Scientific salaries.

October 22, 2008

And this is why you don’t go into academia for the money.


Seminar Flow Chart

October 8, 2008

If I were inclined to say it in that special Intertubes way, I’d say:  OMG!!@!  Thiz is sooooo me!!1!1!


Where are the NDP on science?

October 5, 2008

I’ve been paying attention to Canadian politics as I look forward to exercising my democratic rights ina couple of weeks.  I’ve never been seriously interested in the NDP, for the simple reason that they never seemed to be in a position to take power, but with the Liberals melting down in the polls recently, I’ve come to view the NDP as a serious contender for (at least) the opposition.  Since I would normally vote Liberal, this now leaves me pondering my choices more carefully.

To help figure out what I’m going to do, I sat down tonight to review the platforms of both the Liberals and the NDP.  Mr. Layton’s was interesting, with many ideas on important issues like climate change, the economy, and so on.  But if you’ve read this blog for any time at all, you’ll know that I’m a Ph.D student in Biology, and that science is very important to me.  So what is the NDP stance on science and scientific research in Canada, you ask?

Beats me.

The NDP platform is weirdly vague to begin with.  But doing a search through the document reveals a single mention of the word “science”, and that’s in regards to climate-change.  Searching for “research” leads to such vague platitudes as:

[we will…]  Encourage the best young minds to stay here in Canada by increasing funding for university and college-based research, and for graduate and post-graduate studies.

and

[we will…] Introduce measures to ensure that new drugs are evaluated through evidence-based research to be more effective, before they are prescribed by doctors and paid for by Canadians.

and

[we will…] Work with the provinces and territories to encourage research and develop strategies to minimize the effects of climate change on communities, vegetation and wildlife.

and

Stop the hollowing out of Canadian industries by strengthening the Investment Canada Act. Foreign takeovers of Canadian companies will be subject to more stringent tests respecting job protection and creation, head office location, and the promotion of research and development in Canada.

That’s literally every mention of the word “research” in the NDP platform (and every single mention of “university” as well, come right down to it), yielding not a single concrete item on the matter.  Contrast that with this section of the Liberal platform:

A Liberal government will increase support for the indirect costs of university-based research to $500 million a year, which at full implementation will represent a more than 50 percent increase over current levels.

For researchers and graduate students, a Liberal government will increase the budgets of the three granting councils by 34 percent over four years.  Support for the Canadian Institutes of Health Research (CIHR) and the Natural Sciences and Engineering Research Council (NSERC) will both increase to $1.275 billion a year from the current levels of $960 million.  Funding for the Social Sciences and Humanities Council (SSHRC) will be increased to $450 million a year from the current level of $320 million.

We will also create an Interdisciplinary Sustainability Fund of $100 million.  This Fund will be available to scientists, researchers and graduate students for projects that reach beyond the barriers of their discipline.  Interdisciplinary research is the way of the future.   It is how we will address complex scientific challenges – like adaptation to the climate change crisis – that affect our economy and our society. government will increase the budgets of the three granting councils by 34 percent.

You see, now there’s a set of hard targets that I can vote on.  Seeing as I’m funded (well, I *hope to be* funded) by NSERC, knowing that the Liberals would increase their budget is useful information.  Since NSERC and its sister agencies fund much of the public scientific research in Canada, this is a sign that the Liberals would take basic and applied science seriously.

But the NDP?  I have no idea what they would do.  They’re going to “encourage the best minds”?  How?  I might be interested in voting NDP, but I just really need to know more than this big steaming pile of nothing that I’ve got before me right now.  Jack Layon, or one of your supporters, if you’re reading this:  help a guy out.  Help me vote for you.  Explain what the hell you’re talking about.


In defence of accuracy (Science on TV).

October 2, 2008

I have to admit it:  I’m a tab collector.  Despite my best intentions, and productivity be damned, I inevitably find myself surfing my RSS feeds, popping open new tabs for interesting looking stories, and then winding up doing something else and forgetting about the tabs until I wonder why Firefox takes twenty minutes to come to the foreground.  Which is why I just got around to reading Jennifer Ouellette’s fantastic post about science on prime-time television, and also explains why I’m just getting around to forming my thoughts on her argument.

