %)
13. Bill Richardson (59 %)
14. Ron Paul (54 %)
15. Kent McManigal (campaign suspended) (52 %)
16. Rudolph Giuliani (34 %)
17. Elaine Brown (34 %)
18. Alan Keyes (32 %)
19. John McCain (31 %)
20. Mitt Romney (28 %)
21. Tommy Thompson (withdrawn, endorsed Giuliani) (27 %)
22. Newt Gingrich (says he will not run) (24 %)
23. Chuck Hagel (not running) (24 %)
24. Mike Huckabee (24 %)
25. Tom Tancredo (withdrawn, endorsed Romney) (24 %)
26. Fred Thompson (22 %)
27. Jim Gilmore (withdrawn) (19 %)
28. Sam Brownback (withdrawn, endorsed McCain) (18 %)
29. Duncan Hunter (18 %)
30. Stephen Colbert (campaign halted) (8 %) did you need more evidence to demonstrate Colbert is satire? I mean he out right-winged Tancredo, Romney and Huckabee!

One thing is that quiz did not deeply deal with many science issues (or any other issue for that matter). So how do the top dem's fair in science? Well it just so happens that this week's Science has the following News Focus "SCIENCE POLICY: Science and the Next U.S. President" by Jeffrey Mervis. You should go read it and the subsequent responses from the candidates. Some highlights:

Clinton: "promised an executive order that would 'ban political appointees from altering or removing scientific conclusions in government publications without any legitimate basis … and prohibit unwarranted suppression of public statements by government scientists.'" and a "doubling of the $30-billion-a-year National Institutes of Health budget during the next decade."

Obama: states that "his policies would be based on 'evidence and facts.'" and that "He'd like to double federal spending on basic research." again with the doubling

Edwards: "would 'eliminate political litmus tests for government scientists' and forbid political appointees 'from overriding agencies' scientific findings unless the chief White House science adviser concludes they are erroneous." nice that one advisor can override an entire agency Further, he "supports budget increases 'substantially better than the pace of inflation' for the National Institutes of Health (NIH) and the National Science Foundation." I like this better than another doubling and the problems that arise when the doubling ends

There's a lot more for each of these candidates as well as the other candidates including the republicans. From this information I find no reason to disapprove of Obama, so I'll wait this thing out longer before making a stronger decision.

Course Evaluations Part II

Previously, I discussed the nature of student evaluations. Where they can help (course improvement) and where they can hurt (evaluation of instructor effectiveness). Here, I want to discuss the outcome of my most recent course evaluations focusing on some specific questions on the evaluation. I will post a comparison between my current course and the previous course I taught and my non-scientific analysis of the evaluations between these courses in a third post.

Our evaluations are a series of questions that the students rank aspects of the course from 1 (very poor) to 7 (exceptional) with 4 being satisfactory. These are fill in the circle questionnaires so there is no chance of a 7 being misconstrued as a 1. There is also a section of instructor teaching characteristics that students rank as either strength or weakness. Finally, there is an empty box for specific comments. My class is small (~20 students) and everyone turned in an evaluation, although only a few entered specific comments (there was a reason for this I'll discuss later).

Once the evaluations are submitted, they are scanned and the Office of Measurement Services (I picture one or two undergraduate students feeding these forms into a scanner and stapling the resulting output sheets together between rounds of Halo as the Office of Measurement Services.) generates a set of summary sheets that is put in your permanent record and sent back to the instructor. So let's see what the evaluation entails and how I did.

How would you rate the instructor's overall teaching ability?
Mean 6.2 SD 1.1 Median 6.6
In my opinion this question has less to do with teaching ability and more to do with student satisfaction. I benefit from a small advanced class plus that I have great teaching ability.

How would you rate the instructor's knowledge of the subject matter?
Mean 6.0 SD 0.9 Median 6.2
In fact I am surprised this one was so high, some of the subjects I felt like I barely had my head above water.

How would you rate instructor's respect and concern for students?
Mean 6.4 SD 0.8 Median 6.7

How much would you say you learned in this course?
Mean 5.2 SD 1.5 Median 5.6
One of my lower scores although I am not too surprised here. This course is different than most courses I think students take since I do not emphasize the facts. We spend most of the time discussing how to go about doing the science to learn something and I assume the students come to class with the necessary facts to participate in that discussion. So I hope the students learned a lot and got something valuable from the course even if they didn't know it.

Instructor's clarity in presenting or discussing course material.
Mean 5.7 SD 1.3 Median 6.0
I thought i would do little better here, although there were a couple of outliers not found in other similar questions.

Instructor's rapport with you as a student.
Mean 6.3 SD 1.0 Median 6.7

Instructor's use of technology to enhance your learning experience in the course.
Mean 6.1 SD 1.1 Median 6.5
In other words, no problems plugging in the computer

Instructor's success in getting you to think.
Mean 6.2 SD 1.2 Median 6.6
SUCCESS!

