July 31, 2006

Circus of the Spineless #11 at Words & Pictures

The latest Circus of the Spineless is up at Words & Pictures, exploring mountain mollusks, ancient spiders, sex and cannibalism, exploding jellies and other wonders of the invertebrate world.

Read the 11th edition here.

July 30, 2006

DNA's Underlying Code; Erudition #12

From "Scientists Say They've Found a Code Beyond Genetics in DNA," by Nicholas Wade of The New York Times:

The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself.

The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.


I blogged about another discovery made a few months back involving nucleosomes/histones (DNA segments) and their function in determining growth in children and adults:

Imagine this: fundamentally, our DNA is spun around little protein spools called histones. These histones provide a structure for DNA and assist in gene regulation, or the process of turning genes on and off. Genes, obviously, cause development.

There are two histone sites where the methyl-marking (methylation) occurs; the K4 site and the K27 site. At the K27 site, the DNA is bound very tightly to the histone complex, not allowing any strands to become available for transcription (expression of DNA into protein). These sites are marked in adults.

At the K4 site, the strands are loosely bound, more accessible. K4 sites are marked in young, undifferentiated cells, like embryonic stem cells.

What this says, in a nutshell, is that they have found the areas where gene expression is a go (marked K4 region, in young cells) and where it is shut down (K27, in adults).

Certain genes do not have to be "turned on" when we are fully grown - especially genes that direct limb or organ growth - and the marked K27 site prevents that area of DNA to be accessed.

However, the K4 site would need to marked in the blastocyst and the DNA made available in order to start the differentiation process, so the cells could be directed into whatever is needed: liver cells, muscle tissue, bone, neurons, etc.

We're getting closer by the month, it seems.

July 28, 2006

Ayn Rand Institute Fellow Misconstrues Environmentalism

I want to share a quintessential mistake of rhetoricians: This article, by Onkar Ghate - fellow of the Ayn Rand Institute, professor, and writer for Capitalist Magazine - is so horribly skewed and misinformative, it is hard to believe that the institute allowed it to be published in the first place:

After reporting the arrest of several ecoterrorists from the Earth Liberation Front (ELF) earlier this year, Ghate says:
Despite common belief to the opposite, the ideology of environmentalism is not concerned with improving man's life on earth. If it were, it would not oppose but champion industrial progress--luxury homes, dams, highways, bioengineering, food irradiation, etc.--and the individuals who create it.

Environmentalism instead champions wilderness (including wild animals). On this premise, science and technology are irredeemably evil. If the supreme value is a world untouched by human hands, then in logic man and industry are destroyers of value, to be eliminated by force if necessary.

Committed environmentalists openly voice this hatred of man and industry. The founder of Green Peace reflects: "I got the impression that instead of going out to shoot birds, I should go out and shoot kids who shoot birds." A biologist with the U.S. National Park Services states: "Until such time as Homo sapiens should decide to return to nature, some of us can only hope for the right virus to come along." The head of the 1992 Earth Summit wonders: "Isn't the only hope for the planet that the industrialized civilizations collapse? Isn't it our responsibility to bring that about?"

Environmental terrorism is a consistent expression of environmentalism's worship of wilderness. By making the preservation of untouched nature the ideal, environmentalism necessarily makes man, who survives by exploiting nature, the enemy.

If we value our lives, we must never make common cause with environmentalism, no matter how appealing a particular environmentalist project may seem. We must fight not only against particular environmental terrorists but also against the ideology that inspires them. But even more important, we must fight for rational values: man's life and industrial civilization.

Ghate places all environmentalists (apparently including conservation biologists and ecologists) in the same boat, assuming that all accepting that title are no better than self-destructive anarchists with murderous intentions, wishing for the day that industrialized society collapses. While I was reading this essay, I kept waiting for some distinction to be made between the criminals from ELF that were apprehended and prosecuted and the conservationists concerned with protecting our wild areas and maintaining biodiversity through sound science and economics. Ghate acts like human beings aren't inhabitants of the biosphere.

