Thursday, January 28, 2010

Overwhelming evidence, education and obstructionism

My favorite Obama quotes from the State of the Union Address:

“I know that there are those that disagree with the OVERWHELMING EVIDENCE on climate change. But, here’s the thing; even if you doubt the evidence, providing incentives for energy efficiency and clean energy are the right thing to do for our future…”

“In the 21st Century, the best anti-poverty program around is a world class education.”

“Neither party should delay or obstruct every single bill - just because they can.”

Thursday, January 14, 2010

Gharials and cobras - Water conservation

The gharial and king cobra are two of India's most iconic reptiles, and they're endangered because of polluted waterways. Conservationist Romulus Whitaker shows rare footage of these magnificent animals and urges us to save the rivers that sustain their lives and our own.

Sunday, January 10, 2010

Insinuations of Lamarckian Evolution and a Lamenting First Impression

I just had a read of Meet your viral ancestors - how bornaviruses have been infiltrating our genomes for 40 million years over at Not Exactly Rocket Science, and then promptly made a follow-up, though cursory, pass at the associated publication from Nature:

Horie, M., Honda, T., Suzuki, Y., Kobayashi, Y., Daito, T., Oshida, T., Ikuta, K., Jern, P., Gojobori, T., Coffin, J., & Tomonaga, K. (2010). Endogenous non-retroviral RNA virus elements in mammalian genomes Nature, 463 (7277), 84-87 DOI: 10.1038/nature08695

Sine Ed has already accomplished the task of detailing the paper (at the above link), I won’t bother to do so here, rather I’ll just provide my initial, perhaps somewhat imaginative, take on it.

My first impression of the work, once again emphasizing that I sometimes express imaginative tendencies, is that it suggests a Lamarckian process of evolution.

The paper reports on a genera of RNA viruses called ‘bornaviruses’ that seemingly have the capacity to enter, and remain in, in the germlines of their hosts. In the instance of primates, for example, the researchers indicate that bornaviruses have been passed to humans from a lineage stretching back 40-million years. Although the authors don’t make specific reference to Lamarck, they do add to the argument that in addition to demonstrating “functional, albeit weak, evolutionary conservation,” the viruses “may have some function in their host species,” such as being a causative agents of psychiatric disorders, AND EVEN being “a source of genetic novelty” as to become “a new source of genetic innovation”!

So, is the paper saying that the introduction of ACQUIRED CHARACTERS into the germline of a lineage has lead to GENETIC NOVELTIES with the demonstrated ability to translate to the expressed PHENOTYPE of an ANIMAL, thus acting as a source of INNOVATION. That seems to have a tinge of Lamarckism…

Fascinating findings and bold suggestions, but in my interpretation the word ‘innovation’ goes too far in that it implies adaptation, fitness benefit and positive selection. Let’s not forget that Lamarck’s theories also relied on the idea of progression; the belief that evolution advances form towards specific functional goals. The research ‘is what it is;’ but, I can’t help but think that its speculative portions could have written a little differently… I’d be surprised if the ‘tinge’ in this paper isn’t abused by the fundys; there might be a pattern emerging over at Nature

Saturday, January 9, 2010

Arrested Development in Socratic Parasites

Arrested Development since the Arrest of Socrates
In the 4th Century BCE, soldier and scholar Xenophon of Athens put to papyrus his arguments contesting charges by the Athenian court that his esteemed mentor had been corrupting the City's youth with inappropriate religious teachings and an anti-democratic message. The defensive rhetoric laid out in his document included transcriptions of past dialogues made by the accused that served to demonstrate allegiance to the accepted religious dogma of Athens. By detailing the religious notions of his indicted teacher, Xenophon was confident that he'd prove the court's charges to be unjustified and thereby win his teacher's freedom. In one of the work's incorporated dialogues, the accused teacher - Socrates - affirmed his religious adherence by describing what he believed to be evidence of divine creation:

"Do you not think that he who created man from the beginning had some useful end in view when he endowed him with his several senses?... The eyeballs, being weak, are set behind eyelids, that open like doors... with such signs of forethought in these arrangements, can you doubt whether they are the works of chance or design?... do you suppose that wisdom is nowhere else to be found, although you know that you have a mere speck of all the earth in your body and a mere drop of all the water?