I urge you to read her post first – she’s the kind of writer I wish I could be, and reading her material is a treat of itself – but if you can’t spare the time, she summed things up in a comment near the bottom:

Stripped of excess verbiage above, my argument is this:

1. TV is quite possibly the most powerful communication medium in modern American society.
2. Anyone who is interested in broad communication to the general public ignores TV at their peril.
3. There is an unprecedented demand for science-themed shows right now, and hence a corresponding need for scientists to serve as technical consultants or participate in other efforts to better acquaint Hollywood with what “real” science looks like.
4. This is made more difficult by an enormous cultural gap between the two worlds: there is fear and distrust of science in Hollywood, and often open disdain by scientists towards mainstream TV, which writers and producers naturally find alienating and irksome.
5. We need more exchanges between the two worlds, and a shift in attitude on both sides, or we will lose an excellent opportunity.

This argument, alone, is one that I find convincing.  I’m happy that science is finding a place in the schedules of prime-time programming, though I won’t be too terribly surprised if we’re back to nothing but Survivor-clones when the networks over-use the “science show” idea and the public’s fancy shifts again.  Yet along the way to making this argument stick, Jennifer ends up saying two things that bother me somewhat, and I wish to address those points with my own thoughts.

First, she suggests that accuracy is less important than the popularization of science itself (reminiscent of the “framing” arguments which have stirred up so much trouble in the sciblogosphere):

True story: a year ago, I met one of the writers for Bones at Grae’s birthday party. He was initially pleased to find that I really was a fan of the show, and not just being polite. (I knew all the characters and plot twists — a dead giveaway.) But when I mentioned I was a science writer, he suddenly became guarded and defensive: “Yeah, yeah, I know, we take liberties with the science, DNA test results never come back that fast….” I reassured him that I wasn’t one of those sorts who compulsively nitpick the writers to death, and he relaxed a little. But the exchange saddened me a little. Here was this very smart, really nice guy who loves his work and finds the scientific elements fascinating. Yet his personal encounters with actual scientists have been unilaterally negative and alienating — so much so, that he physically recoiled upon first learning about my science writing credentials. That has to change, or the cultural gap will just continue to widen.

I sympathize with the writer who has run into prickly scientists.  Yet I would maintain that a higher level of accuracy is necessary on science-based dramas, for reasons both practical and philosophical.  Practically, a lack of accuracy leads to things like the by-now-well-known CSI effect, where people have come to expect things of forensic science that are simply not feasible or practical (like the seemingly 8-second DNA analysis and database search that they routinely employ on that show).  Responses to this problem typically fall into the “poetic license” category or employ the “sure, but we need to focus on communication over accuracy” argument as Jennifer obliquely makes in the quoted section above, but these responses ignore the real problems that a public misperception of what science can do may lead to (as a prosecutor frustrated by a jury demanding DNA evidence for a simply break-and-enter might attest to), and they also ignore the fact that it is possible to do both accuracy and entertainment.  There are shows that are true to the science;  as Jennifer notes, The Big Bang Theory has a realistic image of the science and the environment of science itself, and Numb3rs is great for focusing on real mathematics.  Writers of science-y shows might do well to learn from Law & Order, which (as I have been told by people involved in law enforcement) presents the best depiction of the real process of justice that is on television, even if it glosses over the more repetitive aspects.

The related philosophical problem with Jennifer’s statement above extends past the purely practical problem of the CSI effect and into the “science is magic” problem.  Jennifer criticizes Fringe for flirting with the “science is magic” viewpoint, but doesn’t really take this to its logical conclusion even as she notes the most important part when she says:

Uh, no. That is not what science is about; it’s what science fiction is about. I love both, but let’s not confuse the two.

