consider the platypus
In lieu of anything sensible, I present the platypus:
We who are about to defend salute you. Open an umbrella, and wish for rain.
In lieu of anything sensible, I present the platypus:
We who are about to defend salute you. Open an umbrella, and wish for rain.
I just finished the final revision on the first draft of my thesis submitted to my committee. Put that way, it sounds a little less final, but it is an important milestone along the end of the road.
I am almost done.
Now I just have to defend it, revise it with their comments until it meets their approval, and then render it down into its component parts for publication, a process I have already begun.
With a new year, new deadlines. My life for the next four months, summarized (all apologies to Bungie):
I spent the latter part of this afternoon converting excerpts from my thesis' literature review into the Wikipedia entry for Scirtothrips dorsalis, so now the truly bored can learn more about this critter than they ever possibly wanted to know. I am probably going to continue to expand the article, adding sections on management of the thrips - but converting all of those citations makes my eyes want to bleed, and I keep finding things that should be linked into other things. I mean, I can't leave a section on putative Tospovirus transmission in S. dorsalis without first improving the page for Tospoviruses, now can I?
Please feel free to contribute to or to vandalize these articles as necessary. This information needs to be shared, and right or wrong, Wikipedia has gradually become one of the most prominent references for common knowledge. It is amazing what ten minutes of expert opinion can do to improve an article, and conversely, what ten seconds of vandalism can do to ruin it.
My old company just axed another quarter of their staff during the weekly meeting this afternoon. It was an unpleasant surprise to most of the assembled staff, and apparently the CEO was too craven a coward to make the announcement himself this time. I am rapidly running out of people that I met there who still work there. This is their third round of layoffs, and each one has cut staff by at least twenty percent. This does not bode well for the future of the company, but I suppose that they are slimming the workforce in order to concentrate all of their diminishing resources on one of their three drug candidates currently in clinical trials.
Once again, I must reflect and recognize that I am lucky to have left when I did. I almost certainly would have been fired in the first round; I was in a superfluous and overstaffed department, and was a malcontent and rabble-rouser. I do wish that it hadn't unemployed so many of my friends quite so suddenly.
I wish them all the best on their roads ahead, and I even hope that the company does survive this latest downturn. Whatever reservations I have about the conduct of certain scientists employed there or the management team, the biochemistry recorded was amazing in its breadth and depth. Many of their drug targets show incredible promise as treatments for debilitating and terrible diseases, and I suspect that given sufficient time and resources, Lexicon will eventually produce a product of note and value.

I feel that I am finally done with the preliminary writing for my literature review, and with any luck I will not feel the need to drastically revise or add to it again in the near future. Of course, barring a miracle, someone else will probably have a few suggestions for improvement. It currently masses in at approximately thirty and a half pages in length when double spaced at twelve-point "Times New Roman" font, and is followed by a little more than eleven pages of single-spaced citations and references. It will probably still undergo some trimming and slimming in places, and some expansions in others - but for the most part the whole of the thing is written and done and out of my way. Now I just have to avoid plagiarizing myself while I finish writing chapter introductions to experiments and then in discussing my results.
You know, there are very few moments in cinematic history that actually pull a truly emotional reaction from me. Stephen Spielberg's Jurassic Park is one of them. You know the moment. It's the one where you meet your first live dinosaur for the first time. John Williams' score begins to swell, and the brachiosaur comes over the rise, trumpeting mournfully.
I've probably been waiting for that particular moment my whole life.
I really am in the wrong field.
The man was filled with shadow,
the land was bathed in sun.The afternoon was waning,
the man was on the run.He had to get to Reno,
his future there to find.He had to get to Reno,
before he changed his mind.If life is but a gamble,
and each is dealt one hand,
he had to get to Reno
to play his one-man band.Truth may prove elusive,
old beer may lose its fizz,
but a man who leaves his shadow
can change his was
to is.
My father, ever the poet.
A special thanks to Fred Wightman for his thoughtful gift. Now I just have to learn how to tie it!
Of course, I ended up at the gallery of paleontology and anatomy. I suppose it says something about my person when I have but a day to explore all of Paris, and the two major sites that I visit are a library and a museum of natural history.
The museum itself is something of a wonder. It has over four hundred years of collections, brought together and studied by some of the best scientists that the world has to offer. These are amazing and historic samples in a sturdy building designed to last for the ages. They are also poorly labeled and displayed behind scratched plexiglass. The roof leaks, and samples and displays all suffer from water damage. This approach pales when compared to the educational presentation of even a modest American museum of natural history.
