Importance of being dumb - oh science...

Taking break from student horror stories for a minute I recently came across an interesting article, which I have linked at the bottom (free access) for those that are interested.  The gist of the article, which we will go into more detail about in a moment, refers to the need of stupidity in graduate school and to be successful in science.  I had an interesting applied moment when I read this in light of my graduate career so far.  I remember reading an opinion paper (which I cannot find now for the life of me) in a journal that talked about how being in graduate school makes you feel stupid, even though being in school means to some degree you are pretty darn smart.  Recently, with my comps (ideally) looming next semester I've heard more than a few talk about the need for absolute humility while taking the oral component - in short explain what you know while never appearing as though you think you know everything.  Let's discuss.

First off, graduate school does make you feel stupid.  Part of this level of education is not taking regular classes but having them as seminar or discussion - to integrate advanced topics and reasoning.  Prepare as you will, the professor will always lead the discussion in a way that you never thought of and there's always someone else that says something profound (well, it's not always actually profound, but you're little brain makes it feel that way).  You'll find yourself scrambling to write down every word and still walking away only half following what the hell just happened.  This mixes very interestingly with the societal pressure to cut the tall weeds (aka it is often socially unacceptable to be the really really smart one) and the academic pressure to weed out the scrubs (aka figure out who really doesn't know much).  Most new students are too afraid to say anything, afraid to sound stupid or to come across like they are "attacking" another idea.  So you sit, smile, and nod your head.



Of course, this doesn't last.  Here in my 3rd year of my PhD I find myself participating more often, especially in classes or seminars with a large proportion of graduate students.  Still keep pretty pursed lips though in large scale settings with lots of faculty.  I'm not really a shy person, but what do you do?  Just try.

Now onto the comps piece.  We talked a little bit about this before but for the conversation to continue we all need to be on the same page.  For a PhD student, the only way to move from "student" to "candidate" (aka even be considered for grants or graduation) is to take comprehensive exams.  This differ from department to department and school to school.  Usually there's a mixture of written and oral exams.  Some use a mock grant proposal and defense.  Others use large scale tests.  My department has a week of essay papers for the written.  Each day a different committee member (minimum of 5, and trust me that's ALL you need) will send you a set of questions each day.  They will require you to produce facts from papers you have read as well as extrapolate and apply them to the questions.  Assuming you pass these there is a day of orals, whereby you sit in front of your committee and for 4-6 hours they verbally ask you questions.




Okay, enough on that drama for now.  I am more than sure as they approach and I sink in deep for survival there will be more on that.  The point of that conversation is to move it further.  Another student in the department (with another adviser) was telling me horror stories of her first failure and her second try (you only get 2) in which she passed.  She told me one of the biggest differences was attitude.  She's a smart cookie and going into her first one felt confident.  Responding to this her committee became very aggressive and would outwardly tell her that they didn't like whatever thought process she had followed to get to an answer, even if it wasn't technically wrong.  Afterwards her adviser berated her for her performance, leading her to almost quit.



Thankfully she didn't quit and when she tried again she went in with her head down.  She was still able to think through answers but by being less confident she got more positive responses and received much less aggression from her committee (plus she passed).  Now take any story with a grain of salt but it seems to me that part of the point of comprehensive exams is to show you how much you DON'T know (or can't know YET) and look for you to show signs of humility and "absolute" stupidity.  Keeping in mind of course that these exams also look for you to prove you do know the basics in your field and would be a respectable representation of it (not "relatively" stupid).

This brings us to the paper I mentioned at the beginning of this conversation.  The author actually teases at my assessment above, stating if a student is able to answer all the questions posed to the fullest it is the committee that failed the exam.  By that feeling of absolute stupidity it pushes us to question and inquire, to keep moving beyond the bounds of current knowledge to learn and regain the feeling of shock and awe at the complexity of the universe.  If we ever feel like we know anything, then we stop learning and stunt the learning of those around us.  In the universe of science, you shouldn't feel like you know what you're doing because that's what leads to the big discoveries.  So feel absolutely stupid but know that you're not relatively stupid.  You know a lot, but you can't know everything!

Check out the article.  It's a well written essay that is easy to follow, even if you don't get into science itself per se.

Swartz, M.A. 2008. The importance of stupidity in scientific research. Journal of Cell Science 121: 1771.
http://jcs.biologists.org/content/121/11/1771.full.pdf+html-

Let me know what you think or share related experiences.  Your story can only lead to inform others coming through and make those who have felt it feel less alone.


"Do not be afraid of defeat. you are never so near victory as when defeated in a good cause" Henry Ward Beecher

Paleoecology: A long-term complicated relationship. I can't break-up, my CD's are in his truck

Sorry about the delay, I was on a bit of vacation. Not thinking about school or work in real life and the internet universe as well. I'll make it up to you though!

Now, continuing on my previous train of though.  There are many ways in which ecology gets complicated and tends not to look as pretty as the previous post shows.

Let's look at some of my MS (Master's of Science) work as a starting point.