---Socrates (from Xenophon's Memorabilia, circa 371 BCE)

In the mind of Socrates, the mutually beneficial relationship exhibited between the feebly endowed human eye and its divine door-like benefactor the eyelid, represented mechanistic proof positive of heavenly design. The relationship of biologic form and function that he observed seemed too perfect and far too complex to have been borne of a lowly, earthly apparatus. Giving what we know today as the scientific method a miss, Socrates explained his observations from the teleological perspective; meaning not through the organic processes of nature, but from a preconceived notion of a god-governed intent. To Socrates humans weren't a byproduct of physics, chemistry and biology; rather they were the realization of a blueprint rendered from the draft table of the gods. Unfortunately, and despite Xenophon's heartfelt efforts, written accounts indicate that not all of the gods Socrates had credited with nature's humane work were deemed acceptable to the 501 Athenians gathered as jurors during his trial of 399 BCE. For the sins of his impiety Socrates was sentenced to drink a poisonous concoction of paralyzing hemlock; thereafter he numbly passed into the void of history.

Although Socrates has long gone, his teleological arguments and the idea of 'irreducible complexity' still persist to the modern day. Unsurprisingly, far from being refined with time, these archaic arguments remain utterly the same - as if frozen in time. In terms relevant to developmental biology, the process that is actually responsible for the making of Socrates' divine doors, we might even say that irreducible complexity has suffered an induced a state of 'arrested development.'


Beyond its analogous application to the petrified argument of irreducible complexity, the term 'arrested development' as applied in the biological sciences can be interpreted in a variety of ways. In the sense of modern medicine, arrested development generally refers to a condition of ceased physiological growth or maturation. In this meaning the expression may be used, for example, by a doctor to describe an embryo that has failed to reach the benchmarks associated with its growth to a fetus. Slightly more broadly, the science of developmental biology often uses arrested development in detailing the phenomena of 'neoteny' - a process in which adults of a species come to express the physical characteristics previously exhibited only by its juvenile members. Also referred to as 'juvenilization,' neoteny played an important role in course of human evolution; however, because that's a big topic in itself, I'll mention another frequently cited example of neoteny - the species of salamander called the axolotl.

Even when adulthood and reproductive maturity is obtained by the axolotl, a lack of thyroid stimulating hormone causes them to appear as though they're still in a larval stage of growth. Instead of looking like sure footed terrestrially adapted salamanders, axolotls look more like jumbo tadpoles, complete with feathery external gills and a fully aquatic lifestyle. Although, axolotls come across as juveniles frozen in time, they can still reproduce; they obtain sexual maturity without ever enduring metamorphosis or without ever 'growing-up.' Just like Socrates' original suggestion of irreducible complexity, their continued development has been arrested.

Although, a pronounced lack of adult refinement characterizes the arrested development displayed by both axolotls and creationists, I admittedly find the comparison between the two species somewhat inaccurate, and in all honesty, disrespectful. After all, axolotls, unlike creationists, are physically and behaviorally adapted to their environment - the high altitude lakes they call home. Creationists on the other hand, have suffered from such complete and total developmental arrest that they remain today only as anachronisms, psychologically better suited for long degraded and extinct habitats; like those settings more common to the time of Socrates. To show a little respect and give axolotls their due credit, perhaps there is in existence another developmentally arrested species that creationists more closely resemble..? I'll come to that shortly.

Over the nearly 2500 years since Socrates' less than elucidating interpretation of the natural world, the science of biology has - to put it mildly - grown by leaps and bounds. And, although the process of science is (and will always be) an ongoing endeavor, it has been un-tethered by the self-defeating presumptions of irreducible complexity for quite some time... Despite this, since the Socratic inception of the irreducible argument, the only evolutionary journey embarked on by archaically-minded creationists has been to vary the organic structure pointed to as proof of divinity. As science sharpens its resolution of the nature world, refuted creationists seek their holy grail at an ever dwindling scale. In the time of Socrates it was the eyelid, later the eye itself, a few years ago it was bacterial flagellum and the intricacies of the immune system; recently (with Stephen Meyer/Discovery Institute's latest contrivance ) it's the structure of DNA.

