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.
April 14, 2009
January 16, 2009
status: in progress
With a new year, new deadlines. My life for the next four months, summarized (all apologies to Bungie):
- Deadline for degree application
January 30, 2009
Begin processing the paperwork on ISIS.
Status: Complete! - Submit thesis to committee
scheduled for February 10, 2009
Submit thesis to committee in whole.
Status: three quarters written, pending first approval and edits. - Defense
scheduled for March 5, 2009
Sit down and be electrocuted by committee for five hours.
Status: rebuild graphs and display files, practice discussion of data and results. - Entomology department deadline
scheduled for March 16, 2009
Thesis first submission (defended, signed, formatted, on paper) to Department for review. - Thesis first submission
scheduled for March 30, 2009
Thesis first submission (defended, signed, formatted, on paper) to Editorial (160 Grinter) for review. - Final exam form deadline
scheduled for April 20, 2009
- Final exam form deadline (Editorial, 160 Grinter) for dissertation or thesis degree award.
- Final submission of thesis or dissertation.
- Deadline for “Final Clearance” status in the Editorial Document Management (EDM) system, to qualify for degree award this term.
January 13, 2009
keeping myself busy
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.
December 16, 2008
done and done
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.
November 20, 2008
on the road to lake tahoe
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.
November 12, 2008
more trouble than it is worth?
To be presented on November 17th, at the Entomological Society of America meeting in Reno, Nevada.
October 31, 2008
and a happy Halloween from Derksen
A special thanks to Fred Wightman for his thoughtful gift. Now I just have to learn how to tie it!
happy halloween from the Cambrian
Pumpkin courtesy Danielle Long and Anomalocaris.
October 9, 2008
a namesake of sorts
A cranium of Protoceratops andrewsi, collected by the infamous Roy Chapman Andrews during his Mongolian adventure. He went seeking human origins, and instead came back with some of the first evidence of dinosaur nesting behavior.
You might notice something familiar in his name, but look to something even more familiar in his hat. This notorious adventurer, explorer, scientist, soldier, spy, and some would say grave-robber and thief of rare antiquities was one of the inspirations for another adventurer in a beaten fedora hat. You can either read of his excellent adventures in his own hand above, or try Charles Gallenkamp and Mike Novacek's biography of the man, Dragon Hunter.
burgessia etcetera
The Burgess shale occupies a unique location in paleontological history, and has played a significant role in both posing and answering questions for evolutionary biologists. It represents a small snapshot of life on the edge of a coastal shelf in Cambrian seas. Its discovery by Charles Walcott in the early 1900s was significant in that it was one of the first sites to yield up a large number of difficult-to-preserve soft-bodied organisms from a period when life was making the transition from simple to complex multicellular organisms. It has been referred to as a period of "biological experimentation", as evolution tossed up a number of innovative body plans, not all of which were adopted. Many of the critters uncovered are... weird... for lack of a better description. They are difficult to place within context of modern taxonomic groupings, as they are either "failed experiments" that went extinct, or their ancestors are so derived that it is almost impossible to detect the familial relationships.
Of course, many of the hypotheses set forth by the original site have now been supported or expanded by additional finds in the Chengjiang formation in China - and elsewhere around the world, but the wonder of remains are still being excavated from the original Global Heritage site that inspired so much thought.
These two creatures have wandered quite a distance from home to live in the muséum national d’Histoire naturelle:
This is Burgessia, a small and early crustacean from the eponymous shale. They probably lived a life similar to brine shrimp or krill, swimming and filter-feeding in the open ocean.
This is Naraoia, an early soft trilobite. I sometimes wish that these had not gone extinct, as I would like to try eating them. On the other hand, few folks eat horseshoe crabs, so...
It is sad to note the extensive water damage on both of the cards labeling these important fossils. All of these valuable fossils were stored in simple and poorly lit plexiglass cases, and not all of them were labeled. There were no educational or supplemental materials to really place the organisms in their evolutionary or historical context. They were simply objects to be appreciated for their natural beauty, and it was sad to see such an amazing resource callously gathering dust in an empty display case. Even my own personal collection of odds and ends from the natural world is better organized and placed in a more meaningful context.
