September 30, 2006

The Plight [Blight] of the American Chestnut

Paleoecologist Margaret Davis' work has become legend among ecologists. She analyzed layer upon layer of pollen buried in lake sediments in the Appalachian Mountains to determine the natural history of trees in the area.

She found an interesting pattern:

Spruce (Picea) pollen dominated the area 12,000 years ago.
Beech (specifically Fagus grandifolia) pollen appears 8,000 years ago.
The American Chestnut pollen did not show up in the sediment record until 2,000 years ago; it quickly vanished around 1920.

Cryphonectria parasitica, a type of blight (type of fungus), was transported to North America on the Chinese Chestnut, which had evolved defenses against the blight. The American Chestnut had no such defenses, and has been all but obliterated.

The blight usually only affects the trees when they reach a certain growth point, leaving the roots of the tree intact. Essentially, it attacks the sporophyte (spore bearing generation) of the organism when it reaches a certain height above ground.

This will be an interesting phenomenon for evolutionary biologists to observe over the centuries. How will the chestnut adapt and evolve to avoid the detriment of infection by Cryphonectria? Is there any way that ecologists/dendrologists can assist the population in a natural, evolutionary recovery?

There were once 3 - 4 billion indigenous chestnut trees in NA, 25% of which were concentrated in the Appalachians. Today that number is scant comparatively, though there are several organizations that are specifically supporting the chestnut, including The American Chestnut Foundation and The American Chestnut Cooperators' Foundation. Both organizations have great information at their websites (you can even buy seeds to plant with instructions on protecting the tree from infection).

Consequently, Davis continued her research across North America, and found evidence that the Appalachians were dominated by conifers during the last glaciation 18,000 years ago. It was a very different world not so long ago.

September 29, 2006

Update on the LGBT Hunger Striker

The LGBT hunger striker at FSU that I discussed here, here and here has officially ended his strike because of health risks.


So much for heroism. I hope that he has found that there are safer venues for getting attention.

September 27, 2006

TVG Print: The Devil Comes 'a Calling

I have been a huge fan of Isaac Asimov’s work since I was a teenager. For those who don’t know who I’m talking about, Asimov was a biochemist and a prolific author who started his career writing for his school newspaper (the man wrote professionally on just about everything starting in the 1940’s, from the Bible and politics to science and science fiction, over 400 books in his lifetime). He is considered one of the great popularizers of science and one of the most legendary science fiction writers.

Asimov is almost single-handedly responsible for all of the science fiction that we read in books and watch in the movie theaters, especially the works of fiction dealing with robots. I, Robot was the first of these books, exploring a world where man constructed robots that abided by three basic rules of functioning, the Three Laws of Robotics:

-A robot may not injure a human being, or, through inaction, allow a human being to come to harm.

-A robot must obey the orders given it by human beings except where such orders would conflict with the First Law.

-A robot must protect its own existence as long as such protection does not conflict with the First or Second Law.

Asimov fleshed out this future world and crafted stories that dealt with the ins and outs of these laws, which sometimes meant the logical circumvention of them.

At this point, you’re probably wondering what exactly this has to do with the myth of the mad scientist.

Two years ago, Twentieth Century Fox released a film “based loosely” on Asimov’s I, Robot. If by based loosely they meant only the name of the film and the book is identical, I suppose that fits.

The novel I, Robot had a purpose; one much deeper than might be comprehended at first glance. It was written after Asimov—a sci-fi reader as much as writer—had grown tired of the mad Dr. Frankenstein stories that had become fashionable after the scientific horrors of World War I. Human plays God, God punishes human. Human creations turn on creator, usually in the form of robots this time around. Asimov believed in a world where man had the power to control technology utterly, without any divine power struggle or demon contracts (modernism). I, Robot the novel was the creative construction of this world.

Never, never was one of my robots to turn stupidly on his creator,” says Asimov in a foreword to Eight Stories from the Rest of the Robots. “My robots were machines designed by engineers, not pseudo-men created by blasphemers.”

I, Robot the movie was the direct antithesis of the modernist world. What happened in the film? Human creates machine. Machine turns on human, trying to control him/her. The movie was basically another rehash of the Frankenstein story.

Our pop culture in America is rife with these stories. In The Matrix, the creations of humans betray their creators, causing a great rift that destroyed the world and plunged humans into a post-modernist nightmare. The Terminator, sent by his human-hating robo-superiors, travels through time to destroy a temporal cog in the human lineage during another such war between creator and creation. In Star Wars, Darth Vader is Luke Skywalker’s machine-more-than-man (twisted and evil) shadow self. Skywalker must resist the Dark Side that Vader has embraced so easily through his lack of physical being, his disconnect with life.

These stories are dubbed “Faustian,” which refers to a very old story of a man playing God (Faust) and selling his soul to the devil (Mephistopheles) for power. They are archetypal, stories tied deep to our psyche and our inherent fear of the power of science, and therefore the power of knowledge.

They are also unfounded and philosophically unsound.

As a society we are frightened of science and the scientist because of what he/she might uncover. It is okay when science finds new ways to produce an abundance of food or more efficient fuels or time saving appliances. Knowledge is simultaneously our friend and bitter enemy, perfectly illustrated by the Biblical story of the Garden of Eden.

Adam and Eve were evicted from the Garden not because they disobeyed God, but because they could not exist in a place that they knew did not exist. The knowledge from the apple showed them the world as it was, and they could no longer live in ignorance. Once you know something, you can never un-know it.

