Saturday, February 20, 2010

How Enticing Viruses Manipulate Animals

Viruses are ubiquitous to life; they infect everything from the smallest of bacterial cells to the largest of whales. And though these these miniscule pathogens often bring illness, they do not contaminate our bodies out of malice or spite, rather they do so out of necessity. Lacking the prerequisite internal anatomy for self-reproduction, viruses invade the cells of the living as a means of insuring their posterity. They splice their DNA (or RNA) into the nucleus of the host’s cells and effectively subvert its cellular mechanics to meet viral reproductive ends. Hijacked cells are re-programmed by the viruses and become factories dedicated to the task of manufacturing more viruses; viruses which ultimately move on to other victims. In addition to hacking programming codes for the building of replicates, viruses often include sub-routines, or additional programming hacks, that facilitate their journey to new hosts.

By undermining the normal life-processes of the host’s cells, viruses are detriments to health; however, more than just illness can remain in the wake of a virus’s biological sabotage. Sometimes included with the observable symptoms of an ailment are other characteristics of viral infection that serve to promote the spread of disease. The genes that viruses splice into a host cell’s mainframe can code for phenotypes that manipulate unwitting vectors into exposing themselves – purely for the benefit of the virus.

For example, recent work out of Penn State University has shown that a virus common to the squash group of plants does more than just hack a virus-building program into the cells of its vegetative victims - it also includes a program that attracts insects. The cucumber mosaic virus (CMV) infects plants with a gene that causes the plant to synthesize and release chemicals that draw-in hungry aphids. Normally, aphids use their capacity to chemically sense plants as a way to zero-in on healthy and nutritious foodstuffs essential to their survival. By manipulating the aphids’ chemo-sense, the virus’s genes trick the insects into locating and then taking a bite from the diseased leaves of an infected plant. Even though the plant may emit a ‘delicious smell,’ because it has been subjected to disease, it lacks the nutrients needed by the aphids. Luckily for the aphids, after just one bite their tasting-sense overrides their smelling-sense and they’ll bugger-off in search of better food. Unfortunately for other squash plants, the aphids now have a mouthful of CMV virus! Thus, the virus spreads.

The genes of the cucumber mosaic virus can integrate into the DNA of a plant, causing it to produce a chemical compound that manipulates aphids into volunteering their time and services as vectors of disease. This scenario isn’t unique to viruses, plants and insects. Other studies have shown that a similar pathogen to chemo-attractant dynamic exists between sandflies and hamsters; the parasitic protozoa Leishmania causes infected hamsters to produce chemicals that attract sandflies as vectors. And in humans, there is some evidence that Plasmodium falciparum causes more than just malaria, it also hijacks human bodies to produce chemicals that attract more mosquitoes.

Mauck, K., De Moraes, C., & Mescher, M. (2010). Deceptive chemical signals induced by a plant virus attract insect vectors to inferior hosts Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0907191107

Friday, February 19, 2010

Communicating Science: Blogs and the Media

As newspapers and cable news cut science coverage, where can the science-curious get reliable science and technology news? Ira Flatow and guests discuss how the Internet — including blogs and social media — is filling the coverage gap.

Great conversation - Listen to the Audio!

Go to the NPR webpage and click on Communicating Science in the Recent Episodes column: Here

From NPR's Science Friday

Saturday, February 13, 2010

How to Study Invasive Species, a Conservation and Ecological Imperative

The January edition of The American Midland Naturalist includes an essay by Daniel Simberloff (University of Tennessee) that bears the questioning title “Invasions of Plant Communities – More of the Same, Something Very Different, or Both?” As alluded to by the interrogative title, the central theme of the piece is whether or not the ecological characteristics displayed by invasive plant species are similar to those demonstrated by native plants during the natural succession of a vegetative community. In other words, do the strategies and tactics employed by invasives during the conquest of new habitats follow similar patterns of recruitment and regeneration as those exhibited by native plants in moving a community towards maturation? Or, in contrast to natural succession patterns, do invasive species have unique biological or demographic qualities that require a novel or specialized approach to studying their dynamics?