Most environmentalists value human life above all, but feel it is our moral responsibility to protect the products of 3,500 million years of evolution on Earth. Most environmentalists want to make people's lives better, healthier by encouraging government and industry to consider cleaner, more efficient uses of energy. Most true environmentalists realize the power of capitalism and free enterprise to promote new ideas and create new jobs guided by less invasive measures of utilizing nature's resources.

Most of all, environmentalists are thinking ahead, realizing that human beings are capable of great things when reason prevails. Protecting our "cradle," as E.O. Wilson has called the Earth, is as rational a purpose of any I can think. Without science, the foundation of reason, conservation would not be possible.

Environmentalism and humanism are not mutually distinct; rather, much like other areas of thought, they intersect on several levels, from surface values to deepest philosophy. Ghate's essay is as ignorant as it is harmful. As a professor of philosophy and fellow of the Ayn Rand Institute, he should know better than to make sophomoric generalizations about anything.

July 25, 2006

Why Spiders Aren't Insects IV: Adventures in Molecular Homology

Photo by: Gerald Yuvailos

This is the fourth part in an ongoing series discussing the distinction and evolution of spiders and other arthropods.
Part I, part II and part III have led up to this point:

In the last post of this series, we established that spiders descended from marine arthropods called the eurypterids, distinct and separate from insects, appearing in the fossil record in the late Silurian/early Devonian, about 425 million years ago.

The cladogram we used to analyze the spider's history was based on the organism's morphological characteristics, that is, visible structures like chelicerae and book lungs that can be tied to other organisms that possess the same structures. Limulus (the extant horseshoe crab) has both of these structures and predates the spiders, placing them further back in the chelicerates' evolutionary history.

Homologous bones from human (I), dog (II), pig (III), cow (IV), tapir (V) and horse (VI):
r — Radius, u — Ulna, a — Scaphoid, b — Lunare, c — Triquetrum, d — Trapezium,
e — Trapezoid, f — Capitatum, g — Hamatum, p — Pisiforme

Paleontologists call this comparison of physical characteristics homology (coined by Richard Owen an anatomist and, ironically an opponent of Darwin). The mouth parts of a spider are homologous to the mouth parts of Limulus because of the cherlicae's exact form and function. This is a different designation than analogy; analogous structures may function in the same way, but they are different in form because of their different lineage. For this reason, scientists call analogy an artificial classification system.

A good example of analogous structures are wings from bat and bird. They perform the same function in varying degrees, but they have evolved very different forms. A bat's wing is basically a modified mammal hand, while the bird wing is a modified tetrapod arm.

Homology is essential in building an organism's phylogeny (evolutionary history). More recently, geneticists have employed this classification technique to analyze and find similarities among the less visible traits in life, RNA (ribonucleic acid) and the building blocks of proteins, amino acids.

Think of these cellular chemicals this way: If DNA is the blueprint of life, RNA is the builder and its materials are amino acids. When these amino acids are placed in the correct sequence by RNA, they become proteins, the framework of our body. And, since the genetic code for protein constructions is nearly universal*, geneticists can compare entire swaths of RNA from one organism to those of another and find homology at the molecular level.

Here's an example (sequences are greatly abbreviated for the sake of our sanity):

Organism 1: ACGC-CCCCC
Organism 2: ACGC-CCCUC
Organism 3: ACGU-CUCUC

Basically, from noting the differences in each RNA sequence, and determining the homologous sequences (such as the ACGU sequence above), a cladogram can be constructed that shows common ancestry without the murky distinctions that sometimes cloud the comparison of bones to bones, or mouth parts to mouth parts.

The problem with this molecular system of analysis is that it often provides vastly different cladograms than the ones crafted through morphological analysis. This is not necessarily the case between the spiders and and Limulus, the molecular evidence supports the fossil record's interpretation of ancestry, but it calls into question the descent of insects from chelicerates like spiders.

In short, the molecular evidence agrees with the morphological evidence: spiders are more closely related to horseshoe crabs than insects. But where and when did the insects arise?

