Bumper Sticker

I was walking in to lab today and I saw this bumper sticker on a car in the parking lot:

Then I looked up and saw the Duke Chapel looming in the distance. I love living in a free country.

Big Nuts

I thought that the people who read my blog (all two of you) might like to see an example of what it is that I study. My lab focuses on sex determination and gonad organogenesis - or rather, how the decision is made to become male or female, how the organism's cells remember this decision, and how the process plays out. Since humans become male or female depending on whether their gonad develops as a testis or an ovary, we study the particular cellular decisions that must be made for the gonad to commit to a testicular or ovarian fate.

Sometimes the signals get mixed and the decision isn't clear, and as a result you end up with a hermaphrodite, or intersex organism - having both male and female parts. Other times the right signal is masked or lost entirely such that the opposite decision is made and sex reversal occurs.

Inside the gonad (both testis and ovary) special cells, called germ cells, give rise to either sperm or oocytes which are responsible for generating the next generation. These cells represent the immortal line, and through them we can all be traced back to the very beginnings of cellular life on this planet. My focus is on these germ cells, and how they decide to behave accordingly depending on which kind of gonad they end up in.

Particularly I study a mouse that has a mutation that causes germ cells to do something considered very bad in humans - turn into cancer! Germ cells are so special, and powerful, that they are set aside at very early stages during development - so early that there is no gonad for them to live in yet. So they wait for the embryo to develop further and begin to migrate to the inside, up through the hidgut and finally to the site of the emerging gonadal tissue just in the nick of time.

In my mutant males, the germ cells are pretty sick before they get to the gonad and only a few make it. Those that make it to a testis end up transforming a few days later and turning into early cancer cells. By birth the mutant testis is already sick with these growing cells, forming an early tumor. Two weeks after birth the testes look monstrous - even the name for this kind of tumor, teratoma, actually comes from the Greek meaning 'monster'. Here's a picture of normal mouse testes and then a pair of testes from my mutants:



Overall my goal is to study germ cells and learn about how this gene affects their development. One of my sub-goals is to figure out how and why this particular mutation causes these kinds of tumors at this particular point during development.

Cool, huh?

It's Green!

It arrived. I got home from lab about 2:30 AM on Wednesday night and it was there, waiting for me on the kitchen table. My roommate saw that the mail man brought it and he left it on the downstairs table for me to open. A late christmas present ... my brand new GREEN laser pointer!



You see, in the basic science research world, presentations/lectures/seminars are given all the time - and you always hope to get a chance to present your very own data. There's an art to presenting your own data and some scientists need lots of help learning how to communicate their ideas in this open forum fashion. To compound the issue in graduate school, there exists a hierarchy of importance - indicated by the type of laser pointer used.

Presenting data on big screens can be trouble, and no one likes to be the joker having to jump up and down, using their very own finger to point at data on the slides. To go a step up from this, it's common to find hand held red laser pointers in use. These are common among grad students and some faculty. But the color is harsh, not aesthetically pleasing, and let's be honest - it's the easiest color to generate on the electromagnetic spectrum so it's cheap.

If you're really lucky, you can invest in the GREEN laser pointer - I've seen some very famous researchers, including nobel laureates, use a green laser pointer. They're so much more pleasing to the eye to follow on a screen. But they cost more money since it's a harder color to produce. Also, because of the higher energy it's a more dangerous laser and care must be taken not to point it at anyone's eye, or even combustible material!



Only the most elite can move up from here and purchase a BLUE laser pointer! These cost around $500 and are very dangerous. I've only ever seen one used, by a nobel laureate at an important international meeting. Definitely making a statement about status when you show up presenting data with a blue laser pointer.



For now, I'm just happy to have graduated to the next level. I can point it across the street to the treetops and make out the very bright dot when it's nighttime. I can even point it up at the stars and point out a specific star because the beam of green light is visible all the way up to the heavens!

Maybe one day I can go for the gold, I mean blue. :-)

Mario-tastic

I just found this the other day. In college we used to play mario-kart allll the time and had plenty of tournaments. I was a champion every once and while. This is the ultimate love song for mario-kart lovers everywhere:

Woohoo! I'm in!

