Finally….I have a PhD.  *a very exhaused, soft cheer!*  Now I have time to pontificate about science and politics.

Through the Pharyngula blog, I came across a video clip of Palin decrying the use of federal funds for “fruit fly” research in France (of all places!) and talking about how this is a waste of money (to paraphrase).  Here is the original video.  Go watch it, then read.

For the non-biological scientist: “Fruit flies” are Drosophilia, which are one of the most powerful model systems (model system=animal/bug/yeast/bacteria we use to study cellular processes) we have, and are the reason we understand things like Wnt signaling, which has led to cancer therapies, Hox genes, which are how embryos form different body parts out of different tissues, and how we have found many tumor promoters which are great therapeutic targets along with countless other examples.  ”Fruit flies” led the genetic revolution in the early 1900s.  They are also a powerful arguement for evolution, because we are so similar to files….really, on a molecular scale you can study a molecular pathway and then extrapolate that data to humans.  Its uncanny.

Humans are awful systems to study diseases in.  You can’t make mutants (unless nature does it for you), you can’t cut them open until they die on their own, they have small litter sizes and long generation times (or so the joke goes in science, and no one advocates that we do these things - but these are the real unavoidable reasons scientists study diseases in things like mice and FRUIT FLIES).

The McCain/Palin ticket doesn’t understand science….thus, they see expenditures on science as earmarks and/or spending to be cut.

For a relevant McCain reference, think of the 3 million dollar grizzly bear study that he has repeated harped on as an example of earmarks gone awry (I can’t believe he actually called it “criminal”).  This was an excellent study that collected DNA from grizzly fur left in nesting areas and was thus able to map out the range/territories of a number of bears.  Understanding the range of animals is important for their conservation (Perhaps my father could enlighen us on the reasons for this in the comments).  While earmarks are an odd way to fund a study, this isn’t an example of a “criminal waste of taxpayer” dollars.

These are the things about a McCain/Palin presidency that really scare me as a budding scientist.  Because NIH funding is at a particular low at the moment, and they definitely aren’t going to improve funding with their understanding and views about how science works (Correction: Okay, McCain has said that he “supports more funding for the NIH, but of course he has backed off from supporting stem cell research - this is a topic for antother day - Since he didn’t mention this until August-September, and Obama had as part of his policy platform during the primaries, I think we can tell where the candidates’ priorities are).

We are at risk for losing a generation of investigators.  There really is almost no money for new investigators.  Especially R01s, which are the major, large lab funding grants and are necessary for a PhD to attain a permanent position at a university.  Without new investigators, we lose new ideas, new publications, and eventually don’t have quality senior scientists to lead fields.  All of which leads to fewer discoveries to treat/prevent things like Downs syndrome.  That Palin can’t/refuses grasp this, at the expense of future treatments that may help her son, baffles me.

The lack of scientific understanding on the McCain/Palin ticket should disqualify them from high office.  In this respect, I see a direct continuation of Bush’s policies of ignoring science when it doesn’t match his ideology (Note:  article is from 2004, but is illustrative of how science has been treated the last 8 years in the oval office).  Palin has a STRONG incentive to understand the science behind Downs syndrome.  If you can’t understand biologic science, how can you fix the medical system?  If you can’t learn about science, how can you learn about economics?  If you don’t understand the cause of global warming, how can you fix it or address its effects?  With all of the responsiblity that the offices of the president and vice president carries, wouldn’t it be nice if those offices were held by people that were indeed “elite” and understood how the world really works?  Or at the very least…had the desire to understand?  Is that too much to ask?

Hopefully most of you have heard of the Mars Phoenix Lander….if not, go here.  If nothing else the pictures sent back of red, rocky vistas of an alien planet are cool and make good computer wallpaper.  At any rate, this is another little robot sent to our red neighbor.  The purpose of this mission was essentially to see if Mars had the requirements for life (water and/or organic compounds[organic means they contain carbon])….and to find out as much new stuff as possible.  Like any good science mission/experiment there were hypotheses to test and the ability to take advantage of serendipity.

And guess what…the little robot happened upon some water.  The sci-fi geek (and biologist) in me thinks exactly what the title says….cool (Although apparently we already knew that the northern region of mars had buried ice).  Water in other places means one of two things.  1)  There might be/have been life where there is water (which would tell us a lot about biology) OR 2)  water will be useful in other places when we get off of this particular rock (I mean Earth….you really think we’ll be able to keep it sustainable for the next few billion years (until the sun goes nova that is)???  We’ve maybe got a few hundred left…maybe.  Sorry, tangential rant.