She’s right: that’s not what science is about.  But when shows like CSI or Bones play fast and loose with the process of science and how the world actually works, they actually contribute to the problem not because they are science fiction, but because they’re not science fiction.  Science fiction is actually easier, because people can clearly distinguish between science fiction and real science.  When the Doctor says that he is going to “reverse the polarity of the neutron flow”, or when someone’s pattern is stuck in a transporter buffer on Star Trek, most people can easily realize that science as we know it does not allows us to do these things.  If NASA could suddenly achieve faster-than-light travel, people would be rightly shocked!  But though viewers can readily distinguish science from science fiction, they likely have a harder time distinguishing science on television from science in reality.  When the television presents a contemporary drama with science as an important element, the portrayal of science in that show can become the only exposure that people have to the science in question, and thus shapes their view of what science can actually do.  I don’t mean this in a pomo, constructivist-reality sort of way, but in a much more real and troubling this may be the only time that these viewers are ever going to see how this works way.  As Jennifer notes, television is one of the most important mediums of communication in our society today, and the chance that people see a show like Bones is a lot greater than the chance that they sit through a documentary on forensic anthropology on the Discovery channel.  Given that, how can we not hold these dramas to a higher standard?  Jennifer says that we shouldn’t:

Many scientists I encounter seem to incorrectly think that the scientific details are all that matter. While those are important for lending verisimilitude — particularly for procedural dramas like C.S.I., Bones, or House — network television isn’t an educational vehicle. Hollywood’s purpose is not to teach viewers about science, and TV shows are not documentaries, and should not be held to the same exacting standards — although the two are not necessarily mutually exclusive, provided both sides are willing to compromise a little. Good television is ultimately about igniting the imagination with a truly kick ass story. If we can enhance the appreciation of science (and by extension, scientists) in the bargain, so much the better, but that is not the industry objective.

But this paragraph relies on an argument that goes like this:

If we create television shows that employ “lies to children” but spark people’s imaginations, they will go out and learn the real story, and we will have a more educated public.

It is this argument that I reject as unlikely and even dangerous.  Sure, some small proportion of people may go on to have great careers in science or even just learn more in science because of some great drama they watched on television, but the vast majority of people will go no further than their TiVo.  If this is to be their only exposure to these concepts, what do we expect to happen when they are on a jury, or on a school board voting about science eduction, or voting for presidents and prime ministers who will shape science and education policy?  Jennifer is right in that the networks don’t care about this sort of thing, but to suggest that scientists should just give up and go along with it simply to get air-time is, to my mind, irresponsible and ultimately self-defeating.

The second issue that I have with her argument revolves around the depiction of scientists themselves.  Let’s see what she has to say:

Monday night was the season premiere of last year’s breakout sitcom, The Big Bang Theory, which proved to be something of a lightning rod for controversy when it debuted last year, at least within the physics community. (My own take in Symmetry magazine can be found here.) Normally, scientists content themselves with nitpicking various aspects of the science in movies and TV shows, but in this case, the science is largely correct, thanks to the efforts of technical consultant David Saltzberg, a physicist at UCLA. So most of the complaints about TBBT have been of the “negative stereotype” variety.

As I’ve said before, such criticisms might have an element of truth but they are entirely missing the point: these characters appeal to viewers. They are likable just the way they are, and that is a Good Thing for Physics. If the goal is to make physicists feel good about themselves, then okay, maybe this isn’t the best approach. But if the goal is make physics and physicists more palatable to the general public and win their hearts and minds, these characters are fantastic ambassadors. I vote for the latter.

Actually, I’ve used this quote only as a starting point, because I agree with the substance of her argument above (and the argument she advances in a post she links to here) about scientists taking their portrayals too seriously;  no comedy (and few dramas, for that matter), get very far depicting characters who are entirely realistic.  But my problem isn’t with “negative” stereotypes, but rather “positive” ones.  I’ve talked about this before, but shows like The Big Bang Theory, CSI, Bones, Numb3rs, and so on all depict scientists unrealistically as incredibly brilliant people who know just about everything and rarely make mistakes.  This contirbutes to the “science as magic” problem by showing us “scientists as magicians”.  Here we are effectively told that the only people who do science are super-geniuses with an encyclopedic knowledge of everything in their field and in some cases of things way outside it, who can whip up science in a second and come up with answers to just about any problem.  Even one of my favourite characters, Charlie Epps from Numb3rs is guilty of this:  though the methods he uses are real and the techniques are sound, he does the work of a dozen people!  Any practicing scientist knows that science is a team game now because it’s impossible to be a polymath any more;  the days of a single person contributing to physics, chemistry, and biology before lunch and rounding things off with a few contributions to mathematics before tea are gone, and it’s increasingly difficult for people to keep up with the tiny corners of the scientific literature that they inhabit themselves.

