October 31, 2006

Attenborough's "Truth about Global Warming" Clips

I found some great clips from a recent documentary on global warming by Sir David Attenborough (not yet released this side of the pond):T

Part I

Part II

Part III

Anything Attenborough does is gold. Animal Planet should take a hint... Enjoy!

October 30, 2006

National College Media Convention Wrap-up

I'm am sleepy. Two hours in a plane and another three in the car wiped me out yesterday, and this daylight savings time business is always strange for the first few days.

But the conference was good. It gave us a chance to meet some people in our respective fields and find out what's happening in the media today.

Unfortunately, TBL didn't win any official awards at the conference, but we did receive a big complement from a professional critique of the paper; the advisor wanted a copy of TBL to show to her students for content and design purposes and they had a full journalism program and a sponsored newspaper at their university.

I thought I'd share some of the highlights of the trip; perhaps this information could be useful to others out there:
  • Features to Books
    • As I said before, Michael Taylor gave a detailed session on turning magazine/newspaper features into full length non-fiction. Non-fiction is pitched (before the book is completed) in a book proposal, which consists of several parts totally around 30 pages on the average (no more than 50):
      • Synopsis: A two to three page summary of the book, like a lengthy abstract.
      • Annotated Table of Contents: A chapter listing of the book, with one paragraph descriptions of each. It doesn't have to be exact, but the publishers want you to think about organization (about 10 to 15 chapters, typically).
      • Bio: All about you, professionally.
      • Sample chapters: One or two completed chapters from the book.
    • These were the basics (there are a few books written about these proposals). He said finding an agent is necessary, preferably one who handles other authors that you admire. Taylor also said to avoid internet publishing; any agent that tries to charge up front is probably trying to get one over.
  • Resumes
    • This was probably the most useful of the sessions, hosted by editors from the Wall Street Journal, St. Louis Post-Dispatch and the Indianapolis Star. Everyone has a different opinion on the contents, but this is what they had to say:
      • Cover letter: One page, well written. In journalism they use it as a gauge of your writing abilities in addition to clips.
      • Resume: One page, neat, simple, to the point. Include three references (education, professional, personal)
      • Clips/Media: Six samples of writing, either from photocopies of the print article or a website printout. They recommended supplying commentary with each clip, describing your process or problems briefly. One of the editors recommended sending a disk containing any edited pages or designed pages or graphics. He liked to see "the whole package."
      • No folders, nothing fancy: Just a paper clip and white 8.5 x 11 paper. No staples.
    • The session was geared towards general journalism and never delved into specialist writing (like science journalism), which was a tad disappointing. They recommended "overdoing" your online resume if you have more information, and giving the link in the resume for further info.
  • Blogging for the Serious Journalist
    • I had mixed feelings about this session. The woman who hosted the session had been a journalist for 30 years for one newspaper, and her political blog was anything but personal (or interesting, for that matter). It was basically a way for her to include smaller stories in another format (does that truly make her a blogger?). She is enmeshed in the machine, however, and said that blogging is becoming a necessary skill in journalism. She felt that it will be the wave of the future and should be included on any resume. Most of her colleagues don't do it because of time.
That's about it for the words of wisdom (I won't bore you with design specs or software alternatives).

The trip was a great opportunity, but I'm glad I'm home. I have a few new tricks up my sleeve and a better sense of the professional writing world. Sort of.

I've been going to these conferences for three years now, and I've only seen one science journalism session given. Unfortunately, the presenter never really delved past the scientific issues people care most about: money, morals and health. I'm more concerned about getting a job at this point.

October 29, 2006

Sensing the World Around Us

We've talked about the contemporaries of our ancestors, modern archaea and bacteria. They communicate, replicate and socially organize into tight societies much like our own.

That is a relatively fuzzy comparison, however. One cannot entirely equate the complexities of our society with the biochemical signaling of such a simple organism. There are interesting similarities, but the argument is hardly conclusive.

At a more fundamental level, however, the comparison can be correlated. Biologically, each one of us is a direct descendant of those bacterial colonies. The framework for communication and organization was already set up for our body plan; natural selection merely condensed and implemented it.