Maybe I'll open my own museum some day.
paleontology and comparative anatomy
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.
wandering free, part IV: jardin royal des plantes médicinales
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.
August 29, 2008
a whole lotta thrips
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?
July 9, 2008
why we transform our data
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.
June 27, 2008
bloodbloodblood
I had thirty minutes to spare before our movie started tonight, and instead of reading colorful but dull lobby cards for films I'll never see, I donated blood. Given the sheer number of times that I've been involved in a life-mangling accident, I figure it is only fair (and about time) I gave a little back. There are plenty of injured people in the world who need blood, and you've got more than enough...
June 16, 2008
"work that is sure to come"
"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.
May 21, 2008
good morning from the sub-tropics
April 10, 2008
publication?
"Greenhouse Canada has requested permission to use your image. This photo will accompany a May feature by Graeme Murphy, IPM specialist with the Ontario Ministry of Agriculture, Food and Rural Affairs."
Well, while I am not certain that this constitutes a traditional scientific publication that will go on my CV or resume, I do have to admit that I am thrilled to hear that someone is making use of the photo. I took them so that someone might make use them. Kudos to the University of Georgia and their Center for Invasive Species and Ecosystem Health for hosting and sharing the images, and kudos to the Creative Commons licensing that helps to make such sharing possible.
All of this just makes me want to take more and better photos.
March 10, 2008
driven to the water's edge
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?
February 13, 2008
a good day for mail
Well.
Hunh.
I guess it turns out that I am not totally incompetent after all, and that my thesis research has the potential to be interesting to somebody outside of the academic community. It seems that I have recently been awarded the "Dennis Carpenter Memorial Fellowship", sponsored by the Dade County AgriCouncil.
This is kind of odd, and kind of flattering.
I've never really received money for writing up an idea before.
It kind of feels good.
February 12, 2008
darwin day again
Well, happy Darwin Day all over again. Had the man survived like his work has, he would now be a year shy of two hundred years old, and all the stronger for it. Next year, his Origin of the Species will be one hundred and fifty years old - and while it has undergone considerable refinement as additional data has been collected, the central tenets of his observations about the processes affecting populations over time still remain the same:
- Individuals within populations must possess variable traits. For whatever reason, not all critters are identical. Some of us are slightly taller than others, or shorter, or hairier, or a slightly different shade of mauve.
- These variations must result in differential performance. Maybe being shorter helps you hide in your burrow and helps you avoid being eaten by hairier folks, or by being slightly more mauve you are slightly more attractive. Performance is often measured in terms of reproductive output, because the ability to reproduce yourself and to continue or expand your lineage into the future is the only real measure of "success" for a population.
- These variations must be heritable. It doesn't matter to the population's success over the long term if your individual success cannot be shared with the generations of offspring ahead of you. They must be able to inherit your performance.
January 27, 2008
weekending
Adult Geiger beetles aggregating on the underside of a leaf on a Geiger tree just off of US1 on the road to Key West. The beetles are precinctive to the area, and the Geiger tree is their only known host. A friend of mine is working on some of the interesting defensive behavior that the beetles' larvae display.
October 9, 2007
an inconclusive phylogeny for family Thripidae
Inoue and Sakurai's 2007 paper represents some excellent work, but as the figure simplifying some of their results demonstrates, it also shows how little effort has been placed on sequencing the genus Scirtothrips when compared to other genera of thrips. One of the obvious conclusions that the authors reach from their results is that sampling more sequences from broader populations and different species of genus Scirtothrips (which inspired the figure above, having "an ambiguous phylogenetic position in this study") would help to better establish the position of the clade in relation to other groups. Curiously enough, a much larger sampling of genus Scirtothrips already exists (Rugman-Jones et al, 2006), but it focused on sequencing samples for ITS1 and 2, and not COI or EF-1a. Furthermore, the Rugman-Jones et al laboratory were using RFLP to establish a standardized amplification protocol, and had not yet attempted to construct the inevitable phylogeny that is sure to follow for the group. I am uncertain as to whether species of genus Thrips or Frankliniella have already been sequenced at these alleles, but given their economic importance, it would not surprise me and those observations should be compared to the work that is sure to come from the Rugman-Jones lab.