I suppose my father puts it best:
" As I often preach in my geology lectures, a rock is no more exciting than a page in a book. It's the story that matters, and the challenge for a museum is to tell the story (as well as warehouse data).We've probably told you this before, but in 1976 we visited the Cairo Museum of Antiquities. It was like the government warehouse scene at the end of the original Indiana Jones -- an immensity of stuff, dimly lit, dust-covered, few labels (fewer in English). There was much of the King Tut material, what you could see of it, and endless mummies and caskets. Years later we saw a a traveling exhibit of Egyptian material including a fraction of the King Tut stuff from Cairo - but viv're la differance! It was a very well-displayed collection that really made an impression. So, there is probably a moral here somewhere, but I will settle for the thought that one good idea - well communicated - is worth more than any old box of rocks."
Emphasis and links are mine.
Lamark, I am here!
Poor Lamark always gets a raw deal when it comes to evolution. While he is frequently remembered for his infamous missteps in early evolutionary theory, his theory was the first real testable hypothesis attempting to explain the generational aspects of adaptive speciation. Moreover, he was an excellent taxonomist of invertebrates, and would become the inaugural Chair of Zoology at the muséum national d'histoire naturelle.
Because this is Europe, the museum is still where it was hundreds of years ago, and is in full possession of those centuries worth of collections. I come upon a signpost, which leads to a fork in the road. Perhaps I should find it revealing as to which path I took on the road ahead.
Perhaps I should always follow my heart in such a fashion.
I have several hours to kill in Paris before my friends get off of work and can join me in frivolity, and so of course while wandering down the Seine, I eventually wind up in a library. I am ever slave to the written word, even if it is not in my own tongue. I figure that even if I am on vacation, I can afford to spend some time looking through the entomological section of the library for a French perspective on les thysanoptères. This rapidly proves to be a moderately amusing exercise in futility: thrips are no more popular in French than they are in English. Out of thousands of pages dedicated to les insectes, I can find perhaps two pages on thrips. My spanish is good enough to make a rough translation of what I read, and it seems that the same problems plague researchers in France as elsewhere: thrips may be incredibly diverse and a significant crop pest, but they're just too damn small to work with.
The rest of the library is of course, more thrilling. This is a building that was constructed around a small forest, and which is flanked on its sides by apartment-building sized towers, all full of books. They have resources in many different languages, and I run through the science section, stopping here and there to flip through a volume on DNA or paleontology. More wonderful is their display of the truly impressive Coronelli globes. This pair of two-ton globes were originally constructed for Louis XIV, the "Sun King". At this, my inner musketeer is awakened, and my ongoing love-affair with globalization continues. They were objects of science as much as they were objects of art, and they expressed the Sun King's power in a very explicit and clear fashion.
I would have taken more photos, but flash photography was forbidden in order to protect the pigments on the star and earth globes. I respect the preservation of such art and science, but one of these days I am going to have to remember to bring a tripod for long exposures in low-light conditions.
A Wordle of my literature review for Scirtothrips dorsalis. I am amused to note that et al displays with as high a frequency as it does.

I have collected and counted 31,785 thrips on 472 3x5" sticky card traps since July 19th of last year. My research thrips of interest, Scirtothrips dorsalis, accounts for 84.04% of all captures. The next two species that account for the largest proportion of thrips collected during the year are Frankliniella schultzei, at 3.59% of all captures, and Gynaikothrips uzeli, who account for another 3.05% of all thrips trapped. I would suggest that this implies that S. dorsalis represents the predominant thrips species on my two host plots throughout the year.
Next week I will collect my final traps for this project, and with sixty weekly sampling periods, this experiment will be complete.
Obviously this project would have been improved if I had access to larger and more field plots from which to sample. This project could have been further improved if these additional sample plots had been from a broader geographic distribution both in south Florida and across the state. It might also have been more informative had it included samples taken from around additional host plants, and had it included an additional variable - measuring captures on traps at an increasing distance from certain host plots.
Officially, this was my "back-burner" project. I did not receive support or encouragement to continue or expand this project during its first three months, and once officially endorsed, it was suggested that I direct my enthusiasm for improving this experiment elsewhere. I was discouraged from modifying the experiment in order to achieve the improvements I have mentioned above.
This experiment is now one of the fundamental planks of my thesis.
Graduate school is all about realizing that you are in charge, and perhaps more fundamentally, that you probably do know what you are doing and where you should be going. Cast off self-doubt, and pursue reasonable research goals that are endorsed by your peers. Follow your heart. Most important of all?