Here is the picture, which nicely shows before and after shots of the ice subliming (going directly from a solid to a gas….no melting at -80C).

Wired had a good article on how the scientists involved in the project can tell that this is water (I mean, it isn’t like they can go and drink it).  However, some of the comments about the article were disturbing.  For example:

“should have spent the money to save life here on earth instead of a futile attempt to prove evolution. you will not find life outside this planet. cant get living stuff from non living stuff, sorry.”

As much as I’d like to think this is some contrary jackass posting on a thread, I’m going to take it seriously.

We really need to fix science education in this country and people need to learn how to cope with large numbers and large time scales.  This particular mission isn’t an attempt to “prove” evolution.  In the lay context used in the quote evolution is already “proven.”  Hence its status as a “theory” in scientific terms.  And actually the odds of life existing outside the planet are pretty high (I’d put it at about 100%).  It is just a  question of finding it (I’d put those odds at very low).  As more earth-like planets are found, and as we find water on the first planet we look at, it certainly appears that all of the building blocks are there for life chemically similar to us to be out there.

And the part about getting living stuff from non-living stuff….yeah, this debate was all the rage until the 19th century when organic compounds (urea [the stuff that makes your urine yellow]) were synthesized from non-organic compounds (I believe ammonia and CO2).  Life is just an organized set of complex molecules that replicates itself.  It isn’t “sacred” or “special” or particularly rare, especially on this planet and probably isn’t all that rare elsewhere.  I mean, where do you think we came from?  Made from clay by invisible beings in the sky?  Well, except for the invisible beings part, that is sorta right.  Our distant ancestors (strings of RNA) came from inorganic (not alive) molecules, until they happened upon a pattern that could propagate itself.  (Just to mollify people horrified by this particular paragraph, you kill a few billion bacteria every time you use Purel or soap on your hands….when I say life I’m not talking about cute little bunnies or anything, more like an e. coli).

As for the lack of mathematical ability in this country, we are spending trillions on war, but a few million on going to other planets is taking money from saving life on Earth.  Holy fucking shit. I just had to pick on the comment because it reeked of ignorance.  Please save us from the ignorant, or at least fucking educate them.  (Sorry for the profanity……ignorance is my biggest pet peeve and seems to be pervasive on the internet).

Okay, back on topic.  Ice on mars = cool shit!  And maybe before I die, I can have a nice glass of scotch on the surface of Mars with some native ice.  Crap, now I’ve got to start working on life extension technology, so I’m around by the time we actually invest in getting off of this rock……although I’d probably be able to get to the asteriod belt first…economics you know…but I bet there is ice there too ;).

The end of the PhD is in sight, things are falling into place, you would think that would make a hooman happy, right?  Ummmm…..no.  For me the end of a PhD is all of the not fun stuff, crammed into one big long procession.  The good parts of the PhD are in the past, and research won’t be fun (or really even happen at all) until after graduation.

I’m currently:  writing a paper, writing my thesis, finishing the last bits of data for another paper, and getting ready for a committee meeting where they hopefully will say “you may defend your thesis.”  What do all of these things have in comon?  They are mostly writing, mostly.  This is the part of science I dislike the most.  I love sharing ideas, but I hate trying to make documents perfect, which is necessary for a scientific publication (at least from my lab, I’ve seen some real crap get published). I miss coming up with and testing new ideas and playin’ around with small volumes of clear liquids in order to understand something about things I can’t see…..stoopid wavelenght of light.

When can I stop writing?  Please….make it go away………

(At least blog wrtin is diffrnt.  Count the speling errors in this entry.  He he…okay now i fell a bit betr.)

If you don’t like my grammer from the title or the article, go here, and please give me a cheezburger…. I deserve one dammit.

When I was in high school, I procrastinated.

When I was in college, I procrastinated.

When I got to medical school, I quit.  It was too stressful, and the sheer amount of memorization required made procrastination, for the first time, unpractical.  I thought I had kicked the habit once and for all.  It left my personal life, and didn’t reappear in graduate school….until now.

Apparently procrastination isn’t a skill you can forget.  I used to be an expert at distracting myself so I wouldn’t think about what I needed to do.  The only problem is that after awhile this becomes a deeply unsatisfying (for me) way to live your life.   So, faced with “fixing” my paper, what am I doing?

PROCRASTINATING!  And it is waaaay easier than when I quit about 6 years ago.  Digg didn’t exist then, the blogs I read didn’t exist then, and I cared much less about the news.  I used to procrastinate using video games….now its the internet.   The internet has an (approximately) infinite amount of material, and thus should be perfect for procrastinating.  This is sadly not true.  After about an hour of surfing for the day, there is nothing new to find.  Even with my wife feeding me new sites, there just isn’t enough for distraction at the rate I consume information.  Maybe I just have my well worn paths that only load new material at a fixed rate and I am missing web gems that are hiding just off my path through the aether.