Moreover, these experiments show precisely why taxonomy and phylogenetics remain critical tools relevant to modern management programs. As both teams of authors clearly demonstrate, phylogenetics can be turned to tasks beyond what some critics have derided as "merely academic interest in the evolutionary history of a group". The primary aim of Inoue and Sakurai's research was to compare the evolutionary phylogeny of the pests to their competence as a vector for several different strains of Tospovirus (Bunyaviridae). Determining the evolutionary relationships between the groups should allow one to predict the suitability of other species within that group as potential vectors for various strains, and perhaps provide a better explanation as to how the Tospovirus made its evolutionary leap from a virus that infected insect-tissue to one that could also invade a plant. The primary goal of the Rugman-Jones project was to provide a quick and dirty molecular solution to the occasionally painful task of taxonomic identification and its reliance on a few trained specialists sometimes using highly variable morphological characters.
The USDA has already launched a similar project, using phylogenetic information to document family relationships and the associated pesticide resistance profiles for several reproductively incompatible demes of whitefly. They are alleged to be in the nascent stages of a thrips-based project which hopes to resolve and establish the missing characters for these groups so that a true phylogenetic comparison can be established...
REFERENCES
- Inoue, T and Sakurai, T (2007). "The phylogeny of thrips (Thysanoptera: Thripidae) based on partial sequences of cytochrome oxidase I, 28S ribosomal DNA and elongation factor-1a and the association with vector competence of tospoviruses." Applied Entomological Zoology 42(1): 71 - 81.
- Rugman-Jones, PF; Hoddle, MS; Mound, LA; Stouthammer, R (2006). "Molecular Identification Key for Pest Species of Scirtothrips (Thysanoptera: Thripidae)." Journal of Economic Entomology 99(5): 1813.
October 5, 2007
this is not an atypical guide to the genera of thrips
"The only reported difference between these two species is the length of the pronotal posteroangular pair of setae (Mound et al. 1995)."
- from Held et al, 2005
The differences between the Cuban Laurel Thrips, Gynaikothrips ficorum, and the Weeping Fig Thrips, Gynaikothrips uzeli, are minimal. This seems to be a typical problem with many of the genera of thrips, and is a strong motivator for other means (Brunner et al, 2002) by which to identify individual species.
REFERENCES
- Brunner, PC; Flemming, C; Frey, JE (2002). "A molecular identification key for economically important thrips species (Thysanoptera: Thripidae) using direct sequencing and a PCR-RFLP-based approach." Agricultural and Forest Entomology, 4: 127 – 136.
- Held, DW; Boyd, D; Lockley, T; Edwards, GB (2005). "Gynaikothrips uzeli (Thysanoptera: Phlaethripidae) in the southeastern United States: distribution and review of biology." Florida Entomologist, 88(4):538 - 540.
- Mound, LA; Wang, CL; Okajima, S (1995). "Observations in Taiwan on the identity of the Cuban laurel thrips (Thysanoptera, Phlaeothripidae)." Journal of the New York Entomological Society, 103: 185 - 190.
October 1, 2007
culture shock
So... tonight I had a halting discussion in Spanish with a Brazilian who only spoke Português and some Spanish and English with the aid of a Colombian who spoke fluent English and Spanish about group selection and whether certain models of sexual selection are appropriate to apply to human social models. With a background in anthropology and evolutionary biology, these are two topics that really interest me and will get me excited, no matter what the language. I can only hope that we were all on the same page and talking about the same thing, and not arguing past one another like ships in the night.
thirty to thirty
This weekend, I needed to run to WalMart to buy a lamp so that my humble room would have light to read by. As I approached their establishment, I found myself incapable of stopping, and instead kept driving. I just kept going until I hit a beach and its accompanying mangrove swamp. Walking amidst the wind-swept mangroves, I found peace for a little while. That, and I chased these poor things all over the park trying to get one or two good shots.
September 22, 2007
nature, red imported mandible and stinger
Ow.
The problem with stopping every now and again to appreciate nature and to smell the flowers is that sometimes you stop on top of a fire ant mound.
In flipflops.
Ow ow ow ow.
Cue profanity.
Ow.
May 12, 2007
saturday morning cartoons
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...