Flight data for Scirtothrips dorsalis around two hosts, Rosa 'Radrazz' and Conocarpus erectus for approximately one year - before and after transformation by the natural log. Kindly ignore the posted trendlines, as they are mostly irrelevant and unduly influenced by start and endpoints.
BEFORE:

There are obviously absolutely more thrips flying around the roses than around the buttonwood year-round, but a more interesting question to ask is whether the rate changes between those notable peaks and valleys are similar for the two hosts. This graph suggests some similarity between the two flight populations, but scale makes it difficult to eyeball an answer. I am further plagued by inconstant variance that increases as a function of the mean - not an atypical trend among natural biological populations. This linear transformation I will apply helps to normalize the data, and it will also remove some of the problems of scale:
AFTER:

While I still need to go through and confirm statistically that these weekly rate changes line up between the two hosts, it does appear a lot more likely that thrips are changing their weekly flight behavior around both hosts in a similar fashion throughout the year. Host is certainly relevant to the total number of thrips available for flight (data not presented here!), but other factors which are constant for both hosts might explain the relative weekly rate of thrips in flight about those hosts.
I obviously need to compare this data to environmental factors, and to the on-plant population densities that I have also recorded during the last year.
Is this progress? I don't really know. It is a hell of a lot of data to poke through.
"The lack of molecular-only and molecular and morphology support for monophyly of the S. dorsalis complex suggests that this 'species' may actually be comprised of several morphologically indistinguishable species which can only be separated using molecular analyses..."
- Hoddle et al 2008b
As discussed earlier, I suggest (as do authors Inoue and Sakurai in the paper described) that in order to better resolve the phylogenetic relationships between the assorted genera of family Thripidae, someone would first have to expand the analysis of genus Scirtothrips by sequencing and comparing several unambiguously defined species for that genus at the always-popular COI allele. Now, the Hoddle lab at UC: Riverside has done precisely that.
"For science to work, clear questions, hypotheses, and testable predictions are an absolute must. Without them, research is blind and typically ineffective."
- Zachary Blount
I have long believed that one of the major advantages of being a geek is that it is much easier to come into contact with your heroes. As an example, this Monday, I drove off to Mote Marine to listen to science writer Carl Zimmer speak on recent developments in cetacean evolution. The talk itself was a quick layperson's review of thirty or forty years of work on the evolution of whales. Much of it focused on the developments of the last ten years, and it was well-expressed for a non-technical audience.
Of course, that wasn't really the point.
The point was getting to meet an author whose works I've been reading for a great many years, and who is good at getting his own point across. In this, the talk was another expression of his writing: to take sometimes complex and arcane science, and to boil it down to its most interesting and exciting elements. It has been fun to follow his keystrokes as he moves from subject to subject in science, first exploring evolution at the water's edge, moving on to parasites, then exploring the social history behind the discovery of the brain, and most recently, our relationship with the ubiquitous E. coli. His blog and his science columns and commentary for the New York Times and Wired Magazine are even more diverse summaries describing the state of the art in a number of different fields.
Science needs more folks like this who are capable of expressing such discoveries in a manner that is at once both entertaining and informative. The entertainment is important, for while the thrill of discovery or the intuitive leap that results in new understanding is the real joy of science, much of the everyday work is like any job: dull, repetitive - full of endless monotony as you grind towards results and conclusions that you hope will be revolutionary and new... but will probably do nothing more than continue to support existing data. Science can also be intimidating, with the primary literature full of needlessly specific technical jargon, sometimes requiring much reading through diverse and obscure papers and journals to understand a single subject.
His writing keeps science fresh, cutting through all of the hard work to the conclusions at the end of a long day (or decade) that are what really inspire scientists to keep moving. This kind of writing may go on to inspire another generation of scientists, and to develop an appreciation for and an understanding of science outside of the technical community in the same way that folks appreciate the work of a farmer, or a mechanic, a dot-com tycoon, or even a lowly politician.
That, and as a lark, he now keeps track of all of the really cool science tattoos. How can you get any more awesome than that?
Ah, Henry Rollins, a man of many talents. Former Black Flag frontman, sometime actor, motivational speaker, and apparently activist in favor of reality based education:

If the eyes are the windows to the soul, then a new pair of glasses must be a bit like remodeling the front of the house with nice new victorian picture-windows. I can see clearly again and live without glare while driving.
Rah!
One of the advantages to my new home is that the sun peeks in through my window as it rises, and very little will keep its persistant determination from lifting the lids of my eyes for very long. As a result, I was up at what might normally be considered an unnaturally early hour of the morning for myself - especially on the weekend. Lacking anything better to do with my time, or failing to want to do anything more than get some breakfast and go back to sleep, I watched my version of Saturday morning cartoons on Google Video.