Yet as intimidating as these characters are to someone like me, who is a scientist and who actually works at this sort of thing, imagine what they look like to someone sitting on their couch at home.  How can we expect to attract people to science if we present nothing but these images of super-people at the lab bench?  Again, we can look back to Bones.  The lead character, Temperance Brennan, is a genius anthropologist, but her assistant is even worse:  a child prodigy, a genius with an IQ of 160+ and packing a “photographic memory” (grrr), yet he always seems to be stumbling behind Brennan (at least in the first season, which is all that I’ve watched so far).  If someone like him can’t keep up with the lead character, how can anyone in the audience picture themselves being motivated to become scientists themselves or even spend any time learning more about science?  Characters like this present such an incredibly high barrier to entry that it seems futile to even try!

Again, the common response to my objections about this is that people either know the difference between fictional depictions of scientists and real scientists, or that the shows will “spark their imagination”, and they’ll flock to the lab for the drama and stay for the science.  And sure, enrollments in forensic science classes surged after CSI became popular.  But if you ask a person on the street if they could see themselves learning anything about the science of physics, or mathematics, or chemistry, or biology, you’ll most often get a self-deprecating laugh and refusal, or a blank stare.  And this is how we’re going to create greater appreciation of science, by portraying scientists as super-men and women who are something Other?  These are the ambassadors that Jennifer speaks of?  It does us no good to win the hearts and minds of people if we’re winning them with the scientific equivalent of demi-gods.[1]

Actually, this is something that I’m sure many other academics and practicing scientists have run into:  mentioning science, or physics, or – God help you – math to someone who isn’t a science person turns your occupation into something untouchable, something to be placed on a pedestal and admired from afar, despite your best efforts to have a normal conversation with the person in question.  And I submit to you that the depictions of scientists on television are a contributing factor for this problem, and that these depictions are something that scientists should be concerned about.  I’m all for the need to show heroes on television, but maybe we could take Numb3rs and cross it with the old Mission: Impossible to get a show where a team of fairly bright people come together to solve hard crimes with some cool math, instead of a show where a single untouchable genius saves the day every damn time.

My word count is telling me that I’ve ranted on for far too long, and my body is telling me that it is time to go to bed, so I’ll leave it here for now.  I’ll just close with this:  instead of satisfying ourselves with what we see on television, perhaps we as scientists, should try even harder to push realistic images of science and scientists out onto the airwaves.  I think that society might thank us, in the long run.

___________

Back to post [1] I think that Chad Orzel at Uncertain Principles may have said something similar in recent months, but for the life of me I cannot find the relevant posts right now.


A few things I hate about science in Hollywood…

August 22, 2008

I don’t watch a lot of TV anymore;  when I moved to Montréal, I never hooked up the cable and my television doesn’t even have an antenna, so I haven’t seen anything I didn’t download (legally) or buy on DVD for quite some time.  But I do tend to watch seasons of television on DVD, especially when I’m snuggled in with my wife, and recently we began watching Bones together.  Watching the depictions of science and scientsts in this and other series got me thinking about the rage-inducing depictions of same on television and in movies, and here’s a few of my howl-inducing favourites:

  1. Scientists aren’t usually so socially retarded. Many of the scientists depicted on television (including the main character in Bones, as well as most of her team) are depicted as being social morons who can barely manage to wipe their own behinds when left to their own devices.  Having an interest in science apparently turns you into a basement-dwelling dweeb (men) or a retiring wallflower (women), as though you can only like science if you’re suffering from Asperger’s.  Don’t get me wrong:  I’ve known some scientists with social skills that best resemble those of a paranoid schizophrenic with anger issues, but on the whole scientists are just as human as the rest of us.
  2. On the other hand, scientists are not that pretty (at least, on average). Again, I’ve known some attractive scientists – both male and female – but come on.  I know that Hollywood is responding to what the viewers want, which is usually “attractive flesh”, but scientist are usually shown as jaw-dropping gorgeous (or, to really shake things up, hideously unattractive – see point #1).  CSI is particularly bad for this one, Grissom notwithstanding.
  3. Scientists don’t know everything about everything. The Stargate series, both SG-1 and Atlantis, are great examples of this.  The scientific members of the team, Samantha Carter and Rodney McKay respectively, know just about everything it is possible to know.  They’re both physicists by training, but in the field they magically acquire deep and broad knowledge about not only all of physics, but also chemistry, engineering, biology, etc., etc.  Their range of knowledge is, frankly, ludicrous.  If you know anything about modern science, you know that the amount of knowledge has exploded in the last few decades.  These days, it’s increasingly hard for people to keep up with their particular corner of their own subfield of their chosen major field.  There’s a reason that most of the polymaths that you hear about were active in the early 20th century or earlier…
  4. Not all scientists are l337 hack3rs. This one really bugs me.  Being a scientist does not mean that you can find yourself plunked in front of some random computer with “encrypted data”, pound a few keys furiously, and declare “we’re in!”.  Frankly, even most people who work with computers for a living can’t do this.  I’ve been programming for 20 years, on and off, but I’ve never cared about security and I know that I wouldn’t be able to decrypt that terrorist hard drive just because you had to save the world.
  5. While we’re on the subject, computers (and technology) aren’t magic. It turns out that the mere introduction of some computers and a little lab equipment can make absolutely anything happen.  I love CSI (or, really, just about any other show ever made) for this:  apparently, they can blow up grainy, low-res surveillance photos to arbitrary sizes, pull details out of pixels that don’t exist, and then compare the subject’s toenails to a massive database of toenail clippings in less than half a second before generating a match.
  6. And another thing:  where the hell do they get all that money? Just about every lab I’ve ever seen on TV or in a movie that wasn’t located in someone’s basement (and honestly, a few that were!) is dripping with beautiful, gleaming equipment that would cost millions of dollars in the real world.  I wish that they could send a bit of that money our way.
  7. Science is all about failure and uncertainty. This is a more subtle issue, because I’m not using the words in a pejorative fashion:  publish or perish aside, the driving force of science is failure and uncertainty.  You try an experiment and don’t get the results you expect, so you find out why.  When it turns out that you did the experiment correctly the first time and the results are still inexplicible, you get excited – something new, something you can’t explain!  Your model doesn’t match realistic outcomes, so you have an excuse to build a better model.  You see nature doing something that nobody expected or that nobody can explain, and it makes your year because now you have something to work on.  This is the process of science, in which we chip away at the limits of our own ignorance and push back the darkness.  If everything came up roses every time anyone asked a question, science as an enterprise would have been largely wrapped up in or around the 17th or 18th centuries.  Yet when you look hard at scientists on TV, most of them do nothing but succeed, and when they don’t immediately have an answer, it’s cast in a negative light.  Entire scientific careers can be made out of consistently asking questions to which there as (as yet) no answers, but this fact is lost on television and in the movies.  Actually, it’s lost on undergrads as well, but that’s the subject of another post…
  8. Science is a cooperative, community effort.  This is somewhat related to the issue in point number 3, where scientists are depicted as gods of knowledge, standing alone amongst the ignorant plebs.  But in reality, scientists are part of a larger community working together on problems of interest.  Sure, there are superstars in every field, but even they don’t stand alone:  they build on the work of others, who in turn build on their work in a web of knowledgge.  There’s a reason that scientists look forward to academic conferences so much;  aside from the social element (which is pretty important when most of your closest intellectual colleagues are scattered across the globe), it’s a chance to connect with and immerse yourself in the cutting edge of the work being done in your field.  Science isn’t advanced by the loner working in his or her basement anymore, despite what the comic books would have you believe.  It’s done by a whole bunch of people, who are greater collectively than they are individually.

Those are just a few of the more egregious problems I see in the depiction of science in popular media these days.  I can forgive a lot of them for the mere fact of dramatic necessity, but I worry some times that the images of science put forth are driving the public away from understanding that scientists are people doing a job, as opposed to these semi-magical beings who do things that no normal human could contemplate.  The CSI effect is bad enough, but the more that we turn science into an inaccessible, mythical pursuit, the more difficult it is to recruit otherwise talented people to join us.


I passed!