So, in the spirit of enabling…what are some good procrastination websites?  I’m really trying to avoid this paper.

As you may have noticed, I haven’t posted to the blog in a long time.  Points if you can guess why.  Scientific writing is draining, and that is my main (practically only) activity at work lately.  The results are in, the data looks good (really fucking good), so now I’m on revision 3 of the paper.  Only one problem.

Scientific writing sucks!

Here is my short list why (I could write a PhD on this too):

1)  When you write scientific articles (at least in my lab and my dicipline) everything is in the passive voice.  Not “We examined” or “I competed this nearly impossible experiment!”, but “The hypothesis that …. was tested by …”  Not only does this make the sentences overly cumbersome, but also BOOOOOOOOORING.  Which is impressive when you are the one writing it and the topic is exciting to you.

2)  No one ever agrees on how things should be done.  Everyone has different suggestions for order, ultimate content of the paper, and how to get favorable reviews.  This is very frustrating.  Combine that with not being the person with the final say on how “your” paper gets treated is a recipe for wanting to throw laptops across coffee shops.

3)  NO ONE WILL READ LARGE SECTIONS OF THE PAPER THAT I STRUGGLE OVER.  Also, these sections don’t add a lot to what readers will learn from my paper.  This is the most vexing part.  While I struggle over word order in various parts, most of the readers will skim various parts of the paper.  For example, as long as my methods are accurate and allow experimental reproduction, who cares how I write them and if I use the word immunoblot or western blot.

4)  Arguments over what constitutes “Jargon.”  I get nailed for using jargon in my paper writing all the time.  However, what is jargon is highly debatable.  For example, the word “phenocopy.” Look it up. It perfectly explains what I am trying to say in various parts of my paper, however, even though it is a well-defined genetic term, it gets deemed jargon and I have to cut it out…..inevitably replaced by “loss of protein x recapitulated the biochemical and functional effects of loss of protein y….”.  Not the prettiest sentence in the world.

5)  I hate the separation of the results and the discussion.  I understand that this is a very important part of scientific papers.  Results are…well…..the actual data.  Discussion is what you think the data means.  However, the division between the two is artificial.  My results come from experiments that were designed to test part of my hypothesis, which was modified by the previous experiment, which modified/confirmed/expanded the previous hypothesis, and so on.  To make any flow between my experiments requires some explanation.  The easiest way to write the paper would be Abstract, Introduction (here are my proteins and why they are cool), Results with discussion incorporated, Short conclusion and model.  Not how it works, unfortunately.

Basically, I suck at science writing.  This, above anything else, is my fatal flaw as a scientist.  However, I dislike the way papers in my field are generally written, I am forced to learn and follow the “rules” and feel like I’m not getting any better at them.  Hopefully, this attitude is mostly just my despair at the vast amount of writing between here and the summit of my PhD.  Maybe I’ll learn someday, after all I am just an uppity graduate student.

P.S.  I want that damn degree already, so sick of telling post-docs how to do and plan experiments.  If I have to tell one more post-doc that they forgot a fucking control I’m going to go crazy.

Hi everybody!  I’ve been underground, working in the mines…..I mean working on my thesis.  Anyway, this isn’t what this post is about.

I got a new book from Amazon, Octavia Butler’s Fledgling.  However, it wasn’t in the typical azw format.  It is in a .tpz format……

I wonder what this means?  And can I not decrypt my books now, except on my kindle?

I hate DRM.

Update:

Okay, so TZP stands for topaz, which is another type of AZW file with embedded fonts and *crap* different encryption.  As far as I can tell, this particular format has not been broken yet, however, not many books use this format right now.

Starting my PhD was hard, apparently finishing it won’t be any easier.  I’m basically one figure away from publication (and hence graduating)…….but I don’t know what that figure/experiment is.

I thought I had it last week (see my very happy post), but further experimenting showed I was on the wrong track.  FUCK!  Sorry, sometimes the frustration just slips out.

I love research, really.  I just want to finish my PhD, and sometimes it is quite difficult.  This sounds really corny, but right now the only way I am getting through this is my new wife.  She’s my rock, who works hard, makes all of our money, and takes care of me when I come home from a day of disappointing results.  I don’t know how I was able to start down this path without her, and I know that if she hadn’t come along, there is a good chance I wouldn’t have been able to finish.

I just finished Cory Doctorow’s newest book, Little Brother. Um….wow, it was really, really good. You’d think I’d be a bit more eloquent after reading some absorbing fiction, eh?