Next time we'll tackle the more recent movements to elucidate the phylogeny of arthropods, including a discussion on the significance Hox genes and evolutionary-developmental biology (evo-devo).

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Only One Month Left...

...and I still have loads to do.

School starts back up in a little over a month, and I am a bit behind in my article writing. For those that don't know, The Voltage Gate is going to print starting this school year as a hard copy supplement to this blog.

Anyway, I told myself at the end of last semester that this summer I would crack down and have six or so non-timely articles ready for publication by the end of August.

Publishing gets to be a bear when you fill multiple roles. At the beginning of last semester I was news editor, music editor, managing editor, layout design and, of course, staff writer. By the end of the semester I had passed several of those roles to our most competant staff members. Hopefully this semester I can keep it to layout, columnist and editor.

I have a great handful of ideas for the column, discussing everything from evolution in plain terms to the science of homosexuality to the general misinterpretation of science. The list goes on almost indefinitely.

The Bottom Line's new website is finally coming together, and even in its early stages it is leaps and bounds beyond our last set up (although in defense of our old website, it was entirely created and run by one student; College Publisher does not have such limitations).

So, all in all, expect a lot of cross traffic here at TVG, from The Bottom Line website to its blog to the new blogs of our columnists. I have high hopes for the coming year.

July 21, 2006

Right Compares Al Gore with Hitler; Erudition #11


But, I would like to point you in the direction of a post from Jen at Studying Biology and Environmental Science who quotes an article about the general denial of human-induced climate change, even going so far as to compare Al Gore with Hitler.

It's worth a read for both sides of the fence; conservatives can see what nonsense their representatives are spewing on television and in print, and liberals can continue to build up their ammo stores for 2008, platforming about environmentalism as if it we just another political issue. Enjoy.

As a side note: There are very few blogs that I read on a daily basis; Jen's in one of them. Go check it out.

My brother is coming up this weekend, so I won't be blogging until Sunday evening.

July 19, 2006

"Crossing the Moral Boundary": The Science Behind Bush's Stem Cell Veto

This situation is unfortunate. Bush is foolish on so many levels, but mainly in the fact that other countries will get the jump on us if NIH is not properly funded to begin research. Bone marrow transplants (aka adult stem cells) are incredibly painful and extremely limited in variety of function. Adult stem cells are what is called "unipotent," which means they can only differentiate into one type of cell at a time.

Embryonic stem cells are "pluripotent," which means they can differentiate into all types of cells, from muscle to neuron, to germ cells - eggs and sperm. They are the mutable macro-building blocks of an organism, but undirected by its genes.

So, adult stem cells are undifferentiated cells residing in differentiated tissue, and therefore limited; while embryonic stem cells are undifferentiated cells in undifferentiated "tissue," and potentially limitless in capability to replicate, well, anything for anyone.

If you take nothing else with you from this post, consider this: embryonic stem cells are taken from a literal ball of cells (the blastocyst, below) in such an early stage in life that it remains unattached to the uterus. No nervous activity, no "parts," only cells.


This is another scientific issue dragged into the political arena, like evolution and climate change, discussed and debated by people who don't even understand (or want to understand) the real science behind the curtain.

All is not lost, however. State institutions like Johns Hopkins in Baltimore was recently given the go ahead by Ehrlich, and $15 million was given to Hopkins for research. And Maryland is not the only state that is bypassing the federal government. We'll get there eventually; then maybe we can save some lives and make some technical headway.

Hopefully I can tie this post in with a discussion of Hox genes when we tackle part IV of "Why Spiders Aren't Insects."

July 18, 2006

Why Spiders Aren't Insects III: The Evolutionary Advantages of Mass Extinction

So far we have established that spiders are distinct from insects for two reasons: physiology (mouth parts, body plan, respiratory structures) and more importantly, evolutionary history (or phylogeny, as scientists call it).

But where did spider's come from? How did they crawl out of the water as euryterids and speciate (become a distinct organism that cannot interbreed)?