I'm so excited! I found out today that my paper was just accepted for publication in the journal Developmental Biology! And I'm first author! For a grad student this is a wonderful milestone to pass during the graduate career. Every department has an unofficial/official requirement that you must not ONLY have a thesis written and defended, but your research published. Our department's going rate is two first-author papers. A few revisions need to be made, but I've now got one down and one to go :-)

To celebrate, I'm offering to you one of the most kick-ass videos on youtube. It's of James the Amazing Randi, a very famous magician, debunking the claimed 'psychic' James Hydrick on primetime television! It's a butt-kicking worth watching; you begin to wonder how deluded or evil he is - perhaps both? It turns out, just pure evil - as he confessed to an investigative reporter after this very failed performance. Oh, and you get to see Bob Barker in his younger days - hope you enjoy it as much as I do!

god(s) of the Gaps

Be afraid. Be *very* afraid. Answers in Genesis is warning us that the upcoming celebrations of Darwin's 200th birthday and 150th anniversary of his publication of On The Origin of Species will not be honest about the 'true' origins of life. Specifically they claim:

During the “Year of Darwin” and “Darwin Day” celebrations on February 12, our hope is that many souls will dig a little deeper and discover the true Source of Life, whose Book holds the key that unlocks the mysteries of life.

Of course they're talking about their holy codex (La Biblia), which they apparently seem to think was meant as a science book from god.

In the article, they link to free samples from their latest issue of Answers Magazine, (I imagine they're having trouble selling it) pulling perspectives from creation 'scientists' who 'research' the creation 'model'. Sorry for the quotes, but I don't want you thinking I consider those true to their definitions.

In the article God of the Gaps, they point out that transitional fossils still do not exist in the fossil record, and according to Darwin's text himself his hypothesis is thus refuted. I think because they've repeated this drivel so much that they actually believe it.

It's painful to read through the many errors in the text, not least of which when they continue to purport evidence from fossils laid down by 'the Flood'. Most interesting about this particular article is how, instead of completely ignoring the evidence (as they normally do), they twist and lie about what it represents by misleading the reader to think it's an interesting anomaly:

Likewise, groups of animals that purportedly link reptiles to mammals, or fish to amphibians, are fascinating cases to be studied. Rather than being transitions, they appear to be brushstrokes from God’s creative palette, examples of wonderful designs suited for their unique, pre-Flood environments.

'Cases to be studied'? 'Brushstrokes from God's creative palette'? Wtf? There are SO many examples of transitional fossils - invertebrates to fish, dinosaurs to birds, evolution of whales, horses, and human primates. Here's an example of the transition of fish to tetrapods:



I got the pictures from Wikipedia - they are artistic renditions based on the fossils discovered. I took the liberty of organizing them into a timeline with names and dates. Note how every 2-5 million years there's another advance to the tetrapod form.

Of course Ken Ham would have you believe that these are not transitions, but instead 'brushstrokes' of a creator. This is what you call 'moving the goal posts' - this is what happens with true believers. Because they start out with their conclusion, they claim that there are no transitional forms because a god created the world 6000 years ago. They are admitting that transitional forms would refute their 'creation model' so they are forced to claim that they simply don't exist, but implicit in this is that should transitional fossils be presented their model would be invalidated. So now when we have them, and when new ones are discovered, instead of being intellectually honest and admitting what they are, they simply move the goal posts and say that they aren't really transitional 'enough'. Some creationists think transitional forms mean cats giving birth to dogs, etc. That just shows their complete ignorance when it comes to the subject in general.

Go be motivated - google search transitional forms and see all of the awesomely cool links that we DO have. Don't let someone fool you into thinking that we are missing all transitional forms. Imagine how many others might still be out there ...

Biologists Rule

In case you weren't aware, in the hierarchy of science there's a particular order for making fun of different disciplines.

Biologists make fun of Social Science.
Chemists make fun of Biologists.
Physicists make fun of Chemists.
Mathematicians make fun of Physicists.
Philosophers make fun of Mathematicians.

This is all predicated on how 'hard' the science is for each discipline. Don't ask about the philosophers - I reckon they just question all premises and refute all claims.

In honor of this hierarchy, here's a post from xkcd.com representing the only way for us biologists to get respect from those other disciplines:

Oxygen Deprivation

One of my favorite YouTube users, Edward Current, has recently uploaded a new video that I must share.

Mr. Current is an expert in satire, particularly concerning fundamental christian believers. He's also quite adept on the computer machine and inter-tube. In this scenario a christian is about to die, but before he bites the dust, as his brain is deprived of oxygen, he hallucinates and a bit of truth is revealed to him ... isn't the saying 'better late than never'?

Boom!

Happy 2009!

I hope that everyone had a lovely 'ring-in-the-new-year' event. My evening was spent with friends and spirits, so it was a fun time indeed.

One of my new year's resolutions is to stick to a routine with my blogging; so that I can get better at writing and so that I can have an archive of the things I think about. And what better way to start off the new year, than with an exciting example of how science works?!

Just recently, published in the Astrophysical Journal, scientists have managed to test hypotheses concerning the formation of supernovae, using as a case study an event just a mere 13 million light years away from us.