We are each a giant walking colony of organisms; each of our trillions of cells has its own role in the larger organism, much as Donovan stated last week, and has become specialized to perform distinct operations in the interest of the larger organism (not to mention the many species of bacteria that inhabit our skin, mouth and gut). This is essentially a compartmentalized, specialist version of the basic bacterial colony.

We have muscle cells that provide the framework of motion, blood cells for nutrient dispersal and defense, cells that regulate hormone levels in the body, cells that absorb and digest nutrients, etc. Perhaps the most important of these are the nerve cells.

Nerve cells help the larger organism sense the world by distributing sensory information along a fabric of neurons (nerve cells) woven through our entire body. Eventually this information is trapped in brain cells for later use (memory).

It is interesting to note that objects we encounter in the world-fruit, pavement, pencils-have no inherent scent, feel, taste, sound or even appearance; we assign the qualities of an object according to their usefulness to us. We are nauseated by feces and rotting garbage because it is dangerous for us to consume. The "scent" of garbage was contextualized in ancient times, and our brain is genetically wired to send waves of repulsion through our body, driving us to turn away in disgust or even vomit.

Similarly, we are attracted to certain foods. Our mouths water at the smell. We are compelled to eat more of a food because its taste and texture indicate that it is nutritiously viable. Our bodies love lots of high energy, fatty foods.

The funny thing is, most of the information about the world in which we live is never "consciously" processed.

I'm sitting in the spare bedroom of my apartment typing this article. Loads of sensory information is coming in through my five senses:

I see alternating images, the keyboard, the desk and the monitor.

I feel a faint wind through my open window, the pressure of my tongue on the roof of my mouth, the chair pressing on my back, my feet on the floor, fingers exacting the pressure required to press each key and a dull pain in my head from staring at a light source for too long.

I smell the carpet, my lunch, fumes from cars on the highway, my deodorant; I hear trucks gearing down, my girlfriend shuffling papers, the cats running the hallway, the stilted clicks of my fingers tapping keys. I taste the remnants of my cereal in my molars.

I sense all of it and I haven't even left my seat. In fact, if I wasn't consciously exploring what exactly I was sensing at one time, all of these things would not pass through my conscious mind, since it is much more focused on organizing separate letters into words (lexical arrangement) and separate words into sentences and paragraphs (syntactic arrangement) to match and represent the ideas floating about in the conscious portion of my brain. It's busy writing this article.

But what else am I missing?

A hell of a lot. Food is being metabolized, waste removed, individual cells die and others are replicated, your heart beats, electronic messages race along our neurons, dumping chemical messages of pleasure or pain, telling different parts of the brain to increase quantities of this chemical or decrease quantities of that.

We never even catch wind of these processes in our conscious mind. Can you tell me how much serotonin you need at certain times during the day or under certain environmental pressures? Of course not, that process is autonomous.

Just like our reaction to, pain, or the "fight or flight" response, or sexual attraction to a potential partner. These are all chemically driven responses to the environment for protection or procreation of self that never even make it to your conscious mind, hard wired from our ancestors, reaching back billions of years to the very analogs of the bacterial colonies we discussed last week.

I talk about the conscious mind as a separate entity, and it is in a way; there is a definite section of the physical brain that it occupies. However, it is but one piece of our entire central processing unit (the brain) that has evolved to oversee the conglomerate of separate organisms we call the human body.

Originally published here.

October 27, 2006

St. Louis ACP/CMA Conference: Days 1 & 2

It's been raining for the past three days (I'm soaked to the bone right now), the Cards fans are anxious to see a final win this evening and I could go for a little nap.

Oh yeah, and they transfered several dozen students from the convention hotel (ours) to another one down the street. Apparently, the Detroit Tigers needed someplace to stay. Poor babies.

We had a prescreening of Borat last night (one of the most hilariously offensive movies I've ever seen), as well as Stranger than Fiction (one of the most endearing movies I've seen in a long time).