The answer, like many in invertebrate paleontology, is cloudy. Organisms without hard, thick shells rarely become fossilized. In fact, for any organism's parts to become fossilized, even vertebrates, is a profound rarity, as Bill Bryson illustrates in A Short History of Nearly Everything:
Only about one bone in a billion, it is thought, ever becomes fossilized. If that is so, it means that the complete fossil legacy of all the Americans alive today - that's 270 million people with 206 bones each - will only be about fifty bones, one quarter of a complete skeleton.
Needless to say, invertebrate paleontologists are having a heck of a time piecing things together from such a paltry fossil record. But that doesn't mean there's no evidence.

According to morphological and geological evidence, and therefore directly observable comparison, spiders and their brethren descended from the eurypterids, many of which were sea-going creatures. The eurypterids arose in the Ordovician, a period that began with the decimation of perhaps 60% of all marine life, and consequently ended with another more devastating cataclysm, which which some paleontologists rank as the second most destructive extinction event in the history of the world (by extinction of family). This has become known, quite appropriately, as the end-Ordovician event.

Mass extinctions make room for the evolution of unique characteristics as dictated by an organism's environment, and the environment changed drastically for the eurypterids at the end of the Ordovician. Glaciers began to creep down from the upper latitude, as the greenhouse gas carbon dioxide was depleted from the atmosphere, reducing the Earth's ability to trap the sun's heat energy. As the glaciers encroached, sea levels dropped and global temperatures cooled. This rapid progression decimated habitats, and destroyed a species' equilibrium with its environment.

But the end-Ordovician event was comprised of two parts: glaciation and then a period melting, an interglacial. Temperatures warmed once more, glaciers melted, flooding the land, and raising sea levels once more. The world had completely lost almost 50 percent of the families of life, but the ancestors of the spiders had survived. The Silurian period had begun, and new ecological niches were available for exploitation, a habitat opportunity that eventually would produce the spider.

That's about how it stands from a morphological perspective. But more recently scientists have been delving into molecular evidence and crafting very different explanations of not only the rise of the spider, but the vast diversification of arthropods in general.

Next time we'll address the new cladograms produce by this molecular evidence, and what ramifications it might have in interpreting the diaspora of the most abundant creatures on the planet.

*Interestingly enough, we are in the middle of an interglacial right now, the Holocene. Much like the success of the spider, our current interglacial, which began about 16,000 years ago, may have contributed to the ultimate "success" of Homo sapiens.

Resources:

Pechenik, J. A. (2000). Biology of the Invertebrates. : McGraw Hill Companies.

Gradstein, Felix, James Ogg, and Alan Smith, eds., 2004. A Geologic Time Scale 2004 (Cambridge University Press)

Baez, J. (2005). Temperature. Retrieved July 18, 2006, from http://www.math.ucr.edu/home/baez/temperature/

Webby, Barry D. and Mary L. Droser, eds., 2004. The Great Ordovician Biodiversification Event

University of Bristol. (2004). Fossil chelicerates and evolution. Retrieved July 18, 2006, from http://palaeo.gly.bris.ac.uk/Palaeofiles/Fossilgroups/Chelicerata/fossils.html

July 16, 2006

Tom Brokaw Tackles Global Warming

Tonight at 9 p.m. on the Discovery Channel, Tom Brokaw presents "Global Warming: What You Need to Know," which is less about his journey (a la Al Gore) and more about the evidence for human-induced climate change.

Update: The link above has a listing of the other show times this week.

The program was excellent, as I expected. Brokaw talked to the big climatologists - Oppenheimer, Hansen - plus ecologists and biologists who explained the potential for a mass extinction crisis.

If you have a spare two hours this week and any of those times fit into your schedule, please sit down with your loved ones with an open mind. This issue could unify us as a country once more.

Why Spiders Aren't Insects: II [or] A Primer on Cladistics

So how is it that spiders are more closely related to horseshoe crabs - marine arthropods that haven't changed much in the past 250 million years - than to a more obvious choice, the insects?


The answer to that question is more complex than you might think.