Daniel poses great questions, because, recognizing that we live in a world of mass travel and shifting climates, the study of invasive dynamics is of critical importance to the conservation of biodiversity – protecting natural habitats and native species. In addition to conservation, by researching the interplay of native and non-native species during the establishment of ecosystems we will undoubtedly gain a wealth of knowledge in regards to the feedbacks between evolution and ecology (i.e. how do those species lacking a shared co-evolutionary history come to achieve a stable strategy for survival?).

So, with that in mind, here’s my answer to Daniel’s question: Both!

Cause’ in a nutshell: Although invasive species will exhibit some life-history strategies comparable to those of plants from the newly invaded habitat (growth pattern, time to reproductive maturity, etc…) they will also be subject to environmental factors of a temporal nature that do not influence the natives (at least to the same extent).

Said differently, because the growth, reproductive habits and resource needs of an invasive likely mirror those of at least one native plant, the invasive could theoretically replace the native with little ill effect to the ecosystem; the invasive could fill the niche left void by the out-competed native plant without disrupting the energetics of the plant community as a whole. BUT, at the same time, a newly arrived invasive species may have a distinct advantage over a native transient because it is completely foreign to the ecosystem. For example, being unrecognized by its new environment the invasive may, for a period of time, be buffered against attack by herbivores, parasites and other stressors that may be actively reducing the fitness of the locals.

Similar to the above potential advantages, the invasive could also be subject to the detrimental affects of being an outsider - brought about by a lack of co-evolved pollinators, ect…

I would also argue that the above temporal effects associated with being a novel addition to an ecosystem, though only short-lived, can be magnified greatly by stochastic events. I would suggest this because – generally – variability in initial survival rates contributes greatly to ultimate establishment; often more so than reproductive strategy, which is subject to greater phylogenetic constraint (i.e. initial survival is more important than in choosing to produce many low-quality seeds when young, or to conserve energy and produce fewer higher-quality seeds when older).

Daniel’s essay is a great read and offers plenty of real-world case studies to emphasize his points; definitely check it out!

Simberloff, D. (2010). Invasions of Plant Communities – More of the Same, Something Very Different, or Both? The American Midland Naturalist, 163 (1), 220-233 DOI: 10.1674/0003-0031-163.1.220

Thursday, February 11, 2010

Online Recommendations for Darwin Day

It’s Darwin’s birthday!

Linked below are a few videos, a website and a paper that I plan to enjoy today in celebration of the greatest scientist to have ever lived!

Charles Darwin (Born February 12, 1809)

"Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved. "

A biographical sketch of Darwin by John van Wyhe (Darwin Online)

E.O. Wilson on ‘Darwin’s Four Great Books’ (FSU Mediasite)

Richard Dawkins on 'There is grandeur in this view of life' (YouTube)

Sean Carroll on ‘Endless Forms Most Beautiful’ (Google Video)

Paper (Free, PDF)
Spencer C. H. Barrett. Darwin's legacy: the forms, function and sexual diversity of flowers. Phil. Trans. R. Soc. B February 12, 2010 365:351-368; doi:10.1098/rstb.2009.0212

Wednesday, February 10, 2010

Is the Evolution Debate Over?

A recent blog post at National Public Radio’s Cosmos And Culture by astrophysicist Adam Frank has raised my hackles. The post, titled “The Evolution Debate Is Over; It's Time To Move Forward,” argues that “it's time to put the prejudices that drag down discussion between science and the domains of human spiritual endeavor aside.”

I disagree with Adam Frank and believe that a false impression has caused him to misdiagnose and underestimate a serious problem; as stated in a recent psychology publication (cited below):

“Moreover, academics are largely nonreligious, a pattern anticipated by the negative correlation between education and religiosity. Being exposed to like-minded colleagues, academics may form the false impression that religion is a rather rare and marginal phenomenon.”

Furthermore, let me express that I have doubts as to Adam’s sincerity in this stated endeavor. Most would agree that the best way to “move forward” from a subject is to talk about something else – a different topic altogether. Adam chose a different tactic. He placed religion on even ground with science under the premise that both can “be sources of wisdom” and represent "...the many ways humans encounter the True and the Real." This fallacious pairing of religion and science to me seems more conducive to forming an argument than to dispelling one. That aside, the ‘can’t we all get along’ position is a great sentiment, and makes sense in regards to personal communication, but when it comes determining what is real, and what is true in nature, giving equal standing to relativistic mumbo-jumbo and spiritualism is a nonsensical move for anyone that values what is true.