I finally have a little break between sessions, and I thought I would share a few notes about what I've learned:
  1. It never rains in St. Louis. Except this week.
  2. "Shoulders" is the best drinking game ever conceived.
  3. Non-fiction books are sold by detailed 18 - 30 page proposals as opposed to manuscripts (That from Michael Taylor, who taught a session about turning feature stories into full length books, awesome stuff. He has written several books, some about caving; I immediately thought of Jen. I'll talk more about it later.)
  4. We are one of the best designed 12 page weekly in the country.
  5. We need more white space.
  6. TGIFridays + Drinking Games = Yuck.
  7. SEED Magazine is looking for an Associate Editor of Life Sciences and I qualify.
  8. I wish we published a weekly magazine (or even a one per semester special edition).
  9. There is a new science-centered animal carnival called (what else) Carnival of the Animals.
  10. The college journalist uniform includes horn-rimmed glasses (of many sizes and shapes) and tight girl jeans.
  11. The exact dimensions for effective use of white space.
I'll have more tonight, I hope. I'd also like to do a little bit on Bastesian and Mullerian mimicry, and some new research.

Time for another session. BRB.

October 24, 2006

Erudition: From Fins to Wings

Zimmer presents a nice overview of homology (and some assorted evolutionary mysteries/solutions) in this month's National Geographic.

October 23, 2006

Watch Out St. Louis...

I've been running around like a madman for the past couple of days trying to pack, throw together a makeshift portfolio (with over 50 writing samples; don't ask me where they all came from) and condensing my resumé into a brief review of my journalistic experience.

Why? Because the editorial board and I are leaving for St. Louis to attend the annual Associated Collegiate Press/College Media Advisers conference.

It's set up for student journalists across the country see what's happening in magazines and newspapers, design and layout, covering current issues, portfolio and resumé reviews, how to manage your staff better, website stuff, etc.

All of that's great. But I'm looking forward to the sessions on blogging and podcasting. :-)

In true poor college student fashion, we're cramming all nine of us in two rooms (someone's sleeping on a cot). That in itself will be interesting.

I hope I can keep up the blogging this week, but forgive me if I miss a few days. If I run across anything/anyone interesting, I'll be sure to share immediately (the conference is in the hotel and the hotel has wireless internet in the lobby).

I've read a stack of neat papers lately that I'd like to share; hopefully my mornings this week will be free for blogging.

Anyone been to St. Louis? Is there anywhere I just have to go? Restaurants? Bars? Museums?

October 22, 2006

Autumn in Appalachia

The leaves fall patiently
Nothing remembers or grieves
The river takes to the sea
The yellow drift of leaves.

-Sara Teasdale, Autumn (Pont de Neuilly)

October 19, 2006

Racism, Vandalism and Journalistic Integrity

The paper's been out for less than a day, and already I'm getting e-mails.

We seem to have stirred the pot with this story, about vandals scrawling racially/socially discriminatory messages in marker on the doors of one residence hall (dorm room doors and entrances/exits) and in certain areas of our library.

The messages were immediately scrubbed off by campus police, but we had an anonymous contributor send us photos of the actual content of the vandalism. It's quite clearly a threat, both to African Americans and Jews, and the images, when viewed, are like a slap in the face.

It took a lot of talking and debating to decide whether or not to publish the photos, not just in my mind, not just among my staff, but with people of other organizations and cultures. Among the students, the decision was unanimous, however.

I always have concerns about our readers. I don't want to upset people, but I do want people to see the truth in the fullest extent that we're physically capable of publishing. I even published a letter from the editor explaining my rationale.

I expected a response, and have received a few, most verbal ("Wow, this is controversial. Why did you guys do this?") and one written, in which the writer declares that she is "appalled" by our decision to publish the pictures (and for some reason, the article), especially since the president of the college addressed the incident in his memo to students. She claims that it spreads the message of hatred from a few doors to a few thousand front pages.

That was a point we considered and quickly refuted (I think I explained it well enough in the editorial). Additionally, we are an independent newspaper, not the campus PR rag. The president is the voice of the administrators and the bill collectors, not the voice of the students.

Should CNN have photographed/videotaped 9/11? Those were harsh images, of human beings jumping to their deaths, fire and falling rubble, potentially spreading the propaganda of Bin Laden and his cronies to billions of people across the world (contextually, an extreme analogy, but the principle is the same).