Part of the creationists' outdated strategy is to target features of contemporary science that are not fully understood by the public at large. To these aspects of science, creationists obscure knowledge with misinformation and slight-of-hand. Once the ignorance-countering effects of education have augmented immune response sufficiently enough to resist a particular attack, the creationist pathogens move on to new hosts. Rather than adapting their fundamentalist principles to the reality of contemporary understanding, creationists infest new hosts and shelter as a perpetually reproducing and ever developmentally arrested pestilence. Considering this opportunistic and patient strategy, creationists aren't much like axolotls at all... Now that I think about it, they seem more akin to parasites - perhaps something like trematodes.

The Miscellaneous Misadventures of Alaria marcianae

Trematodes are flukes of nature in that they've evolved an astonishing, almost incomprehensible level developmental plasticity. Like creationists, they can induce a state of arrested development at the drop of a hat. Most have evolved the ability to subtly manipulate their rates of growth and sexual maturation to track the resources available in the environment. For the parasitic nematodes, their environment is manifested by the internal chemistry of their victims. The digestive enzymes, hormones and antibodies expressed through the physiology of their hosts help the trematodes gauge the probability of reproductive success and to tune their own developmental process accordingly. This fantastic capacity for flexibility is of benefit because should a trematode happen to find itself immersed in the body of an unsuitable host, it can induce a state of arrested development and shift its metabolism to complete dormancy while awaiting transmission to a more favorable chemical climate. As a natural corollary, if the trematode succeeds in locating its target host (aka, its 'definitive host') it can quickly push development into overdrive and achieve reproductive adulthood in short order, thus maximizing the opportunity to its individual advantage. Being unrestrained by the ticking-clock of reproductive efficacy, trematodes can migrate from host-to-host and even between species with relative ease. As a case study, consider the misadventures undertaken by the trematode species named Alaria marcianae.


Alaria marcianae is a fascinating organism known to target, as definitive hosts, the kittens of the Florida Panther (Puma concolor couguar). The Florida Panther holds a critically endangered status and, as the common name strongly suggests, resides in the state of Florida. The tawny colored Florida Panther is one variety of a widely recognized group of felids that are also known by the names cougar, mountain lion and puma. The panther-intersecting life cycle of Alaria marcianae is complex with several possible vectors of transmission, but in choosing an arbitrary starting point for the purpose of description, we can assume that its convoluted journey begins within the intestines of an adult panther.

Having recently been deposited in the intestinal tract of an adult feline, members of Alaria marcianae start their lifecycle as eggs. The eggs, unembryonated germ cells, intermix with the partially digested remnants of raccoons, armadillos and other common delicacies found in the panther's system, and are then excreted with the animal's feces. On being submerged by the inundated wetlands for which south Florida is renowned, water stimulates the eggs to internally develop embryos. Once these embryos have achieved sufficient maturation, sunlight triggers the eggs to hatch free swimming, cilia-driven, paramecium-looking critters called miracidia. The miracidia are not adult Alaria marcianae, rather they represent a sexually immature stage of development that is specialized for seeking out a very specific (obligate) intermediate host. To ultimately succeed in stalking a panther, the miracidia of Alaria marcianae must first locate and infect a ram's horn snail of the genus Helisoma.

On locating a ram's horn, the miracidium attaches itself to the soft exposed flesh of the snail and, by excreting tissue-degrading enzymes, sheds its cilia-bearing outer layer. It then penetrates into the snail's body cavity. Having shed its ciliated epithelium, the miracidium becomes an immature sporocyst. Although sporocysts still lack the ability to reproduce sexually, by embedding in the snail's nutrient rich organs they acquire the power to produce additional replicates of themselves - clones called 'daughter sporocysts.'


To further advance on the panther, the new daughters promptly leave their mother's side and venture to the snail's gonads. Mollusk hormones produced by the gonads fuel special cells within the daughters as they morph into tailed, tadpole-looking larval forms called cercariae. The cercariae swim to, and exit from, the snail's shell-producing mantle. From there, they return once again to the open water as free-swimmers.

Leaving the snail behind, the cercariae swim to the water's surface and hunt down the true tadpoles of the leopard frog (Rana pipiens) - their second intermediate host. Hijacking the leopard frog's tadpoles for transport, the cercariae drop their own tail and burrow into the tadpole's skin. There's no need for self-propulsion when riding inside a tadpole. Once inside the developing frog, Alaria marcianae, now at a stage where they're referred to as mesocercaria, cease further development and undergo another round of asexual cloning. As numbers continue to multiply, they patiently rest, waiting for the tadpoles to carry them landward as adult leopard frogs.