Last year, on my birthday (March 28th for all those who want to remember the date and gift me something wonderful :-), a special notice was sent out that supernova 2008bk had been discovered on March 25th. The notice indicated that:

This supernova has not yet been spectrally classified, but the galaxy is undergoing active star formation and a core collapse supernova is possible.

Stars in our universe, like our very own Sun, are sites of nuclear fusion: a process which creates larger nuclei from smaller ones, generating an enormous amount of energy - energy that is necessary to keep the weight of the star from crumbling on top of itself. When a star runs out of fuel, it cannot support its own weight anymore without the release of this energy, and so one of two fates can occur depending on the mass of that star.

In the case of our Sun, a series of steps in stellar evolution will take it through the phases of a dwarf star as luminosity slowly decreases due to the lack of fusion. In other stars that have roughly 8 times or more than the mass of our own Sun, a spectacular event occurs called a Supernova. This is where enough mass collapses down that the implosion leads to the most powerful explosion known in our universe. During this time, unimaginable amounts of light are given off and that is what astronomers observed in March of 2008.

Just recently scientists went back to maps of the sky from BEFORE the big explosion and searched the area for possible candidate stars that could have been responsible. Using a new image of supernova 2008bk taken from the Very Large Telescope they were able to reasonably identify the culprit: a red supergiant. Based on what we know about parameters for supernovae to form, they predicted that the original mass of the star must have been at least 8 times that of our Sun. After careful calculations, the original mass of the star was determined to be 8.5 solar masses.

Question. Observation. Hypothesis. Prediction. Experiment. Results. Hypothesis SUPPORTED. By Zeus, I love the scientific method!

Now, if only I could only see a supernova up close without getting obliterated ...

Anti-science Brought to you by: The Republicans

Last week Christopher Hitchens published a fantastic article entitled "Sarah Palin's War on Science." This topic surfaced as a result of a pointedly ignorant remark by Sarah Palin (the VP nominee for the Republican party) that, "sometimes these dollars, they go to projects that have little or nothing to do with the public good. Things like fruit-fly research in Paris, France. I kid you not." Watch it here.

As a scientist, it's hard to stomach this sort of anti-science attitude, particularly because of the ignorance of the statement. The fruit-fly is one of the foundational research models to study human disease, including disorders such as fragile X syndrome, autism, immune function, sexuality, etc.

This is the VP of a candidate who has denounced spending on grizzly DNA research and projectors for planetariums as "unbelievable." Hitchens summarizes it best:

Scientific American pointed out, there is no way to enforce the Endangered Species Act without getting some sort of estimate of numbers, and the best way of tracking and tracing the elusive grizzly is by setting up barbed-wire hair-snagging stations that painlessly take samples from the bears as they lumber by and then running the DNA samples through a laboratory. The cost is almost trivial compared with the importance of understanding this species, and I dare say the project will yield results in the measurement of other animal populations as well, but all McCain could do was be flippant and say that he wondered whether it was a "paternity" or "criminal" issue that the Fish and Wildlife Service was investigating. (Perhaps those really are the only things that he associates in his mind with DNA.)

Again, Palin has been a past advocate of the idea that global warming doesn't exist, and even if it did, humans aren't responsible. Now on the campaign trail she's said that it doesn't matter what caused it, just that we try to fix it ... what a dumbass thing to say.

And that brings me, yet again, to the things that Gov. Palin DOES believe in - and for that, I'll leave you with Hitchens once more:

Videos taken in the Assembly of God church in Wasilla, Alaska, which she used to attend, show her nodding as a preacher says that Alaska will be "one of the refuge states in the Last Days." For the uninitiated, this is a reference to a crackpot belief, widely held among those who brood on the "End Times," that some parts of the world will end at different times from others, and Alaska will be a big draw as the heavens darken on account of its wide open spaces.

High points, also available on YouTube, show her being "anointed" by an African bishop who claims to cast out witches. The term used in the trade for this hysterical superstitious nonsense is "spiritual warfare," in which true Christian soldiers are trained to fight demons. Palin has spoken at "spiritual warfare" events as recently as June. And only last week the chiller from Wasilla spoke of "prayer warriors" in a radio interview with James Dobson of Focus on the Family, who said that he and his lovely wife, Shirley, had convened a prayer meeting to beseech that "God's perfect will be done on Nov. 4."

Haven't we had enough of religious fundamentalism and anti-science (not to mention anti-reason) in the white house? I'm with Christopher on this one: "On Nov. 4, anyone who cares for the Constitution has a clear duty to repudiate this wickedness and stupidity."