What is real? What is true?

I am typing this piece from the comfort of my couch in Tallahassee, Florida. To type and transmit the text of the post, I’m using a manufactured conglomerate of silicon and plastic that is more commonly referred to as a “laptop computer.” Rather than detailing what precisely a laptop computer is, I am going to assume that the readers of this article are familiar with the technology. Of course, this is a big assumption…

If, for example, you happen to be reading this as a recently arrived member of a primitive tribe from the Amazon Basin or some remote island in Indonesia, a ‘computer’ may be a foreign notion; as would the internet, electricity and many other miracles that I treat as commonplace. In fact, due to its relative rarity in your homeland, your native tongue may not even have the words to describe the luminous rock at which I now peck. Taking it a bit further, the laptop’s ability to conjure light in the absence of fire might even earn it a descriptor with a magical or spiritual connotation! However, regardless if you consider my laptop to be magical or mundane, its nature remains unaltered by our differing languages. It is real - it exists independently of our individual perceptions and doesn’t require faith. It can be held in your hands, measured, weighed and contemplated. The laptop maintains the same physical attributes rather it is in my living room, or it’s placed at a Dani village in New Guinea for use as a backlit fish-cleaning station and object of worship. A laptop is a laptop, is a laptop; thinking that it’s anything other than a laptop is factually incorrect and an artifact of ignorance or self-deception. Believing a laptop to be magic is not insightful, “deep” or quant, quite the opposite - it is something to be remedied through education.

From a philosophical view, does science prove that my laptop is real or that it truly exists? No, science has never, nor will it ever, ‘prove’ anything. After all, it is possible that my laptop is only a figment of my imagination (just as it’s possible that it has magic); but, just because anything is possible, it doesn’t follow that everything is equally likely. There is an ‘objective reality.’ Individual phenomena are labeled as true or un-true based on that objective reality as measured by observation, rationality, discourse and methodical inquiry – reality is measured by science.

Science isn’t in the business of determining certainty; instead it applies a probability based on all available evidence. For example, it is not absolutely certain that humans reproduce through sexual congress. But, based on independent experimentation the stork hypothesis seems unviable, and sex appears to be a statistically significant contributing factor to human pregnancy; thus, sexual reproduction is considered a fact by medical professionals around the world.

In strong contrast to science, religion places subjectivity above objectivity, it requires no evidence, and need not be measurable or even rational. Religion affirms that what may be true for one person need not be true for another. Faith is belief in the absence of, or despite of, evidence. Its tenets are as variable as the range of human personality. With religion all things are possible - even human pregnancy without sex.

Superstitious beliefs are used to affront more than just science education. They’re also used daily as justification for sexism, domestic abuse, racism, killing children, terrorism and numerous other immoral behaviors the world over. Rationalizing these behaviors as different ways of experiencing reality or as acceptable consequences of cultural relativism is just as fallacious as staging a debate between legitimate biologists and creationists – it just serves to validate ignorance.

In closing, let me contrast my perspective from that of Mr. Frank one last time. In his post he writes, “it is clear that at this particular moment in history, when we face such obvious and overwhelming dangers, it's time to put the prejudices that drag down discussion between science and the domains of human spiritual endeavor aside.”

Because I fully agree that there are “overwhelming dangers” in the world, I would declare that the very worst thing we could do would be to offer safe heaven (or, safe haven) to ignorance, superstition and irrationality. Our best hope to prevail over danger is to aggressively combat ignorance with the greatest prejudice we can muster. We should strive to eliminate ignorance from every political office and every schoolhouse. There are some things that should not be tolerated or compromsed.

Sedikides, C. (2009). Why Does Religiosity Persist? Personality and Social Psychology Review, 14 (1), 3-6 DOI: 10.1177/1088868309352323

Friday, February 5, 2010

How Science Suppresses the Sex Lives of Republicans

According to Utah State Representative Mike Noel, global climate change is a conspiracy theory. He insists that the whole idea of shifting climates was put together by the world’s biologists, climatologists and other scientists as an elaborate effort to control his sex life.