May 4, 2007
death from above
I know, I should be packing, but the amatuer naturalist in me is continually distracted and inspired by the many wonders (and the occasional atrocity!) of the environment around me. The sheer diversity and entertainment to be found in the ecology present in our own backyard never fails to amaze or entertain me.
The young lady pictured below is about an inch and a half long, and is unquestionably looking directly at the camera. Soon after I took this photo, she tried to remind her paparazzo that he had better things to be doing with his time than harassing a hard-working woman, but she failed to discourage me. She might be known to you by her common names as a "digger wasp", or a "cricket hawk". It probably belongs to the "thread-waisted" family of wasps, the Sphecidae, who have graced these pages before.
A casual google image search reveals that she probably belongs to genus Sphex, but I hesitate to stand more decisively on this point without actually keying the critter out on a reliable document published by a reputable author after a process of peer reivew. Still, she certainly does possess many of the key diagnostic characteristics common to her family of wasp. Most notable among these features are the constricted waist, "simple" unbranched hairs on the thorax, and a pronotal "collar" that fails to reach the tegula - the "shoulders" of the wings.
Sphecids are far more interesting for their behavioral characteristics than for their morphology. They flick their wings constantly as they go about their business, and it gives them an odd sense of purpose. As solitary wasps, they spend most of their adult lives serving as pollinators while feeding on the nectar of flowers - a basal behavior that would become emphasized in their descendants, the bees. Of course, reproduction and growth require large amounts of protein for a developing organism - and as a result, these solitary wasps are also incredibly predaceous.
Their predatory behavior can be every bit as elaborate and complex as those of the so-called "higher" vertebrates. Studies on the bee-wolves earned Niko Tinbergen his doctorate, as he established that even creatures as "neurologically simple" as insects were capable of learning sophisticated behaviors, including a positional awareness that allowed them to remember and use distinct landmarks to find their nesting place. Selection has encouraged the evolution of this memory as sphecids drop out of the sky to sting their prey of choice with an immobilizing venom, and then drag them away to an underground chamber they have constructed. The manner in which a given wasp drags or carries its prey away can also be species-specific, and the emerald cockroach wasp, Ampulex compressa, is infamous for its brain-surgery on its host of choice, the American cockroach, Periplaneta americana.
I observed my little girl drag several crickets into that burrow over the next several hours, paralyzed but alive - where they will meet their final grisly fate. That tomb is also a birthing chamber, and once each underground cell is provisioned, the female will lay a single egg on each. Her offspring will eventually hatch, and then slip inside their host, ghoulishly devouring its internal organs - or living like tiny vampires on the blood of their host. You're still alive while they eat you...
April 2, 2007
pocket godzilla
While biking home from the department today, I found a young snapping turtle in the middle of the road. I've always had a bit of a soft spot in my head for turtles, and I felt that I had to get it out of the road before someone less observant ran it over. I also wanted to document the event, but I'd left my camera at home... so I picked it up, and lacking any better place to carry it... I tossed it in my book bag and ran back to a friend's lab to borrow his digital camera:
Photos and "Blair Witch" style cinematography courtesy of Brad Smith, © 2007. Kindly note that no turtles were harmed in the making of this picture, and after thoroughly documenting and harassing the poor creature, it was in fact released on the far side of the road near a nice pond.
February 12, 2007
know your roots
"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.
January 29, 2007
corrupting young minds
As part of my duties as a graduate student, I am required to give the occasional tour of the facility to interested folks from the general public. These range in age and experience from elementary school children to concerned growers from agricultural communities, and it is my responsibility to shed a little more light into the science of entomology - as well as to underline the research that the department here at the University of Florida is responsible for. I personally enjoy these tours, and get an extra-special kick out of the kids because I get to stand up on a podium and have fun talking about the weird diversity of everyone's favorite creepie-crawlies for an hour. It gets even better when the kids know how to ask good and pertinent questions, like "how did you arrive at [that impressively large number] describing the number of different species of insects there are?" - or "how did you figure out approximately how many insects might live in a common acre of farmland without actually counting them all?" I love the little skeptics among them best, and I suspect that they are going to have a very bright future. Anyone who refuses to simply accept facts as they are spoon-fed to them is an awesome and attentive human being - and seeing a fourth grader question methodologies, results, and conclusions is even better. An informed mind can follow a pattern and find their way out of a particular situation - but a critical mind can eventually work its way around overcome any obstacle in the path to truth.