I worked in a field called paleoecology in order to tie in aquatic species with water quality to look at pollution affects on a lake over time.  Diatoms (see Fig. 1) are a form of algae that is made up primarily of silica, and therefore fossilizes in the sediment of the lake they live in when they die. What we can do then is take a core of the lake bed. Each year a new layer of sediment is added to the bottom of a lake. We can take a core of a lake, date it using chemistry (such as Lead 210 dating) and compare what things are in each layer of the core with the associated date.  This allows us to track ecological community changes (the relative number of each species or population of diatoms in a year) through time.  NOW in addition to all that knowledge you can also run chemistry on the surface of the lake bottom (before the chemicals mix or breakdown).  You can compare the water chemistry (things like nitrogen, phosphorus, oxygen, pH, or temperature) with the species found and their relative numbers. This can tell you the preference and tolerance of these species to a given water chemistry factor. So species that have a lot of individuals fossilized at the same level as the water chemistry you tested do very well in those conditions (say high nitrogen, which remember is basically a fertilizer).  Species that are low in numbers (or not in the sample) do poorly under those conditions.  With me so far?
Fig. 1: Diatoms
Fig. 2: A core from the bottom of a lake (depth of mud at bottom)

Okay then so here's the kicker, with the relationship of species to water chemistry, you can look back at older layers of the lake sediment and count the number of species and individuals that are fossilized.  Once you know the community structure, you can use that information to estimate what the water chemistry was likely like!  You can start to understand how a lake has change over hundreds or even thousands of years!!

Now of course, is where is starts to get dirty.  Remember this is still ecology.  So what happened with me is, after 2 years (normal length of a MS program), it didn't work.  But in a way that's what made the project really interesting (and of course at the time very frustrating).  When I ran my estimates and compared them to known emission rates of nitrogen from the area they were exactly inverted! My model checked out well against expected ecological relationships (we call it r squared, or how tightly the relationship of your data is). For something more linear like chemistry or physics you would never accept and r squared value below 0.8 or so (on a scale of 0-1).  In ecology? Remember 0.4 is fantastic and numbers like 0.1 are not even unusual.  The reason is that there are many factors that effect an organism and its habitat and the variable you are testing is likely only one piece of a much larger puzzle.  That doesn't mean it's not important, it just means it's complicated and intertwined.

In my case what we think may be happening is one particular species tends to completely dominate the older sediments, and the problem it this species is a known generalist (often can do well in many different conditions and it quite good at competing with other species for a limited resource).  I proposed that the model needed to be able to ignore such species.  More in depth later.  As a result I have a very controversial paper in lieu since the model has been used for 30 years.  So it's been hard to publish.  See previous Science post for likely reasons why...



"Science is facts; just as houses are made of stones, so is science made of facts; but a pile of stones is not a house and a collection of facts is not necessarily science."  Henri Poincare

Ecology: complicated and delicious, just like your ex's facebook status

Ecology was truly love at first sight.  Now I'm not normally one for complicated relationships, but something about ecology has always made my toes tingle. Ecology is the study of the relationship of species and their environment. Like all relationships, this one is dirty, convoluted, and complicated.  Like a good relationship though, I can also be very rewarding and exciting.  Upfront the idea of ecology may seem very simple. You take a species and see how it responds or affects its habitat.  And it's insanely relevant, answers to those questions can help inform conservation, forestry, zoos, climate change, habitat management, zoning, invasion, biological control, and so on.  You also end up incredibly well rounded, using mathematics theory, statistics, experimentation, laboratory control, cross departmental collaboration, biology, physics, chemistry, aquatics, animal behavior, and evolution. Okay, so now you can see how this can get so complicated.

My bio stats professor once said that ecology will always be a strong career because there's never any way to answer everything about even one question. Realistically, the possibilities are endless.  You could have 9 hypotheses to test and none of them be the correct theory.  Moreover, ecology is almost never controlled by one variable. Let's look at the situation that originally got me interested in ecology my junior year in college as a simple starting point.

I still have the original article, I never got rid of it.  It's a 1997 article in Science (one of the top 2 science journals in the world, likely only second to it's London counterpart, Nature).  "Cichlid Fish Diversity Threatened by Eutrophication That Curbs Sexual Selection."  Okay, let's look at this concept bit by bit.