July 8, 2008

Well, it was a hectic 5 days, but I passed my PhD proposal defence today;  my committee had plenty of questions, but the result was that it was accepted without revisions (which my advisor tells me is extremely rare in our department).  All told, a good day!

And now, I’m off on vacation tomorrow for 3 days.  Hopefully I’ll be able to post a few things tonight, but if not, I’ll see you all on the weekend.


Why I use LaTeX in Biology.

July 7, 2008

[Note:  In some ways I’m putting the cart before the horse here, because I should probably have a post introducing LaTeX before I go on a rant / justification for my usage of it.  However, I’m not in the mood to write that post today, so you can go here or here for further information until I get around to it.]

The title of this post is a little disingenuous;  it should perhaps be titled “Why I use LaTeX in spite of the field of biology.”  LaTeX seems to be less well known here, though I was introduced to it by my M.Sc adviser, who was a biologist (in a psychology department, of all places).  People have no clue what I’m talking about when I mention LaTeX, and many of the journals don’t accept it.  The situation is even worse in the field I came from, psychology, but it’s still bad enough to cause me despair here.  Yet despite the impaired status of LaTeX in biology, I continue to use it with pride, and here’s why I use it instead of Microsoft Word.

LaTeX lets you abstract content from formatting.

To me, this is one of the most important points about LaTeX to be made, and yet it is also one of the most difficult to convey (a good attempt is here).  Computer science people will grasp this point almost immediately, because they’re used to doing this sort of abstraction as easily as they breathe, but it’s not so easy for other people.  So let me take a crack at it:

When you prepare a document, you go through two stages to complete the task.  First, you write the content:

My essay on life.

The quick brown fox jumps over the lazy something or other.  You can tell it was lazy, because it was too lazy to look itself up and put it in my sentence like a good little whatsit, and now I’m very cross with it.  Really, what is the world coming to these days?  Lazy whosits and disrespectful thingamajigs.  Hell in a hand-something or other, I say!

That, there, is content.  The next stage is formatting for the printed page:

My essay on life.

The quick brown fox jumps over the lazy something or other.  You can tell it was lazy, because it was too lazy to look itself up and put it in my sentence like a good little whatsit, and now I’m very cross with it.  Really, what is the world coming to these days?  Lazy whosits and disrespectful thingamajigs.  Hell in a hand-something or other, I say!

That is formatting, or at least some version of it.  Real documents would probably have a lot more formatting in them, like margins and figures and carefully placed page-breaks and the like, but the essence of the argument can proceed from what you see above.  Now here is the step that Microsoft Word slaves users have to pay attention to:

Formatting and content are two separate steps!

Content comes first, and it is the responsibility of the author;  formatting comes second, and it is the responsibility of the typesetter.  In many cases this will be the same person, but scientists need to pay attention to this because often the journal has its own ideas about how a document should look!  The beauty of LaTeX is that it allows us to mark-up our content so that typesetting can be applied by a journal without us having to do a single thing to it (well, often the journal will give us a document class file to use like Elsevier does, but the point is that the class file does all of the work for us).  If we structure our document properly when we generate the content –  placing appropriate tags like \abstract, \title, \appendix, etc., the journal can manipulate our content as it wishes to create the final product that you see.

Microsoft Word has the unfortunate problem of mixing up those two steps so that people who use Word do the two logically separate steps above at the same time, and it does so without any abstraction.  How do you mark part of a Word document as the abstract, or an appendix?  You can’t, and so there is no way of making those parts of the document accessible for separate handling.

Who cares, you ask?  You might want to look around at the web page you’re looking at right now, because it was the adoption of the same sort of model that allowed standards compliant web pages and the explosion of Web 2.0 to really come into their own.  HTML as it used to be mixed up content and formatting, so that you’d have content tags like <body> and <head> mixed in with formatting tags like <b> and <em>.  It was only when they took the step of separating the content (HTML and XHTML) from the formatting (CSS) that the mess that was web-design could sort itself out.

Using LaTeX (or TeX) allows you to use BibTeX.

Oh. My. God.  What did I ever do before BibTeX?

Actually, a lot of the reason I get so much joy out of using BibTeX is because I use BibDesk and Skim to store, cross-reference and annotate my .PDFs of journal articles as well as manage my citations.  That said, though, BibTeX all on its own is a compelling reason for scientists to use TeX/LaTeX.