This inherent desire for ignorance in our culture is not justifiable. Stem cell research, cloning and gene therapy are the Faustian blasphemies of modern times, but the scientist investigating the benefits of such research is not mad Dr. Frankenstein. She/he is a member of a progressive scientific community, seeking to know human beings inside and out, and to use that knowledge to our benefit.

It comes down to this: Knowledge can be dangerous, especially if it is in the wrong hands, but what are the alternatives? Asimov can only answer with more questions:

“[Is] the response to be a retreat from knowledge? Are we prepared to […] return to the ape and forfeit the very essence of humanity? Or is knowledge to be used as itself a barrier against the danger it brings?”

Originally published here.

September 26, 2006

BBC Interview with Richard Dawkins

Dawkins' The God Delusion just came out recently, and I tried to find it at Walden Books in our tiny mall outside of Frostburg. It is ranked as the #1 bestseller in England and the #12 bestseller in America so I [stupidly] thought it would be in plain sight in this conservative Christian Republican area.

Surprise, surprise. They didn't even have a copy in stock.

So, I settled for this interview from the BBC, and several excerpts from their website. I really don't have time to read it anyway with all the tests this week (ecology today, physics tomorrow). Enjoy.

Off to physics lab...

September 25, 2006

Clearing the Forest to Spite Wildlife

Did anyone see this story from the AP?

BOILING SPRING LAKES, N.C., Sept. 23 (AP) — Over the past six months, landowners here have been clear-cutting thousands of trees to keep them from becoming homes for the endangered red-cockaded woodpecker.

The chain saws started in February, when the federal Fish and Wildlife Service put Boiling Spring Lakes on notice that rapid development threatened to squeeze out the woodpecker.

The agency issued a map marking 15 active woodpecker “clusters,” and announced it was working on a new one that could potentially designate whole neighborhoods of this town in southeastern North Carolina as protected habitat, subject to more-stringent building restrictions.

Hoping to beat the mapmakers, landowners swarmed City Hall to apply for lot-clearing permits. Treeless land, after all, would not need to be set aside for woodpeckers. Since February, the city has issued 368 logging permits, a vast majority without accompanying building permits.

The results can be seen all over town. Along the roadsides, scattered brown bark is all that is left of pine stands. Mayor Joan Kinney has watched with dismay as waterfront lots across from her home on Big Lake have been stripped down to sandy wasteland.

This kind of stuff makes my blood boil. Instead of waiting for the details surrounding the legislation (not to mention understanding the need for preserving these birds) landowners wanted to spite the environmentalists and so jumped the gun, assuming that the mapping would completely take away their rights to own land.

But this isn't the first time that endangered species listings have backfired.

Back in 2003, there was a study published in Conservation Biology about the endangered Preble's jumping mouse (excerpt from Conservation in Practice):

The researchers surveyed 379 landowners to find out how they responded to the 1998 threatened listing of the Preble’s jumping mouse, which lives in riparian areas in parts of Colorado and Wyoming. Much of the mouse’s known habitat is on private land.

While some landowners worked to help the listed mouse, others worked to discourage it from living on their property. The survey showed that a quarter of the land in the study had been managed to improve the mouse’s habitat, but another quarter had been managed to keep the mouse from living there. Landowners were more likely to have improved the mouse’s habitat if they had received information from conservation organizations. Landowners who depended on agriculture for their livelihoods were more likely to have destroyed the mouse’s habitat.

The survey also showed that most (56 percent) of the landowners would not allow a biological survey to determine the abundance and distribution of the mouse on their land--information that is essential for developing and fine-tuning conservation plans.

The University of Michigan research suggests that listing the mouse may have done more to harm than to help it. The researchers suggest better approaches could include letting landowners know how conserving the mouse’s habitat can benefit them; reimbursing landowners for the cost of fencing to keep livestock away from riparian areas, thus protecting the habitat; and reducing landowners’ fears of regulation by including them early in the conservation decision-making process.

These private landowners should be the main focus of educational environmental efforts. Since it has been estimated that 90% of the endangered animals' natural habitats is on privately owned land, attention must be focused on these landowners in order to make headway in preserving these animals.

September 22, 2006

Extremism and Sacrifice

As I mentioned in a previous post, we have a student on campus who has not eaten in almost two weeks. He has been on hunger strike to fight for LGBT rights.

I think he's addressing the issue in a way that the neo-cons want and expect. They can ridicule his impulsivity and dramatics, demeaning both his personal crusade (as an attention seeker) and the umbrella cause, gay rights.

Before I continue, I want to make it abundantly clear that I think it is atrocious that we have gone this long without granting all American citizens the full extent of their rights and privileges.

Don't get me wrong, I think Correa is a nice guy, and his intentions are in the right place. I just hope he comes to his senses before he is seriously harmed. Catabolysis is probably gripping his system by now, breaking down lean muscle tissue instead of fat.

From the Merck Manual:

In adult volunteers who fasted for 30 to 40 days, weight loss was marked (25% of initial weight), metabolic rate decreased, and the rate and amount of tissue protein breakdown decreased by about 30%. In more prolonged starvation, weight loss may reach 50% in adults and possibly more in children. Loss of organ weight is greatest in the liver and intestine, moderate in the heart and kidneys, and least in the nervous system. Emaciation is most obvious in areas where prominent fat depots normally exist. Muscle mass shrinks and bones protrude. The skin becomes thin, dry, inelastic, pale, and cold. The hair is dry and sparse and falls out easily.

