A thousand taxonomists cried out into the night…

Whoever said cladistics were useless?

Certainly I haven’t.*

An example has just surfaced that shows the importance of taxonomy to this day. Sadly, taxonomists’ vindication may come at the cost of a species of fish, the flapper skate, now recognized as critically-endangered. Classification of this fish as the same species as the related blue skate has allowed the flapper to be fished almost to extinction, and all because of a classification error.

Pictured: The Flapper Skate. So cute!

So while the fact remains that taxonomy is mostly an outdated field, there might still be some role for the science of natural classification yet. Just not in any of the important sciences.

Wired Science: ID Error Leaves Fish at Edge of Extinction

*This may be a lie.

Fear the Biologists

xkcd on biologists:

 
Source: xkcd.com

Awesome comic find from xkcd

New cartoon to go up on my lab bench:

Source: xkcd.com

Awesome photography – ISS with shuttle in front of sun

 
Credit: Thierry Legault

This image was snapped of the ISS and shuttle endeavour as they passed between the Earth and the Sun. Incredible, no? Its amazing to see a human construction in this light (pun oh-so-intended). Humans rock. They’ll take over the world someday.

  Credit: Thierry Legault

Scientific Literature in Undergraduate Education

Larry Moran at Sandwalk asked a a few weeks back about how undergraduate education exposes students to scientific literature:

Exposing Undergraduates to the Scientific Literature

As a rough analogy, I liken the initial experience of learning of the scientific literature to landing in a foreign country and learning the language without guidance. One flounders around a lot, having difficulty with the simplest of tasks, and there’s a lot of exaggerated waving of hands involved. The process is tedious, frustrating, and difficult because there is not much help provided with regards to how to navigate the complex webwork of publications to find the information you need. And next thing you know you’re stuck in an Slovakian jail for reasons unknown. And your cellmate is starting to get just a little too friendly…

Anyway.

I’d say my own problems getting used to research in the literature stems from several places:

1. Newly published papers require a background of knowledge to understand that the initiate doesn’t have.

2. Old papers use obsolete methods, have hypotheses that may have been proven wrong, and use terminology that has been changed or discontinued. This is rarely ever corrected in the literature, one needs a background to know what to trust.

3. Licensing on papers makes finding information difficult as one can spend 10 minutes obtaining a paper just to discover it does not have the information needed.

4. Research takes time, and when deadlines loom, it becomes less and less reasonable to take the time and read through 10 papers to get the understanding needed. The focus often shifts to picking through and skimming for details, which doesn’t teach anything about proper research, and you’re left no better off.

When I consider the time I spent learning how to research (if you’re generous and assume that I actually can now), there aren’t many good memories. Much of my exposure comes from looking for specific facts in an obscure paper published in the 1960s. This sometimes comes as a result of being required to look up references that are obscure, just for the sake of reporting a technique that is widely accepted in practice today. I don’t know how many times I’ve referenced A rapid and sensitive method for the quantitation of microgram quantities of protein or Cleavage of structural proteins during the assembly of the head of bacteriophage T4.

It wasn’t until late in my undergrad when I really came to appreciate that the list of references on a paper are not just there to give credit, but more often to lead the readers to where previous information has been published, if desired. This basic idea of how the scientific publishing system works was never really introduced to me, and I went a long time before learning to properly follow the breadcrumbs to find the information I wanted.

So how might the process move more smoothly for undergrads in a course?

I’d say for beginners, a list of “classic” articles would go a long way to making things easier when looking for a reference on a technique or system. For a given project, a handout of some relevant papers could be provided. This would be pampering upper-year students, but certainly would help ease in new initiates.

To help get them familiar with the infrastructure and process of physically or digitally finding a paper, provide the information for the paper, but see that the students obtain the papers themselves (by, say, requiring method information from the paper). This would help ensure that students could learn to use respective web and library resources, hopefully before any real crunch time came down and the actual science had to be done.

In later classes, this list could be scaled back or removed, but in introductory science classes, this sort of help could be a useful way of easing into learning the system.