Speaking to climate change, Republican Mike Noel (at left) explained recently that, “This is absolutely, in my mind, in fact a conspiracy to limit population not only in this country but across the globe."

Being both a Republican and an enthusiast of the equestrian arts, Noel isn’t the type to quietly lie down and let the lefties fondle his reproductive liberties! To the contrary, he has been an outspoken proponent of Utah’s House Joint Resolution 12; a proposition that aims to stop the Environmental Protection Agency from establishing policies that reduce carbon dioxide. Noel’s good friend, Republican Kerry Gibson, sponsored Resolution 12 because… Well…

Well, because there’s a global conspiracy going on!

Here are a few proofs of the conspiracy as listed in House Joint Resolution 12:

1. “…Climategate, indicate[s] a well organized and ongoing effort to manipulate and incorporate "tricks" related to global temperature data in order to produce a global warming outcome…”

2. “…there has been a concerted effort by climate change alarmists to marginalize those in the scientific community who are skeptical of global warming by manipulating or pressuring peer-reviewed publications to keep contrary or competing scientific viewpoints and findings on global warming from being reviewed and published…”

3. “…the Intergovernmental Panel on Climate Change (IPCC), a blend of government officials and scientists, does no independent climate research but relies on global climate researchers”

4. “…the climate change "gravy train," estimated at more than $7 billion annually in federal government grants, may have influenced the climate research focus and findings that have produced a "scientific consensus" at research institutions and universities”

In addition to deducing the above listed ‘hard facts,’ Noel and Gibson also arranged for a hired gun to testify as an expert witness at Utah’s legislative proceedings. The hired gun was non other than the infamous Roy “shunned by the system” Spencer, a climatologist from Alabama whose work has been continuously rejected by the scientific community – yet further evidence of the conspiracy!

Checking Roy's facts during the proceedings was a group of 18 scientists from Brigham Young University. The group unanimously concluded that he was full of crap and even “patently false.” Accordingly, they put their findings into an open letter (available here), which each scientists signed. The letter was mailed to the State legislature in hopes of dissuading them from passing the resolution.

What was the result of this unified effort?

Republican chairman of the Utah farm group Randy Parker publicly demanded a formal apology from Brigham Young University. Parker in part stated that, "I guess the bottom line here, from my perspective, is that science is an open process of ongoing research and debate, and a group of scientists should not make these kinds of statements about another scientist…” (Note: I couldn’t agree more with this sentiment. The art of debating without debating is under-appreciated.)

So unfortunately, it looks as though Mike Noel, Kerry Gibson, and Randy Parker’s fight for breeding rights has paid-off for the republicans. House Joint Resolution 12 passed committee yesterday morning. The state of Utah is about to tell the Federal Government that climate change is nothing but a conspiracy theory, take the EPA regulations and shove 'em!

This should be great for tourism: Welcome to Utah – the State of Denial!

References & Credits:
Sovacool, B., & Brown, M. (2009). Scaling the policy response to climate change Policy and Society, 27 (4), 317-328 DOI: 10.1016/j.polsoc.2009.01.003

Chris Vanocur-ABC Channel 4

Judy Fahys- Salt Lake Tribune

Photo: Mike Noel

Wednesday, February 3, 2010

Rush Limbaugh: How the existence of god disproves climate change

Yesterday, Rush Limbaugh - a proponent of creationism and intelligent design - detailed to his radio listeners that because his god wouldn’t have created us humans with a capacity to destroy our own environment, he doesn’t ‘believe’ in climate change.

As scientific evidence of this assertion, he explained that plants need carbon dioxide to produce oxygen for humans; thus, there is no way that carbon dioxide in the atmosphere could be a harmful thing…

Who needs science, when you have such astute republicans! I wonder if Rush would be willing to be sealed in a carbon dioxide filled chamber with a lovely bouquet of flowers to prove his point?

I hereby rest my case against the fallacy that evolution progresses towards human perfection.