I put a bagel in the toaster, spread some peanut butter on it, and sat down to watch Craig Mello give a talk at Google corporate headquarters on his Nobel-winning research on RNAi as part of their continuing seminar series on emerging technologies. The tech talks are interesting because they give you a look into what the almighty Google is thinking about buying and turning into their next cash-cow. Dr. Mello's talk is interesting because he is a good speaker and does an excellent job of translating highly technical jargon into plain english that the layperson might understand and appreciate without feeling condescended to. That, and he is talking about RNA interference, one of the single most interesting and important topics to hop along through molecular biology in the last ten years. To say that I am excited by its potential application in various subfields of biology and chemistry would be something of an understatement.
If you have an hour and ten minutes to kill, I highly recommend that you check it out...
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"My dear, descended from the apes! Let us hope it is not true, but if it is, let us pray it will not become generally known."
- attributed to the wife of the Bishop of Worcester, in reaction to the infamous debate between TH Huxley and the Bishop Wilberforce
While I do not subscribe to the "great man" theory of history, there is no question that Charles Darwin happened to be the right scientist in the right place at the right time. Spurred on to publication by Alfred Russel Wallace, the "father of biogeography", his observations from years of collected research led him to conclusions that shook the foundations of biology and the society built atop that platform. His work brought forth a mechanism by which the whole of diversity might be explained within the context of geological history. When linked to the evidence of heredity first explored by Mendel, and then confirmed at the molecular level by Watson and Crick (and Franklin!), it provided the unifying synthesis of modern biology.
As I am dedicating my life to following the science that he helped to establish, it is with some interest that I note that my own life has from time to time, accidentally fallen into Darwin's footsteps. I have touched the same armoured glyptodontids that he helped to unearth in Southern Argentina at the Museo de la Plata. I have stood in the home he kept, and looked through the study to the desk at which he wrote much of his work. Lately, I have seen the villainous vinchuca that was to bring him low in his later years with Chagas disease in a new light, and finally, I have stood atop his grave at Westminster Abbey in London.
Everyone has their heroes.
Happy Darwin Day, everybody.
Thursday night last week was one of the better days I have had in a long time. Not only was I looking at a three-day weekend due to the observance of Veteran's Day, but the seminar speaker for the afternoon was Dr. Jim Marden - a guy I think of as famous for his work on the evolution of flight in early insects. He has done a lot more work on a lot more integrative biology since then - pushing the science at the level of the gene into its effects on behavior and population structure. One of the projects he is exploring looks at the frequencies of certain genes in a metapopulation of butterflies. These genes are responsible for the butterflies' ability to convert sugar to energy and stay aloft for long periods of time, and inadvertently represent the butterflies' ability to migrate from one area to another. Butterflies who express one form of this gene tend to be very good at staying in their natal patch and reproducing there. Butterflies who express another form of this gene tend to disperse and migrate out onto new patches.
Continue reading "grad school rocks! grad school is going to make my brain explode!" »
Okay... as of today, it appears that I have a new major advisor for graduate studies in entomology, and a new project focus for my education. I will now complete a lifelong goal by defending America from an alien invasion. Admittedly, this will be an invasion of small biting arthropods known as thrips, but they're strange enough to be from beyond this world.
They are tiny parasitic insects of about a milimeter in length whose wings can only be described as feather dusters. They are incredibly prolific, and once a colony is established, it can be extremely difficult to eradicate. Worse still, they are promiscuous parasites, readily leaping from a preferred host to an alternate host when environmental conditions demand. Most important of all, they can also act as vector to several commercially important plant viruses, and to top matters off, they will bite human beings when they run out of plants.
It appears that Florida stands poised on the brink of invasion by a creature that could only be described as an enemy to all I hold dear - the Chilithrips, Scirtothrips dorsalis. It will be my duty to develop a management strategy to control and identify their advance across the nation. Millions stand to perish if I fail.
I am actually looking forward to the challenge. I mean, it isn't mosquitoes, but it still will be ecological control of a potentially harmful species, and it presents all sorts of interesting opportunities to explore the evolution and adaptation of an invasive species: resistance, founder's effect, structured competition, host-shifting and sympatric speciation. As in all such things, only time will tell.