Up until the middle of the 20th century, before evolutionary theory was completely accepted by mainstream biology and supported by genetic analysis, taxonomists (scientists who place organisms in groups) classified organisms according to their modern anatomy. If organisms shared common physical structures (like chelicerae or mandibles) they would be placed in groups (like subphylums and classes) that put like with like. The Linnaean system of classification is still used today, but a more recent mode of classification has been able to answer how evolution plays a part in giving rise to new anatomy, and how organisms are related through common ancestry.

Common ancestry is what evolution is all about when it comes down to it, and this relatively new way of studying common ancestry is called cladistics (links to a great BBC explanation).

Open up this evolutionary tree into a new window/tab and follow along with me. This tree, a cladogram, represents the evolutionary history of all the chelicerates; spiders ("other arachnids"), horseshoe crabs ("Xiphosurida"), eurypterids, and scorpions. The cladogram labels time periods at the top from approximately 550 millions years ago (the Cambrian era) to about 250 millions years ago (the Permian era). We're mainly interested in that bracket on the bottom encompassing the "true chelicerates."

Notice on the cladogram that you can trace each group back to one point where it splits between one group and another. Take the "other arachnids" branch for example. You can trace its branch back to the split with the scorpions, and at that split there is a common ancestor from which both other arachnids - including spiders - and scorpions descended.

So basically, cladograms are family trees that evolutionary biologists can use to determine the ancestry and hierarchy of modern organisms.*

Ernst Haeckel's artistic representation of two species of eurypterids.

Keep tracing that line back from the common ancestor of spiders and scorpions. The next stop is the eurypterids (image above) the extinct relatives of the spider. Go even further back and there's a split between the common ancestor of eurypterids (and subsequently spiders and scorpions) and another extinct group of chelicerates, the Chasmataspida.

Finally, follow that last split back, all the way back to the Ordovician period, over 400 million years ago, to where the horseshoe crabs arose. That is where the true connection between the horseshoe crab and the spiders lies, in their common ancestry, not merely in their modern anatomical similarities.

Nowhere on this cladogram do you see insects giving rise to the spiders. In fact, modern insects would arise in later periods, millions of years after the first spiders crawled on land, although the details of the appearance of insects is still debated.

But how did spiders become distinct from their marine ancestors? The transition from water to land (and sometimes from land back to water) for all organisms is one the most interesting aspects of evolutionary biology, and though it remains somewhat of a mystery for spiders, we'll delve into the facts tomorrow.

*Cladograms are closer to what Darwin suggested for phyletic analysis in Origin of Species than the Linnaean system.

July 15, 2006

Why Spiders Aren't Insects: I

This is the first in a series of discussions on the evolutionary significance of the spider and its relatives.

Perhaps nothing will spark a lengthy dissertation from an entomologist more quickly than calling a spider a "bug." And lengthy can be well, hours.

Truly, spiders do seem rather buggish; they're creepy, have loads of legs and the thick outer structure (an exoskeleton) that other bugs possess. In short, if it looks like it, feels like it, tastes like it (?!), well, it must be...

That rule doesn't apply here. When you look more closely at a spider, one thing becomes immediately clear: it only has two segments, the most important of which is called the prosoma. The prosoma in spiders is the smaller segment and bears both the spider's head and all of the spider's walking legs, while the larger part, the abdomen, bears another part spiders are famous for, silk-secreting spinnerets (we'll discuss silk production in a later post).

The major distinction between spiders and insects is in the mouth. While insects have evolved leaf and flesh shredding mandibles from small appendages on the head evolved from a common ancestor of both spiders and insects, spiders have more primitive feeding parts called chelicerae tipped with well-known and well-feared fangs with which spiders subdue and tear prey into digestible pieces. Chelicerae can be used like knives or scissors depending on the species of spider.

For this reason more than any other, spiders are placed as a class under the subphylum Chelicerata (Greek: claw) and insects are placed into the subphylum Mandibulata*, (Greek: jaw).