1. The species: Cichlid fish are found in many places in the world, although warm water.  They are well studied for their species divergence by population.  In other words, often when a population of cichlids becomes isolated in a lake or water way they specialized and diverge.  If they are reintroduced to the population they come from (the source) there will no longer be any breeding between the populations.  
2. Eutrophication: In aquatics, the water quality and clarity is often generalized into 3 majors groups
1. Oligotrophic: clear crystal water with little algal blooming or fertilizer
2. Mesotrophic: moderate clarity with some algal blooms likely giving the water a hue of blue or green for parts of the year
3. Eutrophic: murky, dark water with little clarity and high algal blooms giving the shoreline a very green color. SO when we say "eutrophication" we mean a lake that is moving (or being pushed) towards poor water clarity and quality.  In this case reducing vision within the water column. 
3. Sexual selection: Alright so this term should be more familiar since we talked about it in my evolution post.  Specifically here it is important to know that females choose their male mates based on color and color brightness.  So there is selection pressure on the males to be a certain color and to be a very bright variant of that color.  Think about how this would be different if there were a predator? 
4. So the kicker with this research is that over time, as the lake becomes more euthrophic and more murky, the females have less ability to visually choose their males and often do so indiscriminately.  They breed across the lines of sub species as well, no longer able to choose by color.  As a result, there is no benefit for the male to invest a lot of energy in being colorful so there is a reversal (another term you know!) to being dull fish.  The males and females were becoming dull grey in color and the populations were almost completely intermixed again as a result!!!

Alright, I will continue to talk about ecology next week and how it becomes more complicated.  If you have any questions so far, let me know!

"Science is one thing, wisdom is another. Science is an edged tool, with which men play like children, and cut their own fingers." Sir Arthur Eddington

Science-how the study itself adapts and evolves!

Science!  One of the things that is often misunderstood and misconstrued is scientific theories (and the process by which they are derived).  One of the major problems for this is scientists have established their own little world with its own lingo and set of standards.  The good thing?  These standards have a very good tenancy to hold up (as in relation to society-more on this in a bit).  The bad thing?  Nobody normal gets it.  Mercy sometimes I don't get it, so let's talk about some of the things that science does that incidentally fuels the anti-Darwin fires.

1. THEORY: A theory as the average person thinks of it is a constructive thought process by which a philosophy or belief is based according to perceptions and observations.  Again, I cite the Annunaki (the reptile aliens from a previous post), which is a theory that aliens had intermixed with humans. The theory arose from ancient Sumerian text and carvings.  The beings have traits apparent in certain (select?) humans and the whole shebang.  The term is actually not even caught by spell check it is so common.  They even tie in the the UFO theories and the Builderberg Group/New World Order theories.  They all sound new, they're not mainstream, and honestly some of them are just plain crazy.  
2. HYPOTHESIS V LAW: The problem is scientists don't use the word theory as we just described it.  The term "hypothesis" would tie up much more closely to this definition-a series of ideas or questions built on observational framework.  A scientific theory comes much further down the process line.  First you have a hypothesis, then you propose how to test it, you test it, get results, and draw conclusions based on your test and the subsequent set of results.  For any long standing scientifically accepted theory, that process needs to be performed many times by many different people (repeatable results). Very similar to scientific law.  In fact, the law of gravity is actually a theory according to scientific terminology, but I don't see very many people jumping off the building in order to fly home.   
3. SOCIETY: Science, like every other construct is the black duck of society.  You follow what people want to hear or you get squished.  Example-Ptolemy was able to explain heavenly bodies in motion with an Earth at center basis, he used concentric circles so technically the pattern matched the data.  What was more important was that it matched societies view so it stuck around for 1600 years, even though Galileo figured out the real pattern much sooner than that.  But what happened to Galileo?  Oh, he died in prison...  Now Ptolemy did not screw with data and forcefully misconstrue anything, based on what he had to work with and his observations it fit the pattern fine.  The issue here is that poor Galileo got squashed when he had a DIFFERENT idea, and it took almost 200 years to make it mainstream.  Society also governs what's important, or what types of things scientists should focus on.  AIDS research didn't really go into full swing until the 1990's, but was discovered in the 1970s and named.  However, because of the stigma, it wasn't "important" for mainstream research so it was very difficult to get funding.  It's kinda like that city law that so many accidents need to happen in an intersection before they'll budget in a stoplight.
4. WRONG: Like I just mentioned, sometimes science gets it wrong.  Sometimes it's completely innocent-trying to draw conclusions based on only a few pieces of evidence.  But you have to start somewhere in order to make progress.  Sometimes though, people do bad things, which I'm sure doesn't surprise anybody.  And let's face it, this isn't a construct isolated to the sciences, or even to our society.  However, the example I want to use I've actually seen brought up in a Darwin v God debate.  His name was Johann Meckel.  He made a very famous move in the early 1800s.  Meckel believed development of an embryo mirrored evolution (not that strange of an idea in the early 1800s).  He spent several years of his life studying it.  The issue was (of course) that it just isn't true, the development of an embryo does not mirror the procession of evolution through time.  Instead of admitting his failure, he was so passionate and emotionally tied to his idea that he forged drawings and had them published.  These drawings were even used in textbooks for a couple of years until someone figured out his masking attempt.  That's the perk about science, it has to be testable and repeatable by someone else.  Of course, the drawings have been stricken from teaching and his name only comes up to demonstrate a very bad point.  In fact it took me 10 minutes and 5 pages in google images to find his little faux pas (he went on to do some other quite spectacular things medically).  The point is that even though science makes mistakes, it is able to admit the issue and adapt to new information (even if it takes a while) which is certainly more than can be said of other passionately driven constructs.  No societal construct is perfect!