In time, the mesocercaria-bearing tadpoles grow into leopard frogs and move their parasitic cargo to land. On terra firma the leopard frogs are hunted by a wide range of predators; occasionally falling prey to yet another preferred host (aka, a 'paratenic host') of Alaria marcianae, the raccoon. After catching an infested frog, the raccoon's digestive enzymes make short work of the frog's flesh - in the process releasing the mesocercaria. As with its previous host, the mesocercaria multiply in the raccoon, but continue to maintain a state of arrested development - they are not yet adults.

Did I mention that raccoons in south Florida happen to be a favorite prey item of the endangered panther? Utilizing methods similar to those during the frog-to-raccoon transmission, Alaria marcianae find their way into adult panthers by contaminating raccoons - panther prey. During the process of raccoon digestion, mesocercaria are liberated from tissue and enter the bloodstream by penetrating the intestinal wall.

Now, if the panther they find themselves parasitizing, by chance, turns out to be a lactating female, her hormones will stir the mesocercaria into migrating to her mammary glands where they will transmit (trans-mammary) to the digestive system of her kittens'. The term used to describe the situation in which a mother acts as a paratenic host to her own offspring is called 'amphiparatenesis.'

Here, amphiparatenesis results in the imbibing of mesocercaria-laden milk by the kittens. As with the mesocercaria residing within their mother, the parasites in the kittens will penetrate the intestinal wall and enter the blood stream. They'll surf the blood stream until reaching the lungs where they become metacercaria; as metacercaria they harden the surrounding lung tissue forming protective cysts. Having profitably acquired housing in their definitive host, the cysts in the lungs will eventually be coughed-up the trachea and swallowed into the esophagus. Once back in the intestines, Alaria marcianae accelerates its developmental process, achieves sexually reproductive adulthood (as sequential hermaphrodites), and deposits the next generation of eggs in the intestine. Thus the cycle comes full circle.

Conclusion: A Tenuous Analogy???

Hypothetically, the argument could be made that the reason why Alaria marcianae exhibits such an elaborate life cycle is that its success as a parasite has been rivaled with increased immunity in each sequential host. Deep in its evolutionary past, the parasite might have been able achieve a sexually mature adulthood by infecting just the snail. But, once the snail's immune response blocked the development of Alaria marcianae, its only option was to gain what little it could from the mollusk and to then seek resources in other organisms, like the frog. Likewise, in time the frog's body became incompatible with full maturation and, once again, the parasite was forced to expand its host range. The process repeated until one day the parasite infected the Florida Panther.

Essential to the success of the range expansion in Alaria marcianae was its ability to enter a state of arrested development. While in an arrested condition, the parasite will be tolerated by the host just long enough to gain strength for its continued transmission - its continued assault on other organisms. To ultimately defeat the parasite, and to prevent continued transmission of the pathogen, a host must become wholly intolerant of the parasite. Anything less and the disease will be spread.

This is analogous to creationists BECAUSE...

Davies, S. (2003). Developmental plasticity in schistosomes and other helminths International Journal for Parasitology, 33 (11), 1277-1284 DOI: 10.1016/S0020-7519(03)00161-9

Foster, G., Kinsella, J., Sheppard, B., & Cunningham, M. (2009). Transmammary Infection of Free-Ranging Florida Panther Neonates by Alaria marcianae (Trematoda: Diplostomatidae) Journal of Parasitology, 95 (1), 238-239 DOI: 10.1645/GE-1749.1

Franklin, James (2001). The Science of Conjecture: Evidence and Probability Before Pascal. Baltimore: Johns Hopkins University Press. p. 229. ISBN 0810865697.

Axolotl Photo by Pabloneco

Panther Photo by MrClean

Trematode Photo by Chris Blaner

Socrates Photo by Dithie

Sunday, January 3, 2010

My First Hate Email; I'm on the Big Pharma Payroll

Just got my very first hate mail -awesome!
In case anyone is curious, I didn't vote for Bush and I'm still waiting on my check from Big Pharma...


from: Patrick Russell

dateSun, Jan 3, 2010 at 12:42 PM
subjectre: autism article.....

hide details 12:42 PM (1 hour ago)