Chelicerata incorporates not only the arachnids (spiders, scorpions and mites), but also the extant horseshoe crabs, the extinct eurypterids (perhaps the largest arthropods ever to live, reaching lengths of over six feet) and the relatively obscure pycnogonids or "sea spiders."

So in essence, spiders are more closely related to horseshoe crabs than insects. Not only do they have a prosoma and chelicerae, but they also respire in much the same way, from a oxygen exchanging structure that closely resembles a book.

Tomorrow we'll discuss the ancestry of spiders; once upon a time, they may have left the sea millions of years ago just to scare the curls out of you in your basement.

*With the inclusion of extinct arthropods into this subphylum, taxonomists dispute whether or not more than one subphylum is required to accurately classify these organisms.

July 12, 2006

More on Coulter: The Nature of the Columnist

Columnists like Coulter are placed in an interesting position. They craft a persona for themselves which typically does not represent who they truly are; pieces of their personality are aligned and emphasized for effect. This is the basis for column-writing. After all, people read columns for the personality, not the accuracy of information.

In fact, we had a dispute with members of Greek life over a scathing column from one of our writers, during which I had to explain the difference between the column and the editorial.

A column is written from the usually unfiltered worldview of one person (or as I stated above, a series of relevant facets of one person). People typically read columns because they appreciate this person's writing in admiration or utter hatred. Columns, in short, are all about the personality and the subject focus.

Editorials are different. They are (or should be) truly rhetorical, lining up facts and evidence through reputable sources (books, internet, experts, studies, etc.) to make an argument. Editorials are all about fact-based rhetoric.

I have seen columnists fall even in college media. A sensationalist columnist creates a two-dimensional caricature of themselves, finds the hot-button issues on campus (administration, Greek life, etc.) and the running commentary can begin (some bloggers are not much different).

They start getting attention for their daring, some good, some bad, all ego-boosting. So the persona they created starts to inflate, exerting more influence over their day-to-day self.

The smart ones can separate themselves from the caricature; the inexperienced can be crushed under the pressure of maintaining the caricature both in print and in day-to-day life. Their own one-sided rhetoric erodes the bridge between themselves and their columnist persona.

It is the same impulse that forges the political leader, the revolutionary and the maverick; and the same force that tears them all down.

Coulter crafts straw men arguments with proficiency, burning each vigorously. She is fueled by our disdain, and coronated with the praise of her rabid supporters. Without these she would shrivel into Ann Coulter the person, an empty wraith starving for attention.

Obviously not all columnists are such creatures; only the envelop-pushers, the liars and the manipulative. And it must be remembered that these people are prominent as entertainers, not advisors.

This coming year I will join their ranks as The Voltage Gate takes a step into print, but my training in science has taught me that not all opinions are equal; those built on a foundation of evidence are much more compelling.

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July 11, 2006

Ann Coulter vs. Evolution Roundup

Ann Coulter seems to be all the buzz this week, unfortunately. I wonder how many people bought the book just to get pissed off.

Ah, well. Such is the nature of American media, I suppose. Politics is a game, and we rush to get in our kicks.

Apparently, Coulter jumped on the band wagon of evolution's detractors, and devoted two (or four, I hear conflicting statements) chapters of Godless to discussing and "disproving" the theory. Of course, the response has been to pick her argument apart, bit by bit.

Here are some good links to those articles:
These are all nicely crafted responses, especially from Media Matters and The Panda's Thumb. But, I do have concerns, as usual.

It seems that evolution needs to be defended and re-explained at every turn. This is unfortunate, because it automatically lumps those who understand and accept the theory (including every scientific academy and institution in the world) in the same boat with the Godless liberalism that Ann Coulter is attacking.

Believe it or not, some of us who accept evolution as fact do not feel compelled to take the philosophical step forward and accept it as a basis for personal philosophy.

Evolution should be viewed as a natural historical mechanism. If historians of human civilization could apply one theory (and maybe they have, I'm no politcal scientist; please let me know if there is one) to the rise and fall of political systems and ideologies, it would be analogous to evolutionary theory.