Will someone kindly remind me to go out and purchase a new set of hiking boots at some point during this weekend? I've quite worn the rubber soles of my old pair of Wolverines down to their leather lining, and the steel toe-gaurds are starting to shine through. It is wonderful to note that the wear patterns of a shoe can reveal much about their user's health and habits. Mine reveal that I have high arches, and that I like to sprint on my toes, rolling across the ball of my foot instead of my heel. They also imply that I usually fence with my right foot forward, dragging my left leg on deep lunges - and that I walk with my toes pointing slightly outwards: a sure sign of lateral chondromalacia...
The abuse and misuse of science in the media by policymakers in order to manipulate the electorate has been a problem nearly as long as there have been elected officials. These distortions inevitably begin almost as soon as the government grants funding to public institutions of science, and the refrain of "don't trouble me with the facts!" has long echoed in the halls of power. In America, the distortion or suppression of science in order to legitimize or justify one's particular ideology has had a long and flavored history. One need look no farther than John Wesley Powell and the United States Geological Survey's scientifically sound settlement plan for the West just after the Civil War.
Next time I say that a girl is "my type", I may mean haplotype.
"Congratulations. The Entomology & Nematology Department's Graduate Committee has approved your admittance into our M.S. program to work under the direction of Dr. Chelsea Smartt."
From the NYT Science section:
Fossil Called Missing Link From Sea to Land Animals
By JOHN NOBLE WILFORD
Scientists found evidence of limbs in the making in the 375-million-year-old fish's forward fins.
The funny thing is that in an interview I listened to on NPR yesterday, one of the scientists mentioned that he hated hearing finds such as this described as "the missing link", because it is merely one missing piece in a long chain of missing pieces, and furthermore, it does not actually represent an ancestral state within a linear progression towards tetrapody and eventually humanity. It is unquestionably a branch that shares ancestors with the line that would lead to amphibians, but its large size, developed neck, and the migration of eyeballs to the top of its head imply that the process towards terrestrialization had already been underway for some evolutionary time.
The other funny bits come later in the article when discussing the relevance of 'transitional forms' to Creation-"Science". There is an argument lifted reducto ad absurdum about how finding this fossil only proves the need to find intermediaries between this 'half-way point' and the next... or to point out that even if amphibians are descended from fish, you still can't demonstrate that fish are descendants of invertebrates, but I suppose that they haven't heard of Pikia...
Last but not least, the idea of giant killer salamanders always brings a smile to my face.
Then I think about the vicious and voracious tiger salamanders I had as a kid, and suddenly I am maybe not smiling so much anymore...
"I figure I've just about got this world buttoned up, so..."
- L. Bob Rife, Neal Stephenson's Snow Crash
This is almost scary in an incredibly geeky-cool sort of way. I guess I'll see YOU on the dune sea...
Our first visit was to the emergency room that once cared for myself and three other travelers, seven long years ago. It was during the return leg of our March 1998 Spring Break road trip to the Western Coast that a careless jackrabbit leapt out into our headlights, and into destiny. It left the four of us suspended upside-down in a ditch: Roy Huggins blind in one eye and bleeding, Elizabeth Tweig concussed with a series of scratches on her head that mysteriously parallel my front teeth, myself concussed with shattered sinuses, and Sarah Olivieri... with a broken fingernail. The Castleview Hospital's emergency room is still right where it used to be, and still ready to take in all visitors at all hours, no matter how far away, or how serious the car wreck.
The second locale was of no less significance, but of greater personal interest. Price, Utah also happens to be home to one of the best dinosaur collections in the world. The College of Eastern Utah maintains a Prehistoric Museum sampling the paleontology and archaeology of the area. This tiny museum in this tiny town is home to some of the richest fossil beds in the world, and as a result, the local natural history museum is better stocked than the collections of many larger cities.
It is unusual returning to this place. The last time I was here, I was still somewhat concussed and using an old pair of glasses that my mother had thought to bring to replace the pair I had lost on the roadside. Between the persistent wooziness and a prescription nearly two years out of date, my memories of the time spent there are a little softer around the edges than usual.
The museum does not appear to have changed substantially in the seven years we have been apart, but many things which were once hidden are now visible. The Utahraptor, once trapped within the matrix of rock that held it, was now free to terrorize the coastal plains running along the Western Interior Sea of North America once more. When last I visited, the Utahraptor had just been revealed to the world in a rare example of science following art: until their discovery, the only members of the Dromeosauridae clan known to be that large hailed from the Steven Spielberg cinematic adaptation of the Michael Crichton novel, Jurassic Park.
In another odd twist of fate, and more proof that the world is a smaller place than one might initially suspect, it turns out that Reese Barrick, a paleontologist I had once hoped would be my advisor at NCSU, had also ended up at this spectacular museum as a curator. As we leave, it occurs to me that I too could settle here and be happy.