Most body systems are affected. Achlorhydria and diarrhea are common. Heart size and cardiac output are reduced; the pulse slows and blood pressure falls. Respiratory rate and vital capacity decrease. The main endocrine disturbance is gonadal atrophy with loss of libido in men and women and amenorrhea in women. Intellect remains clear, but apathy and irritability are common. The patient feels weak. Work capacity is diminished because of muscle destruction and, eventually, is worsened by cardiorespiratory failure. The anemia is usually mild, normochromic, and normocytic. Reduction in body temperature frequently contributes to death. In famine edema, serum proteins are usually normal, but loss of fat and muscle results in increased extracellular water, low tissue tension, and inelastic skin. Cell-mediated immunity is compromised, and wound healing is impaired.

As we noted before, metabolism's function in endotherms is to keep the body's temperature at a level where enzyme activity is maximized. On top of the lack of vitamins and nutrients, Correa's body temperature will slowly decrease over time, limiting the ability of chemical reactions to take place in his body. His systems are already without raw materials; within weeks, they will be robbed of adequate energy as well.

Correa is going about this in the wrong way. His extremism and "sacrifice" will only attract negative attention.

He could work through the system and through non-governmental organizations (NGOs), helping to organize protests and conventions, promoting education and tolerance through positive measures. This is the only way that the LGBT community will make strides in America.

Instead of destroying his body for what he believes, he should be taking measures to make sure he's around to keep fighting with all of his wit and intelligence, influencing people with thoughts and ideas, not threats and melodrama.

But such is the mentality of the young and the revolutionary. They are selfish (not selfless, as they would like to appear), impulsive and egocentric. In an unstable system, they have a usefulness in pushing that system beyond the control of itself; in a relatively stable society, like ours, it is a ego-feeding media parade more than anything else. Pull a stunt and the media will jump.

I did. I messaged him to set up an interview for the sake of campus news. So I can see where the journalist's intentions are good, but the end result is independent of intent, and becomes merely a vehicle for propaganda.

Ultimately, I wonder if he really knows what it means to die for an idea, for a cause. Is he prepared to leave this world at 19, never to know what changes his patience and determination could have made in society?

September 21, 2006

The Scare Tactics of "Save Our Students"

I've talked about Campus Crusade for Christ in the past, and their promotion of ID. (I found out recently that CCC does have a chapter here at FSU. They are incorporated into a group called "On Fire for Christ, whose goal is to spread the word of God "by any means necessary. Sounds welcoming, eh?)

I stumbled across another one of these fundie groups, S.O.S. - Save Our Students.

At this point I'm sure you can guess what the deal is, but I'll let them tell you:

Daily, on college campuses, this country’s future presidents, pastors, professionals, are spoon-fed the strychnine of satan’s soul-damning, Christ-denying, lies, beneath the sugar-coated guise of “science” and “secular humanism.”

Daily, on college campuses, this country’s future policy makers, parents, are injected with insidious ideologies, inoculating them to sodomy, same-sex marriage, sex outside of marriage, abortion, under the demonic deception denoted “diversity” and “tolerance.”

Something must be done to stem this satanic floodtide of lies threatening to drown and damn this country’s youth!

On Monday, September 4, 2006, Michael, Tamika, and Paul Venyah, and Chris Lemieux, of Soulwinners Ministries International, will embark upon an 8 month, 15,600 mile, 27 state, 64 campus, Gospel-preaching trek across the northern, central, and southern United States, entitled “Save Our Students” (S.O.S.). The purpose of this itineration is to present the uncompromised Truth of God’s Word, the Bible, through preaching repentance toward God, and faith toward our Lord Jesus Christ, to the college students of this nation, blinded by satan’s lies.

They also have great catch phrases on the website, like "Hip-Hop Nation: Child of God or Child of the Devil!" and "Repent or Perish!" and "Soon You Will Die!" You know, good Christian values.

I'm living a lie. "Science" has me within its satanic grasp.

My Poor, Poor Impatiens

Every year my fiancé and I buy New Guinea Impatiens for our balconey. They always grow nice and full, and bloom all throughout the summer. This year however, we had a few unwanted visitors, mostly due to the relatively hot summer: Papillo japonica, the Japanese Beetle. This is the first year I've seen them up here...

Here's to you, New Guineas. I will always remember the good times...

September 20, 2006

Evolution and Hunger Strikes: New Articles/Podcast Up at The Bottom Line Online

Hey all, I have two new articles and a podcast up at TBLO.

My column this week addreses some of the common myths associated with evolution (just to get everyone on the same page for the next year), but the best part about it was constructing this cladogram of the hominids:

The podcast is a primer on natural selection. It was a lot of fun to do, and I hope I can turn some of my earlier posts here into future podcasts (like the spiders/bugs posts, and perhaps the red panda).

This week I also covered the story of a student so fed up with the treatment of the LGBT community by the government/media, that he went on hunger strike. As of today, he is 10 days into it:

Ron Correa declared a hunger strike early in the morning of Sunday, September 10. Correa had had enough. He was tired of the rights of lesbian, gay, bisexual and transgender individuals being pushed aside by the media and the government.

Correa will not eat again until sufficient media attention is given to the inequalities between heterosexuals and the LGBT community.

There have been extensive studies on the effects of starvation on the human body. Once the body has been deprived of calories for an extended period, it falls into a state of catabolysis, where it begins to break down muscle tissue for nutrients, leading to a serious reduction of lean body mass, and in eight to 12 weeks, death.