For those of you who don’t know, BibTeX is a bibliographic management system for LaTeX that allows you to cite your papers with ease in a LaTeX document.  Instead of having to keep the citations in your paper straight manually, and manually type them out, you maintain a bibliographic database with all of your citations and then sprinkle citations in your text using commands like \cite{SomeAuthor:95}.  Then, when your process your LaTeX source with LaTeX and BibTeX, you wind up with a document containing properly formatted citations and a complete bibliography which is automatically formatted for you!  As an added bonus, this is type-once-use-forever, because one a citation is in your bibliographic database, it can be used in every document you create at will.

Another bonus is that BibTeX is another example of abstracting content from formatting.  Because your citations are marked up properly in your bibliographic database, you can easily switch from one bibliography style to another.  I recently submitted a paper to one journal after it had been rejected from another;  doing so required changing bibliography formatting and citation style.  Under MS Word, this would have been a laborious process of search and replace throughout the entire document, followed by a complete rewrite of the bibliography.  Under LaTeX, this required modifying two lines of code and took me exactly five minutes. (Most of that time was spent looking up the required modification on Google).

Other advantages to LaTeX.

Those are two of the biggest advantages to LaTeX, and they are among the things that I absolutely cannot live without;  any replacement to LaTeX for me would require having those characteristics, and I’m not aware of any other document preparation system that can do that.  There are also some other advantages that I should mention:

  • LaTeX is great for mathematics.  Really, it is.  You can produce beautiful mathematical typesetting with a minimum of effort.  This is part of the reason that LaTeX is so popular in fields like computer science, mathematics, and physics.  Pick a book in any of those fields off the shelf, and there’s a fairly good chance that it was typeset with LaTeX.
  • LaTeX produces beautiful documents.
  • LaTeX is open-source, free (as in speech and free as in beer) software.  You don’t have to pay hundreds of dollars to have it.  (It also easily produces PDFs, which are great for exchanging documents with people.  Word is not good for document exchange.)
  • LaTeX is cross-platform, and LaTeX source files are just plain text so they can be edited anywhere with just about any editor you can imagine.  On the other hand, there are plenty of great editors for LaTeX (emacs is one I often use on Linux, and if you’re on a Mac, TeXShop is hard to beat for my money).

Disadvantages of LaTeX.

Are there any?  Yes, there are.  To be fair, using LaTeX can sometimes be an uphill battle, for these reasons:

  • There’s a learning curve.  People are used to WYSIWYG editors, and trying to convince them to use LaTeX can be like pulling teeth.  Learning to use LaTeX properly takes some thought and effort, and some swearing every once in a while.
  • Related to point 1, co-authors may not use LaTeX.  That may put you back on the Word train.
  • For that matter, journals may not accept LaTeX.  If you’re in a field with a deep connection to mathematics this is unlikely to be as common a problem for you as if you’re in a field like mine (behavioural ecology).  There’s no easy way to convert a TeX document to a Word document, because Word is a proprietary binary file format that cannot easily be studied to produce such a conversion;  you can thank Microsoft for trying to keep you locked into their system.  Having said that, there are a few things you can try.  Look here for more.
  • There’s no support – well, no official support, anyway.  There’s no one that you can call up to yell at if something goes wrong.  On the other hand, like many open source efforts, there is a fantastic community around LaTeX on the web.  People like TeX and LaTeX so much that they join user groups. But for people used to the world of paid support, this can be a daunting proposition.
  • LaTeX was made by computer people, and the error messages can be … difficult … to parse.  There’s definitely a bit of magic to it.  For that matter, error messages are a downside of themselves, because Word rarely tells you that your document can’t be processed.  (If it does, that’s usually a catastrophe of epic proportions, meaning that your document is probably garbled or gone).

The final words, and further reading.

On the whole, I firmly believe that the advantages of LaTeX far outweigh the disadvantages, and despite the lesser status of LaTeX in biology (and behavioural ecology in particular), I’ll keep using it until they pry it from my cold, dead hands.  If you’d like to know more about LaTeX, here’s a few resources and articles to look at:

Feel free to post your comments with your LaTeX experiences or general thoughts on the matter!