The press are still invaluable to our country. Journalists get a bad rap nowadays - many of them for good reason, don't get me wrong - but they fill a vital role: Keeping the public informed of just what their leaders are doing, and what issues we face as a society.

Social issues like these should never be pushed under the rug. They lose significance if one's understanding of them is vague. It's obvious that racism is still an issue in this country, even among young people. Why hide it?

Here's the extreme example in our community. Now what are we, as students, going to do about it?

What decision would you have made in this position? Why?

October 18, 2006

Listening in on Our Ancestors

What if I told you that with all the structural complexity of our language-written and vocal-at its very base, is no different than communication between bacteria?

It is not too foreign of a concept, considering that the beginnings of life were in fact bacteria, which congregated into giant colonies, forming structures called stromatolites 3,500 million years ago. These stromatolites lined the salty, otherwise lifeless beaches of the planet, rising to heights of dozens of feet, monuments of a greater future under a new sun. Communication between these organisms was necessary for any attempt at joint effort.

Are we any different? Basically our bodies are nothing more than the result of the cooperation of tens of trillions cells passing information-genetic and chemical-to regulate the macro organism, the human being. Every cell is connected, streaming all sorts of vital information-regulation of nutrients, presence of outside stimuli, reaction measures and presence of alien substances.

Recent research exploring colonial bacteria has illustrated the level of linguistic complexity within these colonies. Modern theoretical linguistics has opened studies of communication in many fields, including biology, and given us a view of language as entirely structural; "words" (or chemical signals analogous to words) have no inherent meaning, only the meaning that one applies to them.

From an evolutionary perspective, this rings true. There are myriad examples of one structure becoming useful in another function (exaptations): lungs becoming useful as swim bladders, sturdy fins become useful as walking legs, insulating feathers become useful in staying aloft, etc.

The same goes for biochemical elements. A molecule by itself has no inherent function until it is contextualized, placed in a functioning system.

Communication among bacterial colonies is incredibly complex. They exhibit the same basic social intelligence observed in human beings. (Social intelligence is a term applied to the functions of the mind outside of academic pursuits, specifically the exchange of information to organize in groups, and therefore exhibit a group identity.)

Experiments have exhibited specific examples of such behavior. The phenomenon of antibacterial resistance (a looming, potentially catastrophic problem in the future) has provided scientists with a chance to observe colonial propagation in the face of destruction. The bacteria resistant to the agent are able to exchange chemical information among the survivors, relaying their dire situation. The individuals respond in concert, immediately initiating conjugation. The colony begins replacing the lost members with new, resistant ones.

They identify in this manner as one organism. Mass communication has allowed the United States and other information age nations to respond similarly to catastrophic events. September 11 comes to mind.

The complexity deepens. In starvation conditions, most bacteria are able to assume the form of spores (through sporulation). These spores are incredibly durable (many can survive the vacuum of space), and do not need to feed in order to persist. When conditions become favorable again, the bacteria can change back into a fully function individual. In colonial species, the bacteria can detect the nature of the environment (food or no food) and notify the rest of the colony by releasing biochemical messages. Each individual is able to receive the message, evaluate the circumstances and "vote" on whether or not the colony should sporulate.

Species-specific communication within the colony has to be fine tuned and complex since, in the natural world, colonies coexist with dozens of other colonies of other species, sending their own messages in their own languages.

Our mouths are a perfect example of this. At any given time, you have about 20 species of bacteria inhabiting the tissue of your gums, each trying to organize feeding and procreation (at least until the next time you brush). Their messages need to be clear and purposed-as scant molecules among trillions-to extend the life of the colony.

These are just a few examples among dozens (among hundreds as more research is done). The entire story, however, cuts deeper, closer to home.

In each one of these cells lies the secret to our success: energy producing structures called mitochondria.

Mitochondria generate the flow of energy that makes everything possible, gleaning ions from the constant stream of nutrients into our mouths, absorbed through our digestive tract. They have made our lives as multicellular, eukaryotic organisms possible.