Tree Plantations as Biological Deserts

If I had a nickel for every time a biologist told me that tree plantations are nothing but “biological deserts” I’d be a rich man!

Well, at least a rich-er man anyway…

Industrial tree plantations can be ugly places for those with an eye for the natural beauty offered by mature and diverse forested ecosystems. Plantations are more-often-than-not composed of crowded, densely spaced trees, predominantly of the same species, age, size and condition. The soil surface on which these monocultures stand is heavily disturbed, rutted, bedded & rowed, and laden with fertilizers and herbicides. The compounding effect of these characters alters hydrology, impedes the advance of recruiting plants and strongly restricts use by wildlife.

When compared to pristine natural forests, plantations are like ‘biological deserts;’ but what about when they’re compared to a sprawling urban landscape or an agricultural pasture? What if the plantation’s location in the landscape serves as a corridor for wildlife between a developed residential area and more pristine habitat at a distance?

Plantations do offer important ecosystem services and can often maintain critical ecological functions…

Replace natural forests with plantations? – No, I’ll fight you to my last breath!

Replace agricultural pasture, or a sprawling city-scape with plantations? – I’ll help you plant the trees!

A recently published review by Alain Paquette and Christian Messier has just found its way into a stack of papers I keep as ammunition against the overly broad characterization of plantations as worthless biological deserts (a claim usually made by biostitutes hired to devalue a chunk of land for the financial gain of the owners).

Check it out:
Paquette, A., & Messier, C. (2010). The role of plantations in managing the world's forests in the Anthropocene Frontiers in Ecology and the Environment, 8 (1), 27-34 DOI: 10.1890/080116

Tuesday, February 2, 2010

Buffalos and Birds: Flightless Wings from the KT Extinction to Darwin’s Dinner Plate

Although not an aficionado of fine cuisine by any measure, through persistence and voluminous sampling I have refined my palate to appreciate the delicate subtleties of several dishes. And, while I would admittedly be lost at a wine tasting, when it comes to cheeseburgers, pizza or Buffalo wings, I consider myself a gourmet of the highest standard. In calibrating my sophisticated taste buds, Friday night has been officially dubbed as ‘wing night’ with consumption of the deep-fried, cayenne laden morsels a matter of established ritual. This past Friday as my fiancé and I were blindly obliging our delectable dogma we were taken aback when our usual wing-purveyor served such diminutive wings that we jested they must have been taken from hummingbirds or from an assuredly flightless species. Luckily, the chicken wings’ lack of robustness was mitigated by an ice cold pitcher of beer and a nerd-ish banter about the evolutionary history of flightless birds and their place at the dinner tables long passed.

The current scientific “consensus” is that the vertebrate group we now refer to as birds had origins in the late Jurassic Period more than 145-million years ago. Having evolved from bipedal dinosaurs belonging to the theropod clade into an Archaeopteryx-type winged flyer, birds had conquered the air long before the infamous mass extinction event at the end of the Cretaceous Period. Often referred to as the ‘KT Extinction Event,’ a massive environmental upheaval approximately 65-million years ago wiped-out the majority of animal life on the planet, including what at that time was the dominant vertebrate group, the non-avian dinosaurs. The exact cause of the KT Extinction is still a topic for debate with asteroid impacts and volcanic activity viewed as the likely leading contributors, but what is absolutely certain is that the resulting mayhem collapsed the Earth’s ecosystems into complete chaos. Birds, the only members of the dino-clan to survive the cataclysm, emerged from the ruin to occupy a world in disarray but non-the-less rife with newly revealed opportunity.

In addition to leaving behind a ravaged planet, the KT Extinction also instigated the abandonment of numerous ecosystems that had previously been ruled over by the dinosaurs during their Mesozoic habitation. Though left in shambles, these ecosystems had also been vacated by many of the predators and competitors that initially pushed the theropods to the sky during the Jurassic Period. In the absence of rivalry, birds had been granted access to ‘open ecosystems’ and presented with the option to undertake a second conquest of the land. Several species of birds seized on the prospect of life on terra firma and through evolutionary time traded their wings for the physiology of sure-footedness. One modern grouping of these ground dwelling, flightless dinosaurs is called the ‘ratites’ and boasts the South American rheas among its extant members.