Instructor's attention to what helps you learn.
Mean 5.7 SD 1.2 Median 6.0
I am at a loss, I don't recall spending anytime during the course thinking about what would help individual student's learn. I should have a 4 here (satisfactory). I think this is one of the more useless questions on the survey and likely reflects student satisfaction again.

Instructor's respect for students' individual differences.
Mean 6.0 SD 1.1 Median 6.3
What now?

Overall quality of text(s) and handouts.
Mean 5.4 SD 1.8 Median 6.0
The broadest range of responses and one of the only ones to receive a "very poor" ranking from a student. Not sure what to make of this. There is no textbook, nothing but scientific articles, reviews and primary research papers. Albeit some articles were poor, by-and-large most were very good (a conclusion reinforced by the students).

Helpfulness of feedback given to you about your performances.
Mean 5.1 SD 1.7 Median 5.6
I need to improve on the rate of feedback next year. Right now the students are about half-way through the semester before they get their first exam.

Degree to which evaluation procedures measured your knowledge and understanding.
Mean 4.8 SD 1.3 Median 4.8
Here is the other question to receive a "very poor" ranking from a student. Not sure what to make of this yet

Instructor's encouragement of students to express their views.
Mean 6.6 SD 0.8 Median 6.8
Lots of discussion, so nothing too surprising here

Strength/weakness breakdowns

Instructor ...is available outside of class 100% strength
...effectively manages the classroom 95% strength
...begins class on time 95% strength
...ends class within the time scheduled 100% strength
...effectively facilitates classroom discussions 95% strength
...integrates topics and activities effectively 95% strength
...selects course content appropriate to length 100% strength
...paces assignments and tests appropriately 74% strength two exams, mid-term and final.
...defines academic dishonesty 100 % strength
...explains and clarifies grading policy 90% strength
...effectively uses technology and multimedia 95% strength

At this point a little less than half the class responded, in other words a smaller N and the questions used a variety of ranking criteria, thus I'll just summarize the gist of it.

I provided a moderately/highly structured learning environment.
I emphasized a balanced/many topics.
The course guide/syllabus were accurate in describing learning activities.
I stimulated you to think critically about the course work.
I set high expectations for student performance in the course.You're welcome
I used a variety of teaching and learning strategies in the course.
I provided students with timely and helpful feedback about student performance.
Students attended almost all of the class sessions.
Students would take another course by me. well, except the one student (I deduce) who marked just about everything as a weakness

Course evaluations

Well its that time of year again. My course wrapped up early last month and during the last "lecture" the students filled out anonymous course evaluations which are then sent to some central office for analysis. I just received the summations, so I wanted to share a few thoughts. Before I do (in a later post) I want to spend a minute to touch on student evaluations.

What is the purpose of student evaluations, because in general I regard student evaluations as a necessary evil?

Several potential uses come to mind:
1. provide feedback to the instructors on the course and student's perspectives,
2. provide a "quantitative" rubric to administrators to grade instructors,
3. to allow students an opportunity to vent with no repercussions

1. provide feedback to the instructors on the course and student's perspectives. This seems to be the greatest potential benefit. This could give the instructor an opportunity to determine what aspects of their course worked or didn't work, give some feedback on what teaching approaches should be emphasized and those that should be de-emphasized. This requires, of course, that the instructor actually cares to modify/change the course. I can easily envision a course where change is not necessarily a benefit. So, this is a good use of student evaluations. However, in practice these evaluations tend to fail. Much of this has to do with the USA Today approach to evaluations. The same evaluation is used in a 200+ student freshman English class as a 12 student senior level biological laboratory class. The questions are watered down to the point of homeopathic irrelevancy. However, at least one study has found that this is best approach to get valid student participation in the evaluation process

2. provide a "quantitative" rubric to administrators to grade instructors. This seems to be where evaluations are generally used the most. Administrators love these things, because they simply quantify the not easily quantifiable such as teaching ability. You could argue that the evaluations are allowing you to determine teaching effectiveness, but you would be wrong. Several
studies have demonstrated that course evaluations are related to student satisfaction. Small classes are evaluated more favorably than large classes. Upper level classes are evaluated more favorably than lower level classes. Evaluations also correlate strongly with student grades! In other words, good teachers get bad evaluations from academically weak students and bad teachers get good evaluations from academically strong students. Based on this, it's good to know as a college instructor your tenure, contract renewal, promotion, etc. is based in no small part on these evaluations. Doesn't this imply there is a strong institutional push to give out good grades in order to maximize your evaluations?

3. to allow students an opportunity to vent with no repercussions While tongue-in-cheek overall, in my experience this does appear to be true. There are some students that need to express their loathing of the instructor in no uncertain terms. Well, no uncertain as long as it remains anonymous. Thus, when evaluations come in you should probably be in your happy place (local pub) before reading them. Clearly, student's do not need evaluations for this, there is always ratemyprofessors where you can rail against the machine. However, there is a good chance the instructor may never see it, thus bring in the evaluation form. I do check my ratemyprofessors rating but mostly just to ensure that I am still considered evil.