Mitochondria have their own genetic information, their own blueprint for life, distinct from the blueprint for our own body, making them the odd structure out in the plan of the cell. So odd, in fact, that scientists think that this is enough evidence to posit the mitochondria as a benefactor from the ancient past; in essence, the mitochondria is a separate entity in the cell, a life giving, incorporated bacterium in each of our cells.

We have not left our past behind. Our lives depend on it.

Originally published here.

October 16, 2006

October 15, 2006

Carnival Wrap Up/akacoolpeople.com

Carnival of the Godless #51

Festival of Trees #4

Mendel's Garden #8

Tangled Bank #64

While I'm linking, I might as well mention a cool little blog called akacoolpeople.com (via Thud):

akacoolpeople.com is the website of CrossRoads day-treatment facility.

CrossRoads is a highly structured day treatment program focused on the goal of helping youth facing Level II sanctions and who are long-term suspended or expelled from school. CrossRoads provides a safe environment in which youth can learn alternatives to the behaviors that caused them to be suspended or expelled from school and to be involved with the Juvenile court. CrossRoads actively collaborates with other local agencies to provide an effective array of services for youth in our care. CrossRoads provides afterschool as well as school time programming - reducing the amount of time youth spend unsupervised the program is open year-round so that youth have a place to go during the summer.

Students log in and share their feelings about the material they learn at CrossRoads (including some really neat experiments).

Go and show your support of their efforts! More teachers should encourage this level of involvement in their students.

October 14, 2006

What's Reflected, What's Absorbed

I've been on a serious pigment kick lately (reinforced by my little art excursion last night and my review of all of the fall leaf literature), and rhodopsin came to mind, a light absorbing pigment found in animal eyes, archaea and bacteria (often referred to as bacteriorhodopsin in the case of the archaea).

While chlorophyll is capable of absorbing red and blue light from the sun for much of the year (all year for evergreens), bacteriorhodopsin can absorb wavelengths that much of the plant world reflects, from 490 - 550 nm, or the color green (see chart below).

Bacteriorhodopsin is particularly widespread in the oceans. The depth of the photosynthesizing organism determines the wavelength of light most strongly absorbed; in shallow, churning waters, bacteria will absorb green wavelengths more readily, while blue wavelengths are favored in deeper waters.

When light strikes bacteriorhodopsin, it causes a change in the shape (conformation) of the protein complex, which in turn powers a biological cornerstone: the proton pump. Protons are moved between membranes, creating a gradient of pH and an energy potential. The energy created is in turn used to pluck phosphorus from a cell's cytoplasm to complete the most well-known energy transporting molecules, adenosine triphosphate, or ATP. ATP then can be transported from there for use as energy in any other system.

Photosynthesis runs on different organic systems in the archea, leading biologists to believe that photosynthetic machinery must have evolved twice: once in the archaea, and once in bacteria (cyano; the discrepancies lie in the ETC and in the fixation of CO2 into glucose).

Heather's had her first "core review" session this morning (a pass/fail panel review of her work and one of the reasons I've been delving into pigment), and it went extremely well. I'll post some pics of her paintings at some point today or tomorrow.

October 12, 2006

Slideshow of Beautiful Pics from ANWR

I found a great slideshow today, from NWF, depicting the varied environments and wildlife of the Arctic National Wildlife Refuge.

It reminded me of a short film preview of Oil on Ice I found earlier this year.

Perhaps both were responses to this comment from Rush Limbaugh:

If you put together a video of ANWR, you would see nothing but snow and rock. It is no place anybody's ever going to go. The wildlife that lives there wishes it didn't, but it's too stupid to figure out how to move anywhere. They don't have moving vans sent to their places like people in Philadelphia do when they want to get out of someplace. This is absolutely absurd.


October 11, 2006

A Festival of Leaves

Bundle up and step outside, into the forest. Kick some leaves. Gather your thoughts. Breathe. The leaves have changed.

Poets and artists have pondered the autumn palette, and there is no better place in the country, perhaps, to take in the beauty of October.

It is fleeting, however, as Frost notes:

Nature's first green is gold,
Her hardest hue to hold,
Her early leaf's a flower;
But only so an hour.
Then leaf subsides to leaf.
So Eden sank to grief,
So dawn goes down to day.
Nothing gold can stay.