The problems with learning the literature are not just with learning to be a scientist and review papers, but largely just overcoming the technical, time-limited, and copyright-related drawbacks that come with the current system of publication. It is definitely not an easy system to jump into blindfolded, flailing around. Some basic guidance early on would go a long way.

Philosophical Solutions to Scientific Problems

So a couple of days ago I went to a talk by this guy:

Figure 1: Dr. Massimo Pigliucci.

It turns out that it is not only possible to have three Ph.D.'s in different disciplines, but to actively research in all those at one time as well. Unless you're a Nobel Laureate, this guy likely makes anyone feel like an underachiever. "You only have two Ph.D.'s? That's nothing. Massimo Pigliucci has 3."

Dr. Pigliucci's talk was on the intersection of philosophy and science. He talked on scientific versus nonscientific disciplines, the limits of science, the application of philosophy to scientific ideas.

An important thing that I took away was an understanding that I really do not know very much about philosophy. I guess that is the price I pay for taking intensive science-based courseloads to expand my depth of knowledge in the sciences, specifically molecular sciences; I've sacrificed breadth. Most of my knowledge concerning critical thinking and logic have come from sources outside of my academic career, and of course these don't get nearly as in-depth as postsecondary courses would into the subject matter.

An interesting example that I took away from his talk, while not unknown to the scientific community, was largely ignored by myself until present. The definition of species is in fact quite a difficult task for scientists to concretely do. In fact, scientists remain divided on this seemingly innocuous concept. While intuitively we can know that two different organisms are different species, no one definition is concrete, because every criterion that has been suggested has been broken somewhere in the living world. There is no point trying to ascribe rules to nature, because nature finds a way, somewhere, to break them. And then nature mocks you for being so crass as to tell Her what she is.

We learn in grade school that a species is a group of interbreeding organisms that are mutually compatible. However, by this definition all bacteria would be considered a single species as they can generally swap genetic information with any other bacterium. The definition is not useful in this case. Similar exceptions are observed for any other criterion you may suggest. Dr. Pigliucci suggests an intuitive, though not scientifically rigorous solution, in that of any number of criteria one could use to define a species, if a certain amount are satisfied then a species is present. This thinking comes from the philosophy side of things, and probably won't gain acceptance any time soon by the scientific community, it is much more inclusive than previous methods.

The point is that not everything scientists look at can be completely explained by science. While many a scientist (sadly, myself included) will scoff at the humanities, they are necessary to our understanding of the world. Dr. Pigliucci calls for more discourse and mutual exchange between the presently divided disciplines. I couldn't agree more.

Why Biochemistry?

I'm back.

I want to go through why I chose to study biochemistry, and to pursue it into the future. But to do that we must go back, back, back, in to a simpler time. A time when things were simpler. The pace of life moved a bit slower. People dressed a little differently.

2004.

Figure 1: 2004 Fashion. From Apropos of Something

Back then, a 12th grade high schooler facing the daunting task of selecting the route of my post-secondary education, I had a good idea what school I would be going to for university, but little clue what for. My interest in science went back to grade 2, where I was put on the spot to say what my favorite subject and replied "science" (remembering a recent super-cool demonstration involving milk, soap, and food colouring). However, science alone is not as specific a subject as it may seem to a 7-year-old. When university loomed and choices presented themselves, I found that I must decide between biology, physics, or chemistry, or something that falls somewhere in between (think chemical physics, molecular biology, and quantum ecology).

Being...ahem....a rock nerd at the time,

Figure 2: Rocks are pretty. From tourist_on_earth

I thought that geology - no, geochemistry - might be an appropriate career choice. But so I didn't sound so crazy, I tacked on biochemistry as something similar I may also be interested in. At that time, in one of the most misled moments of my life, I thought the TCA cycle was interesting. Then:

Dad: "It's a lot easier to find a job in biochemistry"

And my decision was effectively made for me.

5 years later, I have an undergraduate degree in the subject, and pretty intricate familiarity with it. Did I make the right choice? Yes and no.