A recent study on hunger striking determined that the psychological effects of hunger striking itself, such as impaired decision making skills and unusually high levels of impulsivity and aggression, can actually prolong the strike unnecessarily.

Correa did not consult a doctor before he made his decision.

"Actually, one of my friends is a nurse," says Correa. "She tried to talk me out of it. Basically, she told me to drink lots of water and take vitamins."

Correa is not taking vitamins. I looked at several studies on both starvation and hunger strikes in particular before publishing the article, which only confirmed my suspicions about the long term physical and psychological effects of starving oneself.

Correa's strike is foolish on several levels, which I will specifically address later today or tomorrow morning. I also have a bit to say about youth, idealism and arrogance. I'll explain later.

September 18, 2006

Binturongs vs. TCM

The binturong is sadly a prime target for poachers due to the continued use of traditional medicine (TCM) in China.

According to Mindy Stinner, executive director of the Conservator's Center,
They are endangered in large part because rainforest locals in Southeast Asia, who used to hunt them only for food, have found an ever-increasing profit in selling them to those who promote the Chinese medicine trade. Their penis bones, ingested as a powder or cooked into food, are said to help men stay virile and to help produce male children. Also threatening to their numbers in the wild is a loss of habitat due to deforestation. At the open markets in Laos they cost around the equivalent of three US dollars. As of 1998, in the exotic pet trade in the US, a young, breedable, healthy individual runs $1500-2500.

Bints are also poached for their scent glands, for use in perfumes. They are being run out of a few areas, recognized by the IUCN. Luckily, there are a few sound conservation efforts in place to protect the animal, including the Thai Society for the Conservation of Wild Animals, the Minnesota Zoo, and WCS India.

Photo by topend.

Binturong Videos!

Here's one embedded, the rest are links. They're so cool!

Another from Youtube (couldn't embed).

Clips from the Minnesota Zoo:

Binturong climbing tree & binturong close up

News clips:

CBS 2 Chicago & KFMB San Diego

Sadly, no webcams... but one can hope for the future. If you find any more out there, please let me know!

September 17, 2006

My Music Binge

The new Mars Volta, Amputechture finally came out this week, which gives me an excuse to show you the video below, where Cedric Bixler (the front man of the Mars Volta) chastises the crowd for their evil ways. It makes me want to hug the guy.

How do you mosh to prog rock? Oh well.

I have bought a torrent of other great music recently:

Redeemer - Norma Jean
Decomposer - The Matches
Broken Boy Soldiers - The Raconteurs (lo fi music = lo fi website)
A Lesson in Crime - Tokyo Police Club
Bitter Tea & Gallowsbird's Peak - The Fiery Furnaces
He Poos Clouds - Final Fantasy. It's not the video game series, I assure you; worth a listen for everyone. In fact, here's a clip:

and finally, Black Holes and Revelations - Muse

New Deftones, Candiria and Blood Brothers due out soon! Woo!

September 15, 2006

Mendel's Garden #6: Straight Outta Compton Edition

Welcome all to Mendel's Garden #6: Straight Outta Compton Edition!

The Compton Science Center, Frostburg State University

For the unindoctrinated, Mendel's Garden is a traveling sample of genetics blogging from all over the 'sphere. This is edition will be short but especially sweet, so I thought I would take you all through the place where I spend much of my time: the Compton Science Center at Frostburg State University.

CSC is the entire reason I decided to attend FSU. It had just been built the year that I decided to transfer. It cost the state just under $27 million, and was worth every penny. I mean, just look at our pendulum:

Enough of my blathering. Strap on your safety goggles and snap your purple nitrile gloves; it’s time to get to the gene candy.

Let’s start in the most obvious of places: genetics lab.

Everyone knows that sex is always on a college student’s mind, especially we biology majors. RPM from evolgen indulges us with a lucid review of the varied sex determining chromosomes in the animal kingdom. It’s a run through the alphabet: XX/XY, ZZ/ZW and TSD.

Paul Decelles of The force that through... sends his students on an NCBI scavenger hunt! There are 51 amino acid in human insulin, so why were the records they pulled up showing 110 residues? His answer takes us on a journey through the data-rich realm of bioinformatics, unearthing evolutionary precursors, the role of cDNA and c-peptide's reduction of apoptosis in pancreatic islet cells.

Down the hall, Chris Patil of Ouroboros awaits us through the magnetically propped door of Cell Bio. His post “p16 vs p16: Preventing cancer, limiting self-renewal” addresses the evolutionary tradeoffs of cell renewal and the development of cancer. Are we truly damned if we do, and damned if we don’t?

After a conversation with a friend debating the sexual orientation of Lt. Commander Data runs long, it dawns on me: we’re late for Animal Phys!

Slink through the back door and grab a seat. PZ Myers of Pharyngula explores the supposed controversy of a recent article published in PLoS Biology providing support for the common ancestry of vertebrates and arthropods through a common set of dorso-ventral determining molecules. This is evo-devo at its finest, folks.

After reading What We Believe But Cannot Prove, a compendium of articles by the contributors over at Edge, Cow from Tethered Cow Ahead applies his knowledge of imagery through mathematical constructs to mutation, asserting five predictions of future scientific findings.

Reluctantly, I plod up to the front of the class, Powerpoint remote in hand, and present my recent post here at The Voltage Gate reviewing the recent molecular placement of the binturong (Arctictis binturong) and the rest of the Viverrids sharing a common ancestor with the extant African palm civet (once a part of Viverridae) based on genetic analyses.