But exactly why leaves change color in the fall is a mystery deeper than any poem has grasped. It also could change the way we think of fall.

For most of the twentieth century, it was believed that autumn leaves were nothing more than a biological wastebasket of sorts. As the light and temperature in our hemisphere begins to decrease, the tree begins to shut down, reabsorbing nutrients from its leaves. A woody cork membrane grows between branch and leaf, cutting off the circulation of nutrients, and the trees stops producing chlorophyll. (Retaining leaves during the winter is not energy efficient for broad-leafed trees.)

Think back to BIO 101. Chlorophyll is a pigment not only responsible for the green color of plants, but also for the production of sugars from captured sunlight. Chlorophyll is also a very unstable compound, constantly broken down by the energy from the sun. So when the trees stops circulating nutrients, the chlorophyll breaks down completely, allowing the tree's other pigments to reflect reds (anthocyanins) or yellows (carotenoids; see sidebar).

Carl Zimmer says it best: "In other words, autumn leaves were a tree's gray hair."

Zimmer says "were" because that notion has changed somewhat over the last decade. Nature, specifically natural selection, allows very little waste, and most traits are expressed through environmental pressures. Colorful fall leaves are no exception. New evidence has birthed two new theories, both provocative in their own right, both controversial among evolutionary biologists.

When biologists discovered that the red pigment anthocyanin was actually produced in autumn, and not merely unmasked by the decay of chlorophyll, this brought up an interesting question: Why would trees waste energy to produce a pigment that would only last for a few weeks, and decay with the falling leaf?

The "leaf signal" hypothesis (or "coevolution theory")seems to provide an answer. The bright yellows, oranges and reds are warning signs to potential aphid invaders, much like the bright colors of poisonous tree frogs.

Trees have poisons and sappy snares of their own for defending against insects, and the bright colors of autumn leaves warn insects not to lay eggs in the trees, unless they want their larvae in the spring meet an untimely demise.

There is preliminary evidence to support the theory. A study of 262 tree species revealed that the trees with the brightest foliage were only subject to more specialist aphids, illustrating that the generalist population of aphids were warded off by the colors. Trees that were duller or remained green until abscission were subject to the generalists. Another study at the University of Oslo studied birches specifically and also found supportive results.

But the leaf-signal hypothesis has its critics. Another group of scientists, pointing out that some trees with bright leaves are not attacked by insects, are suggesting that bright autumn leaves serve another purpose: a natural "sunblock."

As we stated before, trees are dismantling the structures supporting chlorophyll in order to store the nutrient from such structures, and allowing the pigment to decay. There is extra radiation hitting the leaf, with potentially nothing to soak it up. This is where the synthesized anthocyanins come in. They can still absorb light in the absence of chlorophyll, reducing the radiation damage to the leaf, and subsequently, the tree.

Both theories are relatively new, and the evidence is preliminary, but thought provoking. All the beauty of an autumn forest might just be an organic neon sign reading "Back Off."

Originally published here.

October 10, 2006

A Few Early Morning Links

PLoS Bio: Looking into our biological future...

Seed: N. Korea's underground nuclear tests...

NY Times: Giraffe-sized camel fossil discovered in Syria...

The Loom: A short history of Homo floriensis (the "hobbit" hominid), including a review of recent research...

Science Daily: More on Homo floriensis (a new paper suggests that the hobbit was merely a modern human suffering from microcephaly)...

Darren Naish: Tetrapod Zoology: The origins of the domestic dog. Awesome post...

October 9, 2006

Clips > Book Reports

I see students wasting opportunities every day. Every time we lose a writer I shake my head.

"What do you want to do?" I ask.

"I want to write," they say.

Then why are you leaving? By all means, stay, practice, get comfortable with style and diction; these are things they cannot teach you in tech writing or advanced comp. It takes practice, drafting over and over, reading what you've written, reworking it, writing it again.

Plus, when you show up to a job interview, they won't say, "Wow. This is a wonderful double spaced research paper on mythological imagery in Frankenstein. Gee, you even got an 'A.' Look, I need you to cover the president's press conference tomorrow..."