I made a right choice, though i'm sure others would have led me places just as interesting, and carried me on just as far. I couldn't have known at the time that years later I would remain interested in the subject, but I am. I had little idea what biochemistry, or any other sciences (including geochemistry) was actually like. I suspect many others finish high school in a similar situation. However, my choice was a good one. I don't doubt that I would find a niche in any of several other areas, but the one I have is just right for me.

Choices are inevitable, and sometimes lead where you can't know you're going. The trick is to adapt, to learn, and to be happy with wherever you end up.

Did I think that I would enjoy study in biochemistry? I had no idea.
Did I know anything about the subject? None at all.
Am I happy with where my education has taken me? Absolutely.
Might I have been happy in a different discipline? Probably.

Yet here I am. Ready to move on, open a new chapter of my life, and close some more doors as I go. As they shut, the path ahead becomes a little narrower, a little clearer. While those doors don't open again, the ones I walk through take me on. On to new places, new experiences, and new opportunities. I can't wait.

Figure 3: Being forced to make choices is a good thing. From Mikael Miettinen

An Ode to Boring Science

Photo from umjanedoan

I've never been that into dinosaurs and fossils. When I think of space, I think of coldness and emptiness, not "boldly going where no man has gone before". Neuroscience baffles me and as such I have little interest*. And yet, a large amount of the mass media coverage of science revolves around developments in these and select other fields. Not that they're unimportant, but I find it tiresome that the coverage of science is so one-sided.

I would like to see more emphasis on ordinary, bread-and-butter research out there. It seems that if the news isn't covering classic post-Sputnik science such as robots, rockets, and space, it's something contentious like stem cells, vaccines, or climate research. Big news to the media outlets out there: there's more to science than fighting over embryos and forecasting doom! And they often miss great stories, those stories may just unfortunately be a little harder to tell.

I want to celebrate "boring" research. The ordinary, non-press release research that constitutes the bulk of what one will find if they open up a non-Nature or -Science journal. Don't get me wrong, I'm not talking bad research; good-versus-bad is a different classification altogether than sensational-versus-boring research - there's lots of crap at the top and bottom. I want to talk about what you find when you flip open a textbook. What is published on a regular basis in the hundreds (thousands?) of respected journals out there. Just because it's ordinary science doesn't mean that it can't be fascinating once one gets into the details.

Boring research is interesting research that does not necessarily promise to change the world or advance our ultimate understanding or cure AIDS or discover the Caramilk secret. Boring research makes up the bulk of what is published, and while the loudest stories are cried out over the crowd, the progress of boring, everyday research moves forward. It is the blue chip stock in world of science, where the big trading happens in cloning, robotics, and gender studies.

I would like to see the story of boring research told. Research that perhaps is not ground-shattering** but still tells us important things about the world. Things that in time are more valuable than isolated studies that make major headlines. Things that are established to the point that even scientists ignore the interesting story behind them. I want to to celebrate the unsung heroes of research, and what it contributes to scientific progress.

Finally, it should be noted that this research isn't boring to me, nor should it be boring to you. If you think it is, I'd like to change your mind. Dig a little deeper and there is often a story to be told. By celebrating the tons of quality ordinary science out there, we see the true elegance and amazing subtleties of the world around us.

Here's to boring science!

Image from velorowdy

*Hypocracy acknowledged by this biochemist
**Keep in mind many Nobels have been awarded for work not appreciated when it was done

All laboratory research ever has just been invalidated

Well, not quite.

Researchers have found that ordinary laboratory plastics contain contaminants that can greatly affect results of biochemical and other research.

Two things:

1. Of course they do! Plastics and the things we put in them are organic molecules, and biological systems use organic molecules extensively.
2. Why hadn't researchers, or more importantly, manufacturers, thought of this before? I know some definitely have, but

This makes me think of classic situations where one person gets results that no one else can replicate under supposedly the same conditions, or someone gets a result once and can never repeat it, or cells that were happily maintained spontaneously die with no discernible reason. I know that in my experience that if needed, different types of tubes, tips, can typically be used interchangeably, without needing to worry about controlling for this source of variation.