Ah, Microbiology. There’s truly nothing more refreshing than the aroma of hot autoclaves and sexy cultured bacteria in the morning. Keep your Roccal close as we listen in on Coturnix from A Blog Around the Clock. There is evidence to support that endogenous retroviruses (ERVs) are necessary for sheep to become pregnant, evidence that ultimately supports the role played by ERVs in the evolution of the placenta.

After meeting Jen from FSS! (Fighting for Science*; also the author of Studying Biology and Environmental Science) in the Compton greenhouse, she details new evidence for the effectiveness of biodiversity corridors in maintaining genetic diversity within plant populations.

That wraps up this Straight Outta Compton edition of Mendel's Garden. Thanks to the staff and faculty of CSC for ignoring the weird bearded guy snapping photos of room numbers, to Paul Decelles (The Force that Through...) and to all the contributors this time around. If you would like to host the next Mendel's Garden, contact Paul via his Blogcarnival page.

*Shameless plug: FFS! is has a roster of eight science bloggers in varied fields – biology, environmental science, meteorology, physics and astronomy - all sharing the passion for defending and explaining science. I have been blogging there as well for over a month now, and love the thoughtful environment it supports. Props to Eric Ingram for setting it up.

September 14, 2006

New Article Up at The Bottom Line Online

I almost forgot; new edition of The Bottom Line & a new column:

Don't be fooled. There is a political agenda at work here. Behe and Wells do not consider the possibility of an extraterrestrial designer; they mean, of course, the Christian God, which makes them no more than "sophisticated creationists."


I do not believe that all Christians have an insidious plan in place to destroy our public education, but I do believe that they are being manipulated by people who understand their true devotion to the Christian faith and seek to exploit that devotion for the purpose of gaining political power.

That's why ID is dangerous. It is just another power play.

Evolution is not the cause of our moral decline in this country. Like any other issue, it is a combination of factors usually stemming from general societal shifts and a lack of communication between social classes.

Defeating evolution in the classrooms will not make our children any more respectful or pious. Defeating the negative pressures placed upon them by the media and their peers just might.

Something for the Skeptics

Well, one anti-human-induced global warming claim down, a million to go:

Known variations in the sun's total energy output cannot explain recent global warming, say researchers who have reviewed the existing evidence. The judgment, which appears in the September 14 Nature, casts doubt on the claims of some global warming skeptics who have argued that long-term changes in solar output, or luminosity, might be driving the current climate pattern.

*Update: Another one down, 999,999 to go...

September 13, 2006

Tangled Bank #62 Is Up and It's Hairy!

Tangled Bank #62 is up at the Hairy Museum of Natural History, complete with unique little thumbnails for each post, drawn by the host specifically for TB #62.

HMNH is a great resource for any natural history buff. They even sell t-shirts.

September 12, 2006

"Science, Religion and Intelligent Design" - A Review

The forum went well this evening. There was about a 50/50 split between students and faculty (with a sprinkle of older people from the area) but the crowd was diverse; there were science-minded people representing the physics, psychology and biology departments there, but also professors and students from foreign language and other fields.

Raesly started off by describing the principles of the scientific method, but also went beyond the typical observation-hypothesis-experiment-conclusion bit by addressing the importance of different ideas in science. He made clear that "facts" were not necessarily the most important ideas in science - gravity's grip on a pen or the distribution of certain animals - but that scientists seek to unify these facts into comprehensive, applicable principles; in other words, theory.

"Scientists are doing a poor job of teaching people how science is done," said Raesly.

That said, he made clear that the evolution of the eye was possible, by giving a natural history of sorts of the origin of eye proteins.

"The proteins in the eye were not originally designed to be eye proteins," he said. The proteins of the lens were once used in other areas (heat shock proteins, for example), useful in their own right, but became useful to organisms like humans by the processes of evolution.

Rev. Bill Pinches was up next, an eloquent Presbyterian minister from a local church (with several degrees in theology), explaining the differences between theology and philosophy, and trying to place ID in one of those categories. His interpretation of the Bible was refreshing, making it clear that the Bible (biblia, library) is basically a compendium of cultural literature and poetry, not a history or science book.

Pinches also pondered whether or not the conclusions of ID were logical in any sense. To assume that something was designed merely because one does not understand its complexities, he stated, is a false conclusion. He appropriately condemned ID as a "god of the gaps" argument, fearing the repercussions of embracing such a standpoint, and watching the "incredible shrinking God" result.

Both Pinches and Raesly feel that ID is not science (obviously), and should be sequestered primarily to philosophical discussion.

Then the questions began.

Raesly was criticized by a colleague briefly who had a problem with the complete separation of the domains of knowledge (even beauty and morals/values) inherent in Raesly's discussion.

"Can't beauty be explained as phenotypic expression subject to selection?" said the professor. He also questioned the evolutionary significance of morality.

I think Raesly was seeking simplicity in his argument. Of course science can analyze the evolutionary benefits of morality and the physical results of genetic selection (human beauty), but for the sake of clarification, some of these issues can be skipped (it was only a two hour discussion, after all). The professor had a point, though.

Other questions were raised, some about entropy (boring!), others about the validity of the actual arguments (both ID and science's response).

I think the most interesting thing about the forum was the tendency for student responses to begin with "I believe in..." instead of addressing some of the more relevant issues presented in the talk. But at least they were there.