This book is about a government crackdown on San Fransisco after a big attack and follows a teenager whom is caught in the government’s clutches in the aftermath. However, this book isn’t about the plot. It is about the idea of freedom.

In a society where there is information about us everywhere (take a second and think about how much of your information is in computers) and the government reads our email (remember Carnivore?), this book does an excellent job of talking about the ideas of privacy, freedom, disobedience to authority, cryptography and cool technical hacks through an interesting story.

Basically, it was a kick-ass book that was well worth the time it took to read. I even learned a bit more about cryptography :).

Because Doctorow has an excellent philosophy about copyright, his book is published under a creative commons license. If you want to read it online go here. Otherwise, it is available at brick and mortar stores in physical form. But seriously, who actually goes to the book store anymore ;). At any rate, put this book at the top of your pile, physical or virtual, and read it.

Did I mention I still love my kindle?  Now off to install linux on a USB hard drive so I can fiddle on something else for awhile.  The coolest tidbit in this book is a hypothetical linux distribution called “paranoid linux.”  I wish it was real….I’d download it.  So…..sick…..of…..windows.

I was at lab until 9pm last night…not for some cool experiment, not to slog through more of my paper and review that need to get finished, but to help get the new computer set up for our confocal microscope.

I’m the resident computer expert in my lab, not really sure how that happened, but every time there is a new system upgrade I get enlisted to help.  I don’t mind……too much at least.  However, as the finish line for my PhD approaches, I am less and less charitable with my time in lab.  Things like tinkering around with the user management software on the old machine, which was written in the dark ages (2001) is annoying.

What is most amazing is how everyone feels the need to constantly upgrade their computers for fixed tasks.  The confocal software doesn’t really require anymore processing power now than it did 6 years ago.  It is still the same microscope, and the data being dealt with is still of the same magnitude.  However, computer software and operating systems really aren’t backwards compatible.  Unless you are on an upgrade cycle of 4 years or less(give or take), getting a system on Windows XP setup to resemble a system that was set up on Windows server 2000 is a major pain in the ass.  Part of this is incompetence on Microsoft’s part, I’ve always had backwards compatibility issues with them, thus I won’t switch my personal systems from XP (which runs on all of my systems and is tweaked *just right*) to Vista.  The biggest reason is that nothing I have painstakingly setup will work!  (Plus Vista really sucks).

I don’t understand why Operating systems need to be changed all the time.  How much basic functionality does a computer need out of the box anyway.  I don’t see why a good operating system can’t be written that will have a product “lifecycle” of significantly more than 4 years.  I don’t understand why anyone needs Vista instead of XP.  I still haven’t heard of a killer app for Vista that would make me even consider leaving XP.   The most likely reason in my mind is profit.  If everyone keeps their software for 10 years at a shot, you won’t make money.

Don’t get me wrong.  I love that computers get more powerful and cheaper constantly.  I just don’t think that performance improvement should be devoted to running newer, bloated, resource-hungry operating systems.  Crap - sounds like I should just switch to linux.  Of course then I’d have to set up everything again anyway….

I was out for a run earlier, in my current battle to keep my naturally expanding waistline under control. Of course, it was really hot out, and this was a fairly miserable run. This combination made me wish for an easier way to lose weight.

Nearly every American wishes this at some point or other, which is why there is weight watchers, the south beach diet, the Atkin’s diet and so on. However, all of these diets miss a fundamental point: (Calories in - calories out)/3500 = pounds gained or lost. To translate from math into English, if you consume 3500 calories more than you burn, you gain 1 pound. Conversely, if you burn 3500 more calories than you consume, you lose a pound. Simple, right?

So, it follows that there are two ways to lose weight:

1) Eat fewer calories. OR 2) Burn more calories.

Step 1 is where so many diets come in. If you eat less, and can stand feeling like you are starving all the time, you will lose weight. Your body doesn’t like this so much, because it thinks you are literally “starving.” So, as soon as you go off the diet, your weight goes back up because your body wants more food to get back to its “set weight.”

I think step 2 is easier, but I usually like to exercise. If you exercise, you burn calories. If you are careful and don’t consume too many extra calories, you will lose weight this way too. However, as soon as you stop exercising, your weight will start trending back up again.

The only way to permanently lose weight is to make permanent changes. You need to permanently eat fewer calories per day (for me this means 1 pop/day) and permanently exercise 3-5 times a week. This will cause permanent weight change every time as your body’s weight comes to a new equilibrium with the calories you are consuming compared to the calories you are burning. It is just so damn difficult! No wonder nearly everyone goes for diet of the week.