Of course, working and touring around the entomology department has its own unique risks. Little things, like stopping off to let the kids (and their chaperones!) take a bathroom break next to a classroom with a lecture in medical entomology. At which point the professor might stick his head out, and wave you over for a little discussion...
"Oh - sorry, Dr. Kaufman - are they being too loud? I'll move 'em out of here real fast, and get their parents to shush them a bit if they are distracting..."
"No, no - not that at all. I'm just about to show a few slides of sarcophagids."
"Flesh flies?"
"Yes. On hosts. From a... (whispered) crime scene."
"Oh."
"Right."
Disaster averted, we take them into the other room, and instead introduce them to "Sally" and a box full of her friends, giant cave roaches from central america.
For some reason, this always seems to go over well.
November 28, 2006
dead beetles crawled into my eyes
You know what does not enhance your calm?
Trying to identify very small things. I don't care how great your microscope is - microsculpture is still hard to rotate and keep in focus. It helps to have a well-prepared specimen. It helps a lot, but it also helps to know what you're going to need to look at before you prepare your sample, and if your sample is an unknown? You won't know what you need to look at until you can't quite make it out under the scope, no matter how much you rotate and refocus the little monster. This only gets worse when your unknown is under a millimeter in length. Even if you knew what you had to move out of the way to see what you needed to see, getting a hold of a limb and gently moving it up and out and over without also completely removing it from the body as a whole is probably just as tricky as you might imagine.
How sharp are your microforceps?
How steady is your hand?
Now do it for five hours.
Now how steady is your hand?
November 22, 2006
flies in the brain
I just spent a whole day looking at flies under a microscope, and boy - are my eyes tired. I still do not feel confident of my abilities to identify a given family of fly on sight alone, and the keys are poorly executed - only to be followed quickly after developing much familiarity with the individual traits responsible for dividing organisms into one group or another... and I just don't have the practical experience to assess those traits rapidly, and there has been no one to reassure me that I have even reached the correct conclusions for good reasoning - or even the wrong conclusions for the right reasons.
Agck.
Time will tell.
November 13, 2006
grad school rocks! grad school is going to make my brain explode!
So...
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.
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October 27, 2006
terror of the skies
October 18, 2006
if there was ever any question that we were related...
Apparently when given suitable inspiration, my father fancies himself quite the poet:
An entomologist of caddisfly fame
with MS-FLA next to his name
had found his nirvana
with Gobind Khorana
translating the peptide chain.
But Old Holley intervened
and made quite a scene
and said their endeavor was folly.
"I hate to disdain
your nucleotide claim,
but your peptide ain't mono
it's poly!"
Eureka! they said
we'll try this instead,
Old Holley has made it explicit!
So the prize they received
(not quite as conceived)
was not just a double,
but triplet.
hope for me yet
Marshall Nirenberg was the recipient of the 1968 Nobel Prize in Physiology or Medicine, which he shared with Har Gobind Khorana and Robert Holley for their research exploring the translation of nucleotide-triplets on mature messenger RNA into specific amino acids linked along a polypeptide chain. Of further note, and of personal significance, Dr. Nirenberg recieved his master's degree in zoology at the University of Florida. His master's thesis focused on the classification and taxonomy of caddisflies.
He began his career as an entomologist.
There is hope for me yet.
October 11, 2006
greenspace
Amazing what kind of difference one week can make:
The water hyacinth, Eichhornia crassipes, was originally introduced to Florida's waterways to act as a natural biological filter, extracting pollutants and impurities from its waters. It was a successful plan, but perhaps too successful - without any natural predators, the hyacinth has since grown out of control. In certain moving bodies of water, manatees keep it in check, but in stagnant or enclosed bodies of water, it eventually covers the whole surface of the lake, choking off any and all sunlight to other plants.
September 23, 2006
rock of ages
Today was another good day. I spent most of it on a desolate and barren hillside in the middle of a gravel quarry, hunched over a mountain of clay - and armed with only a screwdriver to sift through it - but today was still a good day. I may have burned out my brain in the hot hot sun, but I was searching for buried treasure, and I found it.