My column on ID comes out tomorrow, and I'll have a link to it and an excerpt.

"Science, Religion and Intelligent Design" Forum Tonight at FSU

The forum begins at 7:30 p.m. and is hosted by Dr. Richard Raesly and Rev. Bill Pinches. You can expect a full post here by midnight EST.

I don't really expect there to be any fireworks, but I'll fill you all in later.

September 11, 2006

Confronting the Estrogenic Effect

I am truly half the man my grandfather was.

I wouldn't laugh, gentlemen. You can't hold a candle to pop-pop's sperm count either.

Males - specifically the Y chromosomes that make men, well, men - are under attack. The average sperm count of contemporary human men compared to their grandfathers is dramatically less, approaching the half mark.

Why? Blame it on the estrogenic effect.

Remember that crazy 1980's trend called pollution? It may be time to revisit. In recent years, the mainstream media has all but ignored it.

Think about how many unnatural chemicals that have been introduced to the environment without being thoroughly studied. Think about how many chemicals you use on a daily basis - in your deo, your soap, your food and even your drinking water.

Many scientists believe that these are all having an effect on our reproductive capabilities by causing mutations in our genetic code.

But this "estrogenic effect" is not just harming humans. Just this past week, I found an article about "intersex fish" found in the Potomac River.

The male fish are found with both testes and ovaries caused by the enormous amount of runoff - chemicals and fertilizers, plus hormones like estrogen from birth control products. This stimulates estrogen production in the male fish, disrupting their natural state.

Male alligators in Florida are also feeling the effects of manmade pollution:
In Florida's Lake Apopka, size does matter. Yet it took two years for University of Florida zoologist Lou Guillette to believe his own research findings. His data showed disturbing trends in the male alligator population of this lake, located just outside of Orlando. The most striking finding was the alligators' small penis size: 25% smaller than in normal males. Furthermore, these males had testosterone levels as low as a typical female's--a serious threat to their fertility. How had these "gender-bending" defects occurred? Could manmade chemicals in the waters of Lake Apopka be responsible?
In a word: Yes.

Guillette still remembers when the pieces of this puzzle fell into place. It happened when a colleague told Guillette what he had learned at a recent meeting organized by Theo Colborn. Environmental contaminants, the colleague said, could act like hormones. For example, p,p'-DDE, the major contaminant in Lake Apopka, was known to block the action of testosterone. Suddenly, what Guillette was seeing in Lake Apopka made sense; chemicals were disrupting hormones in these animals.

While the waters of the lake were relatively clean, "gender-bending" pesticides from the spill had moved into the food chain. Alligators were at the top of that food chain, and accumulated contaminants like p,p'-DDE through the fish that they ate. Females then deposited the chemicals in their eggs where they could influence development of the embryos. It all made sense. The population decline, the abnormal hormone levels, the strange structures Guillette had found in the alligators' testes and ovaries...they were signs of scrambled hormone signaling during development.
This is another example of our collective short term memory. Environmental issues are hot when something major occurs: increased number of hurricanes, invasion attempts on ANWR, oil spills, etc. But when the fervor dies down, the media loses interest.

Will they address pollution again when I start growing ovaries?

Second Call for Submissions!

I'll be hosting Mendel's Garden this coming Friday, the 15th. Send me your best posts about genetics.

Mendel's Garden...

...Covers new research in all areas of genetics, not restricted to any specific organism. Everything from transcription to evolution to genetic counseling and social implications of genetics research are welcome.

We'll hopefully take a little tour through the biology department at FSU in the process...

Send me your links through e-mail - thevoltagegate [at] gmail [dot] com - or by using the Blogcarnival submit form.

September 9, 2006

The Evolution [Distinction] of the Binturong

The bints, it turns out, have an interesting evolutionary history.

Recent molecular analysis of the order Carnivora (dogs, cats, bears, seals, bints, etc.) places all subsequent species into two clades (branches): the Caniformia and the Feliformia.

The Caniformia clade contains a staggering array of animals - dogs, bears, seals, martins, pandas, otters and walruses - but interestingly enough, dogs (canids) were the first to split from the group (from the Arctoids), something like this:

The other side of the clade, the Feliformia, starts with the split of Nandinia, the African palm civet. Nandinia was once classified with the other civets in Viverridae, but molecular evidence has placed them in a separate branching.

Here you can see how closely related the bints are to the felids from an evolutionary perspective:

If you consider that the ancestors of the bints arose in the Oligocene, about 30 Mya (about halfway between the dinos and us), that makes the bints are relatively ancient mammals, splitting off with other viverrids from the ancestor of the African palm civet.

During the Oligocene, the world was cooling, but that didn't stop the spread of early forms of extant mammals and the more modern forms of birds:

Early forms of amphicyonids, canids, camels, tayassuids, protoceratids, and anthracotheres appeared, as did caprimulgiformes, birds that possess gaping mouths for catching insects. Diurnal raptors, such as falcons, eagles, and hawks, along with seven to ten families of rodents also first appeared during the Oligocene.

The binturong is the only Old World mammal to evolve a fully prehensile tail, meaning the tail is dexterous enough to be used to manipulate objects, like food items. The rest of the mammals possessing a fully prehensile tail are only found in North and South America (monkeys, opossums).

Only one other member of the order Carnivora has evolved a prehensile tail, the kinkajou (Paris Hilton's old fling).

Next time I want to discuss the ecology of the bints. Unfortunately, that means a revisitation of traditional Chinese medicine.