The good news is that researchers can hopefully take this effect into account and more effectively troubleshoot, finding the sources of error. Who knows, this could even reverse some file-drawering, and research "cold cases" could be reinvestigated if whatever shelved the research may have been plastic contaminants.

The bad news is this opens the possibility for some published research to actually be incorrect, as a common (and necessary) assumption in research is that your tools and implements are essentially contaminant-free.

Though this comes as a big "duh" moment, i.e. no one can be too surprised that this is the case, the publication of real data shows that plastic contaminants can be a real problem. In the past researchers by and large haven't been too concerned about this possibility. Maybe now they should be.


Science 322 (5903): 917

On Wired: http://blog.wired.com/wiredscience/2008/11/common-lab-gear.html

Lingua franca

I'm glad I was raised in English, because working in the scientific field is much more accommodating to Anglophones. Those who naturally speak another language typically have to learn English to work in the scientific field, even if they are in a country where everyone speaks a different language.

In my lab, general conversation goes on in German unless there is a particular reason to include me or one of the other native English-speakers. However, once a presentation is taking place, the default language becomes English. Everyone who works in the scientific field pretty much has to learn English to get by, and I guess I am just lucky that it is my mother tongue. Or unlucky, because while here it means there's less incentive to learn a different language, as I can mostly get by in English.

So I have mixed feelings. It makes a career as a scientist much easier from my end, but I feel like I got ahead without trying when compared to my international colleagues. And I may in fact be losing out on the benefits of learning another language, simply because additional languages always aids understanding of ideas and processes.

I also have to wonder why, exactly, English is the language of choice? Before coming to Germany I did not realize that there would be so much of a requirement for students and researchers to speak English. I remain quite surprised to keep finding so many people who speak English, when in a lab back home almost all other students are monolingual Anglophones. Perhaps the history of science with the British Royal Society? Or the American influence in science in the 20th century? Or just luck?

I seem to recall Dan Brown had some idea about English being the language of science, but I'm not going to go there. I hope to keep the conspiracy theories to a minimum, unless, of course, they are MY conspiracy theories.

Question of the day: If WWII or the Cold War had ended differently, would we all be learning German or Russian to work in science? Or French? Or Japanese?

Göttingen

The University Auditorium

Skipping some other places for now to get closer to the present, this weekend* I got myself to Göttingen, the self-described "City of Science" (Stadt der Wissenschaft). As Hannover is only an hour train ride away I basically had to make it there this summer or regret it in the future. Yes, I am a nerd. I have given up denying, and have decided to embrace it.

Model of the solar system, with the planets proportionate sizes and distances away from each other down the street. Pluto was in a neighboring city.

As you might imagine, it has a particular draw for people like myself, but very little for other travellers, and so I enjoyed an essentially tourist-free weekend. Most if not all other sightseers were Germans. This isn't to say there weren't English-speakers around; quite the contrary as I would say I heard the most English walking the streets there of any German city so far. Presumably, this is because the city is full of students (about 1/5 the population) and English is slowly becoming the international language of choice, aided by its position as the lingua franca of science.

Not a barber shop, this was in fact St. Petri's Church

The city claims its title due to the world-renowned Georg-August Universität which is located in the centre of the city. Gauss, Riemann, and Hilbert all had positions there, and the city boasts 44 Nobel prize laureates.

Because of the university, and what one of my sources referred to as a sort of "mutual understanding" between the British and Germans, Göttingen was spared completely during the war, as were Heidelberg, Cambridge and Oxford. Thus the city still has many original buildings, including lots of 16th-century half-timbered houses. Medieval architecture also appears throughout.