We were digging in a two million year-old sinkhole that once lay at the bottom of a Florida lake. The lake acted as a funnel to the sinkhole's drain, and the depth of that hole promoted an anoxic environment, deterring further scavenging and predation. This created conditions favorable to the preservation of a large number of whole and partially articulated skeletons. You might be surprised by the diversity of life represented in this unusual watery grave - any number of things can fall in a lake and drown over a few thousand years.
September 18, 2006
more florida wildlife
This juvenile specimen was discovered observing a small school of fish in a drainage ditch along the edge of Lake Alice here in Gainesville. It was just over a foot in length, and approximately a quarter-inch in thickness. Some have alleged this beast a rat snake, or corn snake - so known because of their propensity to consume rats in barns, and because their coloration provides for excellent camouflage in the original red-colored strains of corn grown in North America. That said, there also exists a possibility that this is the altogether more fierce Florida banded water snake. My favorite herpetologists wished that I had handled the snake in order to obtain better pictures of his ventral scales, dorsal banding patterns, and his skull morphology - so that they might reach a more authoritative conclusion.
I was far too smart to try handling an unknown (and possibly venomous!) organism without good thick gloves on - and besides, I really am more of a "sit back and observe what happens" than a "poke it with a stick and see what happens" kind of scientist. Call me lazy, but I'd prefer for the organism to inadvertently perform the passive experiments itself than for me to force a situation upon the serpent where it must make an active decision about its lifestyle.
I left the snake a good two or three feet for him to feel comfortable in. Even so, he didn't do much more than move his head four or five inches the whole time I was there - he was nervous. Once I got back up out of the ditch and moved back to seven or eight feet, he slithered slowly forward and around the bend of one of those rocks into the undergrowth with increasing acceleration. He wanted to be gone once he thought I was out of grabbing range...
Besides: after being chased by water moccasins in a former life, I felt justified in leaving a few feet for me to feel comfortable and hope that I would have a good running start to get away from any hornked-off snake...
September 1, 2006
bats in my belfry
In spite of belonging to one of the most diverse orders of mammals, with over a thousand separate species classified, bats remain something of a mystery - often unobserved by the casual naturalist. Perhaps I tend towards a Chinese interpretation of things because of my childhood travels, but I must admit that I have long been rather fond of the nocturnal wonders. While I can not be certain, I suspect that I saw my first real bat long ago at the Denver Zoo, but my earliest memorable encounters with the creatures in their natural environment were never through their direct presence, but always of the carnage they left in their wake.
August 18, 2006
and so it begins
Today, I had a good day.
It began entirely too early - just slightly past six. I am not now a morning person, and I will never be. Still, I managed to pull myself onto the road an hour later after only a single cup of coffee. Sometimes there are reasons to get up in the morning, and sometimes I will find the proper motivating force to drive me forward through the hazy cloud of sleep. Today, I will meet my advisor in the flesh for the first time, and today will truly mark the beginning of my graduate career.
I drive East out of Palmetto, heading towards Interstate 75, which I will follow South to Naples. In Naples, I-75 will turn Eastwards again, and suddenly become "Alligator Alley", a turnpike cutting through the very heart of the Everglades. Endless miles of hungry swamp ensue, with only a thin chain-link fence holding back the horde of hungry alligators - as well as the occasional invasive burmese python. Of course, the truth is actually rather disappointing: the fence is there to protect the alligators and panthers (and pythons, oh my!) from us, and not vice-versa. The "untouched purity" of the wilderness that some would like to romanticize no longer exists. Our greatest natural heritage and our best national parks must be managed, lest their structured ecology slowly phase into the cultured environment of 'civilization'. It leaves them as artificial an environment as any zoo, if not more grandiose.
July 13, 2006
raining and pouring
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.
June 15, 2006
I want a girl with the right allocations...
Next time I say that a girl is "my type", I may mean haplotype.
April 4, 2006
Walking fish is harder than walking dogs, but it still beats walking sticks...
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...
September 5, 2005
Price
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We followed the interstate down the path opened by the Wasatch fault, stopping briefly in Price, Utah to visit two locales of international renoun.
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.
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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.