Phylogeny of the Carnivora (Mammalia): Congruence vs Incompatibility among Multiple Data Sets. Flynn J.J.; Nedbal M.A. Molecular Phylogenetics and Evolution, Volume 9, Number 3, June 1998, pp. 414-426(13)

Mosaics of convergences and noise in morphological phylogenies: what's in a viverrid-like carnivoran? Gaubert P, Wozencraft WC, Cordeiro-Estrela P, Veron G. Syst Biol. 2005 Dec;54(6):865-94.

September 8, 2006

The Binturong's Sweet Tooth

I found a neat little story about the binturong's eating habits in captivity:

They prefer the sweetest foods, with the exception of their taste for meats. A
partial list: apples, melons of all types, cantaloupes, grapes, pears, kiwi, mangos, star fruits,
avocados, oranges, grapefruit, nectarines, peaches, cherries, tomatoes, chicken (raw or cooked), mice and rats, beef, fish, some greens (mostly the stems of anything green in their cage except for grass and poison ivy) and any sweets anyone will feed them. Marshmallows are a big hit, as are chocolate muffins, apple pie, and McDonald’s egg nog milkshakes. Never again will I give any binturongs concentrated sugar when I have to share living space with them. When Edgar and Annika were about six weeks old, they teamed up on us on the couch one night. We humans had been foolish enough to think that we could eat lollipops without sharing. After they each finished gnawing the hard candy off the sticks, they walked around for a few minutes licking their sticky lips and paws, seemingly unaffected. Suddenly, Edgar dove across the couch and tackled Annika. She return-pounced, sending them both crashing to the floor. They sped around their “personal indoor track,” climbed to great heights (for them) and leaped, raced across our laps, and would not slow down. When the sugar rush passed almost an hour later, they both drank a lot of water and slept soundly.

Sounds like a plan... Zzz...

September 7, 2006

The Danger of Siding with Intelligent Design

To surrender to ignorance and call it God has always been premature, and it remains premature today. - Isaac Asimov

Dr. Raesly, our resident evolutionary biology professor at FSU, was extremely gracious in taking time out of a busy day - and a trip to the field - to have a little chat with me about Intelligent Design (ID) before he hosts his forum on "Science, Religion and Intelligent Design."

We talked for about a half hour and Raesly brought up some great points that I would like to share.

We talked about Gould's NOMA model briefly, and he showed me some neat little graphics depicting the filters of religious and scientific filters that people place on the domains of knowledge: personal experience, history, art, religion and science. I definitely want incorporate these into my article on ID next week.

Gould was a proponent of keeping science and religion exclusive; NOMA is an acronym for "nonoverlapping magisteria," specifically science and religion (I differ from Gould somewhat; I personally believe that there is an interpretable yet unexplored cross section of all the domains or "magesteria" of knowledge, but we are so taken with specializations that such an analysis remains out of reach).

Like Gould, Raesly feels that there is no conflict between science and religion.

"Everyone understands the world in different ways," he said. "Science is one.

Raesly believes that most people that identify with and support ID are fundamentalist Christians that are truly concerned with the directions our country has taken towards secular humanism. It's a distaste for what is called "methodological naturalism" that is inherent and necessary in science.

"ID is not science. The fundamentalists perceive the 'materialism' of science as damaging to the moral fabric of our country," said Raesly. "But it's not fear. I don't begrudge people their beliefs. They are legitimately concerned with our society. I believe they do want to see a better world."

If science is robbed of methodological naturalism, the door is left wide open for "studying" supernatural causation of phenomena, which is, of course, what ID is all about. Raesly believes that ID is basically a guise for getting around the church/state separation and slipping creationism back into science.

"ID is counter-productive," said Raesly. "If certain religious groups begin to side with the idea that things are too complex for us to know, when discoveries are made and things are shown to be explainable, this tends to erode religion."

ID seems to have caught on especially well in America, which Raesly attributes to both the sorry state of science education in this country as well as our foundational American philosophy.

"I think ID has gained a foothold here because Americans value all points of view. We believe that we should hear all sides of an issue and then come to a consensus," said Raesly.

"But science is not a democracy," I said.

"Science is definitely not a democracy," he replied.

In this coming Wednesday's Bottom Line, I will have a column about ID, an article about our conversation and the purpose of Raesly's forum, a more detailed podcast about ID, and a blog entry covering the details of the forum on Tuesday evening.

Also published here.

Young Earth Creationists Unite!


There's a mess over at Carl Zimmer's blog worth a look. You won't believe your eyes, trust me.

September 6, 2006

The First Issue of The Bottom Line Out Today

The Bottom Line Online is out today!

It was a lot of work, but it's all worth it; the site looks great, the print edition looks great and I'm really looking forward to the rest of the semester. It can only get better from here.

Today is also the debut of my column. I figured that I should present a rationale - a mission statement - for the year:

The most important of these is, of course, "Why bother?" Scientists are perceived as the only ones who should care about advances in science. They seem to constitute a small cloister of badly dressed, out-of-touch intellectuals whose research only affects the common man when it crosses paths or completely conflicts with modern political, financial, medical or moral issues.

This commonly held perception of science - as a field of "special interest," irrelevant until proven useful or morally objectionable - is utterly false.

But, it is also why I write.

Later this afternoon, we're going on our first field trip in ecology, to Finzel Swamp. Swamps, bogs and marshes are unique cross sections of so many types of ecosystems, illustrative of just how things may have looked thousands of years ago.