There are two species of rhea; the ‘Greater rhea and the ‘Darwin’s rhea,’ which is also known as the ‘Lesser rhea.’ Despite their flightless status, both the Greater (Rhea americana) and the Darwin’s (Rhea pennata) display wings as identifying anatomical features; however, due to the lack of a ‘keeled’ sternum to anchor to their already reduced breast muscles, as well as the presence of a diminished wishbone (furcula) to provide skeletal support, these South American natives are bound to a grounded existence. As an alternative to employment in the aviation industry, the process of natural selection has resulted in enhanced legs that have been optimized for a life on the run. While rhea’s legs have undergone adaptation for speed and agility, they have not yet evolved the ability to avoid entanglement by humans, or for that matter, to steer clear of the occasional dinner table.

On a more historical time scale, one of the most widely used implements of rhea leg entanglement were hunting weapons called ‘bolas.’ Bolas, derived from the Spanish word for ‘ball,’ refers to a weapon constructed with lengths of rope or braided cord with a weighted ‘ball’ attached on each end. The bolas are swung to build-up momentum and then thrown at the legs of fleeing game, tended cattle, or - more to the topic - a running rhea. The momentum of the weighted ends entangles the targeted animal by wrapping the adjoining ropes around its legs; this causes the animal to fall to the ground immobilized, or at least to be sufficiently slowed as to permit dispatch by other means (i.e. gun, knife or club).
Bolas are favorite tools of the South American ‘gauchos,’ which hold a societal role not unlike that of the North American cowboy; they work as ranch hands, hunters, and when the chance presents itself, as wilderness guides. In the year 1833 several South American gouchos were working as rhea-wrangling wilderness guides at the behest of a touring young naturalist from England. In August of that year, the naturalist Charles Darwin documented in his journal a humorous set of circumstances that lead to the dinner table identification of a new species of rhea – the bird now known as Darwin’s rhea.

Rendering of Darwin's rhea by John Gould.

Gould also identified 'Darwin's finches.'

While traversing South America during the voyage of the HMS Beagle, Darwin had observed Greater Rheas in the wild on many occasions. In fact, with the aid of a few gaucho guided bolas, the abundant Greater Rheas had become a mainstay of his diet.

In conversing with the gauchos in regards to habits of these ratites, Darwin had learned that there was a second variety of rhea roaming the continent. This second type, which the gauchos called ‘Avestruz Petise’ was reportedly a smaller version of the Greater and exhibited a darker plumage and skittishness behavior that made it readily distinguishable from the ones he had seen in the wild. Unfortunately, following Darwin’s discussion neither he nor the gauchos were able to collect a specimen of this “lesser” flightless bird for formal description, and in time it faded from Darwin’s attention. The lesser rhea went unspoken of until finally one evening Darwin was enjoying a quiet dinner with Mr. Marten, the Beagle’s contracted artist, who had shot and killed what they believed was a medium sized Greater rhea. As it turned out, the fully cooked ‘medium rhea’ that graced their plates as entrée on closer examination turned-out to be something else entirely; as Darwin himself detailed on pages 108 and 109 of Voyages of the Adventure and Beagle, Volume III:

“When at Port Desire, in Patagonia, Mr. Martens shot [a rhea]; and I looked at it, forgetting at the moment, in the most unaccountable manner, the whole subject of the Petises, and thought it was a two-third grown one of the common sort. The bird was cooked and eaten before my memory returned.”

Fortunately not all was lost. Recognizing the blunder, Darwin quickly gathered the table scraps and remaining carcass from the garbage. He continued,

“…the head, neck, legs, wings, many of the larger feathers, and a large part of the skin, had been preserved. From these a very nearly perfect specimen has been put together, and is now exhibited in the museum of the Zoological Society.”

Phillips, M., Gibb, G., Crimp, E., & Penny, D. (2009). Tinamous and Moa Flock Together: Mitochondrial Genome Sequence Analysis Reveals Independent Losses of Flight among Ratites Systematic Biology, 59 (1), 90-107 DOI: 10.1093/sysbio/syp079

Image from Wikipedia - Public Domain