The publishing world wants to see published clips. I saw a great example of this after my design editor was offered two freelance jobs as a sophomore and her upperclassman friends were passed over. Why? Because she had published clips in her portfolio.

This has been pounded in my head for the past few years by advisors and professors from the Associated Collegiate Press (ACP) and the College Media Advisers (CMA). ACP and CMA hold a large conference every spring, summer and fall, where college newspapers, yearbooks and broadcasting congregate for a giant conference full of info on everything: science writing, blogging, podcasting, newspaper design, website design, editing, management and advertising. You name it, they cover it. We're going to St. Louis for the convention this year.

It's only two weeks away now. I could use the break.

October 7, 2006

Flipping the Aging Switch

Researchers at HU and NCU have found a gene in stem cells that actually "turns off" replication. They noticed a dramatic increase of expression from Ink4a in aging subjects - 10 to 100 times the expression of younger subjects.
Ink4a actively interferes with the ability of stem cells to divide in several different types of tissue, including the brain, the pancreas, and the blood-forming system of the bone marrow.

Under optimal circumstances, stem cells are able to copy themselves and differentiate into other cells, thus replenishing their numbers and acting as a repair system for the body. The Ink4a gene appears to be widely active in locations where stem cells regenerate new tissues.

Presumably as a regulator. Morrison, Sharpless and company suggest that synthesizing medicines to alter the expression of Ink4a could bolster our "defenses" (replication and neurotransmission) against aging.

One gene, one medicine?

Though mice with Ink4a deleted had more regenerative capacity in tissues like the brain and the pancreas as they aged, they started dying of a wide variety of cancers at one year of age. So it canÂ’t really be said that losing the gene helped them live longer.

"If you had a drug that could inhibit Ink4a function, youÂ’d potentially have a therapy against degenerative diseases," Morrison said. "But youÂ’d have to watch patients carefully for cancers. By the same token, drugs that mimic Ink4a function could be used to fight cancer." Ink4a was known to be a tumor suppressor gene that becomes more highly expressed with age, eventually triggering the cell to shut down replication.

*shrug* Every time I have read a statement like that from a geneticist (about medicines inhibiting or increasing expression of one gene) they usually turn out to be largely optimistic. These issues always tend to become more complicated.

The stem cells have a built in balance between replication inhibitors (Ink4a) and promoters (Bmi-1). Disrupting that balance doesn't sound like the best idea. Push too far one way and your body's regenerative ability slows; push too far the other way and your body turns into a tumor machine.

It would, however, be advantageous if the balance and rate of expression at a young age could be maintained into adulthood and beyond (which is probably what Morrison is talking about; he just worded it strangely).

I am hoping that classes/homework/newspaper will lighten a bit this week so I can update here more frequently. Today I have a slightly-less-than-blank Quark template waiting for me in the office. The newspaper calls.

October 4, 2006

TVG Print: Killing the Messenger

I'd like to tell you a couple of stories this week.

A long, long time ago, only God had fire. He kept it close, only for Himself and His most divine creations. Humans went without.

But one day, one of God's cronies took pity on us. He stole the divine fire and gave it to humans, who used the power of fire to craft and build and cook.

God found out and punished the thief by strapping him to a rock and having an eagle pick out his liver. The organ would grow back every day and the eagle would return to pick it out once more.

Sound familiar? It should, it's the ancient Greek story of Prometheus, transcribed into more modern theistic terms. Sound ridiculous? It might, but it is often used as an analogy for a more modernist view of science and the acquisition of knowledge.

This Promethean view of science is the antithesis of the Faustian view, focusing on the gift of knowledge as a rational and technological boon to humanity, instead of the burden of knowledge as a morally destructive force.

We can turn again to our pop culture for more current examples of the Promethean view (of which there are few compared to the Faustian/Frankenstein stories).

Star Trek (in any of its many incarnations) is probably the most well known example of the modern day Promethean story, at least in the mainstream.

When it began back in 1966-amid the tumult of the Vietnam War, the Civil Rights movement and the Sexual Revolution-Star Trek was a fresh idea in the science fiction genre. It depicted a crew of culturally diverse human scientists in the far future exploring the galaxy for no other reason outside of discovery; "to boldly go where no man [had] gone before."