It's damp and soggy outside, and it doesn't look like the clouds are going to let up. So much the better. It's good swamp weather. Maybe I'll snag some pics today...

September 5, 2006

Mendel's Garden #5/Call for Submissions

Mendel's Garden #5 is up at evolgen.

I will be hosting the Garden here in the middle of the month, so this is the official call for submissions. If you've written anything about genetics of late (or you plan on doing so), send your link to:

thevoltagegate [at] gmail [dot] com

The deadline for submissions is September 14th.

Binturongs and the Dexterity/Brain Size Correlates

It's nice when you stumble across some scientific literature that answers a question that's been bugging you. Well, in this case, maybe half of a question.

I've always wondered if there was some connection between an organism's intelligence and its ability to manipulate objects with hands or some analog, and if there would be a way to quantify either attribute effectively. In my mind, cephalopods (squid, octopus) and primates are prime examples of intelligent manipulators, though this connection breaks down as soon as you browse the cetaceans (whales, dolphins).

In my search for literature pertaining to the binturong (which is scant, the animal is a virtually an unknown species), I came across a paper performing just that sort of experiment in a more focused manner. The researchers studied 41 different fissiped (terrestrial) mammalian carnivores, including Arctictis binturong and the red panda, Ailurus fulgens, and did the following:

  • Equated animal intelligence with brain size and brain weight, using a calculation based on such numbers
  • Correlated that number with the "total dexterity" (proximal and distal)

These methods are backed by evidence that the complex use of hands/forelimbs for feeding or manipulating instead of pure movement has lead to the selection of greater intelligence mainly in predators:

[...] carnivorous species within Carnivora may have increased brain size because of a more complex forgaging strategy involving selection for rapid prey detection, pursuit, capture (especially forepaw manipulation) and consumption (Gittleman).

Here's the short version of the results: In this experiment, brain size/weight was shown not to be connected to manual dexterity.

But that does not mean that intelligence and manual dexterity are not connected. A ratio of brain size to body size (called the encephalization quotient, or EQ), while certainly important, does not necessarily accurately describe or denote intelligence. There are other factors, such as the nervous wiring of the brain. The raccoon has a fairly normal EQ, not telling of any significant intelligence or skill with its hands, but we know otherwise; the raccoon can "see" with its hands in the dark. This may be because of how its brain is wired instead of raw brain size to body ratio.

As more brain and neuroscience is done, researchers are finding more and more that the EQ is an insufficient measure of intelligence. Intelligence probably has more to do with the rate at which the brain develops in the womb (think babies with giant heads), than sheer physical mass.

From Carl Zimmer's wonderful book, At the Water's Edge:

Intelligence may not be determined by relative brain size per se but by the rate at which the brain grows in the embryo. [...] primates grow with unusual timing : their brains swell early and quickly, but their bodies grow slowly for mammals of their size.


How skilled are the skilled limb movements of the raccoon (Procyon lotor)? Iwaniuk AN, Whishaw IQ. Behav Brain Res. 1999 Feb 15;99(1):35-44.

Brain size is not correlated with forelimb dexterity in fissiped carnivores (Carnivora): A comparative test of the principle of proper mass. Iwaniuk AN, Pellis SM, Whishaw IQ. Brain Behav Evol. 1999 Sep;54(3):167-80.

Carnivore Brain Size, Behavioral Ecology, and Phylogeny. John L. Gittleman. Journal of Mammalogy, Vol. 67, No. 1, 23-36. Feb., 1986.

Zimmer, C. (1998). At the Water's Edge. New York, NY: Simon & Schuster.

September 3, 2006


I will be gone 'till Monday evening (I need a break!). Be back with an exploration of brain size, intelligence and forelimb dexterity. Sound like fun, eh?

For now, check out some posts from earlier this year that you may have missed:

I'm bullet-crazy!

September 2, 2006

Demon QuarkXpress and Bio Distractions

Busy day, 10 hours of QuarkXpress (a.k.a. Hell). But, the first paper is almost assembled and will be ready to roll by the 6th.

I caught a couple of neat articles on PLoS Biology last night:

September 1, 2006

Thus Ends the First Week of Classes

Well, I think I have a pretty good impression of what the semester is going to be like - hectic, but challenging.

I'm taking ecology, physics, tech writing and world music (I love taking freshmen courses in my senior year) and I have to say, I'm anxiously awaiting trips into the field. We're hitting local forests, streams, ponds, and best of all, a few trips to the local swamps.

I took a little trip to Finzel Swamp with a few friends over the summer and was amazed at the diversity of the environment. Blueberries and raspberries - red and black - were growing in tight copses all along the path. The deeper parts of the swamp were bottom heavy with mud and large freshwater mussels were only noticeable by the tiny bubbles that occassionally made their way to the surface.

The pieces are slowly falling into place for the first issue of The Bottom Line, both in print and on the website. I spent much of the evening uploading articles for release on September 5th, one day earlier than the print version.

Tomorrow we tackle the print template; I hope we can nail it down by tomorrow afternoon so I can actually enjoy the long weekend.

I have some great info on Viverrid evolution, as well as a neat study analyzing correlations between manual dexterity and brain size. One of their subjects was the binturong. I'll have more up on bints soon.

One More Carnival

Festival of the Trees #3 is up at Burning Silo, ladies and gents. The Festival is an interesting, well- rounded carnival, welcoming entries not only from biology centered blogs, but also from poets, photographers and essayists.

I'm looking forward to the Festival in the coming autumn.