Just outside the downtown, featuring the Schwartzer Bär Pub in the foreground

A memorial to Gauss was set up at the southwest side of the city, though I don't know whether to laugh at or be annoyed by the work of some vandals....... (look closely at Gauss's left hand if you can't see)

Gauss Denkmal

The city is also home to the "most kissed girl in the world" - the Ganseliesel (goose girl). This fountain in the middle of the old city square is traditionally kissed by every graduate of the University. It has been illegal for years, but no one actually cares.

The Ganseliesel

All in all, a pretty cool town, recommended to any who find themselves in central Germany and have an interest in the history of science.

Man, I'm a geek.


*Not this weekend at all anymore, started writing this long ago. Ugh, I can't keep up......

The key to imortality as a scientist

No, I don't mean the Philosopher's stone.

I mean having people know your name after you're gone. Sure the big guys have got popular for their discoveries; Einstein, Galileo and Newton are all household names, but they had to do a lot of work to get there.

Think instead of Bunsen and Petri. What did they discover? I don't know either. But, we know their names because they invented a stand for a gas flame, and a circular dish, respectively. Those guys knew how to achieve longevity.

Forget trying to cure diseases, contributing to the advancement of society, or the search for pure knowledge; just invent something useful in the lab and your name will live on in the scientific literature for centuries.

Eppendorf® and Falcon® figured this out a long time ago.

The Immunologist - slave to discontinuous thinking

Everyone's favourite militant atheist Richard Dawkins talked about the "tyranny of the discontinuous mind" in his book The Ancestor's Tale. This concept involves the natural tendency of us, as feeble humans, to try to divide everything into categories. We try to place all that we see as this or that, but never something in between. Or rather, when we do, the something in between becomes a new category, and not just a statement of the continuum between. Often you can find statements that prove this point.

"There are three types of phenomenon X:
a) extreme A
b) extreme B
c) some combination of the two "

Instead of setting up anything so stupid, all we need to say is that X falls between A and B, and ignore all the silliness of that list. However, our natural tendency is to try to divide continuous phenomena into groups of some sort or other. Reality gets forgotten and replaced with a model that categorizes whatever phenomenon we're talking about. This is the gist of the argument Dawkins presents, along with ample evidence of why it can suck.

I've seen first hand how this method of thinking can really harm the scientific process, at least the teaching of it. While In Dawkins' book he used ring species as the example of the limits of this method of thinking in phylogenetics, I have seen it in the context of immunology. This science is still working through its growing pains, still newborn with respect to its old-timer colleagues microbiology, cell biology, and chemistry. But in addition to that, it is a unique science in that the discontinuous, reductionist model no longer applies very well. There are specific instances where in vitro models have been helpful, but the science as a whole suffers from a lack of simplification usually possible in other subjects, that build from the ground up.

Immunologists classically try to break down all aspects of the immune response into discrete categories, but unfortunately, the harder you look, the more often you find that those distinctions are really just fuzzy boundaries, if not just two extremes of an continuum. I ran into trouble when trying to divide up cell lineages at one point because everywhere you try to define a complete group, you find that there is an exception. And in each of those exception groups, there is an exception to the exception. Big fleas have little fleas and so on. This tells me that maybe we're going about this the wrong way. A real revamp of how we look at this system is in order.

This isn't to say that divisions shouldn't be made, but they should never be presented as absolute divisions, as many the instructor seems wont to do. As soon as you start saying "This pathway applies here unless A of B or C or D happens", you're just asking to be proven wrong once E shows up to wreck your day. Its better to explain more of how the pathway actually works, and so predictions can be made. You can say, well based on what I know, if E happens, then I can expect this result. Take that, E.

Immunologists, take note. You're not going to get anywhere until you drop the reductionism and gain a better appreciation of (or respect for) the system you're dealing with. In fact, scientists in general should check themselves for this from time to time. Its all too easy to get caught in a cycle constantly breaking things down into groups until you reach a point where the groups themselves lose all meaning. This is the discontinuous mind at work, and in this case working against you.

The next time a biologist tells you that something falls into one of several categories, tell them they're lying. I dare you. No, double-dog dare you. Given enough time, you'll be proven right. You'll thank me. And to express your gratitude, you know where to send the cheque.