I'm sure by now you've most likely received tons of negative emails about your article, "Bad Science..."....I guess what's so annoying the most is how "scholarly" you try to come off and teach us about "vaccines" and "disease" and of course, "neuroinflammation (’neuro’ = brain; ‘inflammation’ = irritated)", what a revelation, jeez, I didn't know any of THIS!!! OMG!!!!....
Do you ever watch Giant Pharma drug commercials on TV by chance? Do you ever see the parts about all the possible negative side effects? Do you see how people are still taken in by all these nice ads and take this crap at the expense of their health....? Do you see the Legal ads on TV after it comes out that some of these nice Rx's have some rather adverse side effects that possibly might be remedied by a large class action law suit?...
Did you know that some of these nice vaccines that are given en masse to our children are created by Big Pharma? I'll bet you did.
I find it amusing that the "scary stuff" you talk about for solutions for ADHD are actually pretty tame next to the shit I saw in the last Chantix commercial I saw....
So let me understand this , you chastise those for attempting to find a remedy (though in your view "snake oil") for ADHD and it kinda seems like you either are unaware or want to totally ignore the link between Thimerosal used in many vaccines and ADHD...
funny how the CDC notes that there have been no new vaccines by the FDA since 2001 using Thimerosal even though no link has been established between Thimerosal and ADHD...though there are still immunizations routinely given to children WITH Thimerosal still including at no extra charge...
so I don't really get your pompous argument...
kinda seems like your protecting the status quo here which in my mind ain't too good...and poo pooing the notion of looking for solutions like a hyperberic chamber , shades of Michael Jackson!!!....yeah maybe not such a good idea.....maybe you got somethin' better? the alternative therapies for the majority of people with mental health issues are all fraught with some pretty nasty until something better is found, and I hope you never have to deal with your child who has ADHD, people are going to look for something because Big Pharma just ain't doing which Bad Science is worse? - That which is feed to us by travelling salesmen or conventional Big Pharma?...answer me that Mr. Science scholarly dude?

Did Big Pharma pay you to write your nifty little article or are you just naturally ignorant on this subject?
ig no rant, [ig-ner-uhnt]
1. lacking in knowledge or training; unlearned: an ignorant man.
2. lacking knowledge or information as to a particular subject or fact: ignorant of quantum physics.
3. uninformed; unaware.
4. due to or showing lack of knowledge or training: an ignorant statement.

Thanks and gosh I'll bet dollars to doughnuts your probably voted for George Bush in both elections...

Friday, January 1, 2010

Plants to People: the Swift Tempo of Spontaneous Mutation

Research published today in the journal Science serves to further calibrate the ticking clock of genetic mutation. By tediously analyzing the genomes from multiple generations of the plant Arabidopsis thaliana, scientists from the Max Planck Institute have shown that spontaneous mutations can arise rather frequently in the genome. Despite commonly held assumptions of minimally effectual rarity, the study demonstrates that the rate at which novel mutations occur have more than ample potency to drive evolution. Moreover, when considering the total population size of Arabidopsis, the tempo of mutation indicates that evolution likely proceeds much faster than previously suspected.

Although a single seed of Arabidopsis thaliana may only posses a single point mutation (i.e. a single base or ‘letter’ of DNA) relative to its parents, when multiplied by millions of individual plants over multiple generations, that single mutation quickly compounds to produce tens of new base pairs in only a few years time. The rate of genetic change revealed by the Max Planck study not only aids our understanding of how observed resistance to chemical herbicides rapidly evolves within the weedy plants combated by agriculture, its findings also point to possibly underestimated speeds of mutation in other organisms – like those of humans.

For example, back in September a team headed by Sanger scientists published work in which the rate of mutation in humans was estimated at around 1 mutation per 15 to 30 million nucleotides. Comparatively, this estimate translates to about 150 point mutations in every individual as measured against their parents; that’s a mutation tempo 100 times fold that of Arabidopsis thaliana.

Ossowski, S., Schneeberger, K., Lucas-Lledo, J., Warthmann, N., Clark, R., Shaw, R., Weigel, D., & Lynch, M. (2009). The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana Science, 327 (5961), 92-94 DOI: 10.1126/science.1180677

Xue, Y., Wang, Q., Long, Q., Ng, B., Swerdlow, H., Burton, J., Skuce, C., Taylor, R., Abdellah, Z., & Zhao, Y. (2009). Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree Current Biology, 19 (17), 1453-1457 DOI: 10.1016/j.cub.2009.07.032