That may sound incredibly nerdy (I make no concessions for that fact), but Star Trek carried with it the lofty ideals of the Promethean view of science. Human beings in this far-fetched future valued knowledge for its own sake, using the technology gained from this knowledge to explore the galaxy and continue to learn.

It is valuable to remember Star Trek's creator and his purpose behind the story. Gene Roddenberry's intentions were to explore a world where things had no supernatural causation; the crew of the Enterprise always used reason and knowledge to overcome obstacles, even when the phenomena they observed had no immediate or obvious natural cause.

To look further into the Promethean ideal in our society, let's have another story.

In the beginning, God creates man and woman in a grand and beautiful garden. He places a tree in the middle of the garden and warns them not to eat the fruit of this tree or else they will die.

Soon a serpent approaches the couple and persuades the woman to eat of the tree. Her eyes open. She does not die. She feeds her spouse the fruit. He feels the same effects.

They clothe themselves before God interrupts, inquiring "innocently" of their strange new behavior. He becomes angry at the Serpent and damns the creature to a lifetime of crawling upon its belly. He also banishes the couple from the Garden, forcing them to fend for themselves.

Put Prometheus in the place of the Serpent. Replace "fire" with "fruit." Now you see the problem.

The Promethean view of science is seamlessly equitable with the Fall of Man in Western/Christian societies. The Serpent in the Garden of Eden is viewed as the ultimate corruptor for tempting humans into seeking knowledge, while Prometheus is celebrated as the benefactor of human accomplishment.

I am by no means suggesting that Western religious convictions have to be in direct conflict with the acquisition and usage of knowledge, or that Satan should be elevated to a level of benefactor above the Christian God; those are issues for the student of theology.

I am, however, pointing out the significance of these myths. They are inherent in Western culture, stories told over and over again for thousands of years. Their relevance in the modern world, however, is declining.

The only way to combat the detrimental aspects of traditional symbology is by telling new stories - true stories - through scientific inquiry and reason to represent our world and ourselves instead of relying on the fear of knowledge promoted by ancient and irrelevant myth.

The only way to do that is by careful, patient, creative communication between the scientific community and the general public.

Originally published here.

October 3, 2006

The Mythology/Biology of Fairy Rings

Fairy rings are regarded in legends across Europe and North America. In Wales and much of Britain, people thought the rings were leftover from the merriment of fairies. In Ireland they are associated with leprechauns. In Germany, witches gathered around the rings at night. In Scandinavian tales (from which, by the way, Tolkien borrowed heavily), elves danced among the mushrooms in meetings called älvdanser.

In reality, fairy rings are the result of the natural tendency of mycelium (the underground "spreading" portion of the organism) to spread out in a ring shape.

Think of the mycelium like a radar blip, slowly moving outwards in an ever-expanding circle. The only above ground signs of the movement are an early ring-shaped change in the color of the surrounding ground and grass (due to the decay of older mycelium, which releases nutrients into the soil) and a late "bloom" of the cap (basidiocarp) - the spore releasing fruiting body of the fungus.

These basidiocarps, which we call mushrooms, grow from the rings of mycelium, release spores in a circular fashion, perpetuating the fairy ring.

I stumbled on this fairy ring just a couple of weeks ago, just outside of the student union at FSU. I ran around campus (and back into the publications office) trying to find a camera while Heather waited patiently in the car.

I think it is Chlorophyllum molybdites, one of the species found in this area that tends to grow in rings. Chlorophyllum is poisonous, and causes much confusion [and indigestion] among its human and animal consumers:

Of the mushrooms generally considered poisonous, the one far most often consumed is Chlorophyllum molybdites. It is large and meaty; it resembles a generally choice edible, Lepiota (Chlorophylium) rachodes, it tastes good; and it grows in lawns and parks. Chlorophyllum molybdites quickly rewards the unwary with gastric distress, vomiting, and diarrhea lasting several hours.

Hopefully this week I'll be able to get back to the dinosaur/body temp discussion; it's been a crazy few weeks between the newspaper, tests, papers and labs.