Evolution is the mechanism of speciation, the diversification, rise and fall of life on earth throughout history.

Ann Coulter obviously does not understand evolution, as my betters have pointed out in the above articles. Furthermore she, and others that share the same opinion, have no concept of geologic time. It sounds ridiculous to say that my father and mother were mosquitoes because it is a ridiculous thing to say. Common ancenstry as dictated by evolution (and our own DNA) stretches back billions of years, not decades.

The saddest part of this vicious, self-propagating issue is that so much attention has to be paid to the ramblings of a sensationalist. How many times must people like Coulter be corrected? How long will the demonizing of evolution continue?

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July 9, 2006

Great Naturalist Blog: "The Rural Life"

I've been following NY Times Editor Verlyn Klinkenborg and his blog on Nytimes.com for about seven months now and I'm surprised just how many people are unfamiliar with his work.

The Rural Life is a blog about Klinkenborg's day to day life on a farm in western New York. In addition to his own words, he begins each post with an entry from the journal of famed naturalist Gilbert White. The beauty of this blog, however, is the combination of White's brief but descriptive scrawls and Klinkenborg's lucid, insightful observations, and watching how they match up with each other day by day.

Here's one of my favorite entries thus far from The Rural Life, "The Next Generation":

Gilbert White’s Selborne Journal: Friday, 30 April 1784: 29 7/10; 54; NE, E. Grey, sun, summer-like. Cucumbers set, & swell. Polyanths begin to blow well. Tulips shoot, & are strong. Sowed a pint of scarlet kidney-beans. Goose-berry bushes leaf: quick-sets still naked. Pile-wort in full bloom. Rain in April..3 inch: 92 hund:

VK: By quick-set, GW means the new slips of hawthorn that were laid to make a hedge.

***
I often try to explain why my wife and I live where we do. In the country, in nature, where we can raise pigs and chickens — those are the phrases I end up using. But it really comes down to living as close to wildness as we can. I realize that now. What makes it easier is that so many wild creatures don’t mind living near us — so near that we hardly think of them as wild any more. The grace of wildness changes somehow when it becomes familiar, when you know it as well as we know the wild turkeys and the downy woodpeckers.

The other morning, I looked out the south window to see if the flag had dropped on our rural mailbox. I saw a fox just beyond it, standing in the downfall of last year’s goldenrod. The fox paused long enough for me to get the binoculars, and then it moved off the flat to the base of a rock outcrop, part of the orbit she uses to approach our poultry. Something else moved with her. Three, perhaps four young kits were following her.

She turned and led them back to the lip of the den, where they crowded around her. She bent down and licked one of them. They were only a few pounds each, thick with soft, mottled brown fur. In another week the grass will be tall enough to hide them. A week earlier, and they would have been too young to leave the den. The vixen slipped up the hill again, and her young did not reappear.

The den is only as far from the mailbox as our house is, dug into the sunken foundation of a long-vanished outbuilding. I am only a few steps away from those kits whenever I gather the mail. A couple of weeks ago I walked over to that old foundation to see if there were any fox signs, but it is far easier to trace the vixen by her cries in the night — circling around our pasture — than by footprints during the day. I wasn’t even sure the den was really there. Now I know. I won’t go back again until midsummer, but I cannot stop watching.

When I say the grace of wildness, what I mean is its autonomy, its self-possession, the fact that it has nothing to do with us. The grace is in the separation, the distance, the sense of a self-sustaining way of life. That vixen may rely on us for a duck or a chicken now and then, and to keep the woodland from closing in. How she chose to den so close to us is beyond me. The answer is probably as simple as an available hole. But our only choice is to leave her alone, to give her enough room to raise the next generation.

July 6, 2006

Tangled Bank #56 @ e3 Information Overload




Tangled Bank #56 is up at e3 Information Overload!

Check out the carnival and its latest host, an engineering librarian at CWR University...

Carnivals are probably the best way to get your material out there and read by people who share the same interests (even if they are only your fellow writers). Blog Carnival is a neat little site that lists most of the carnivals going on right now by category, and how to get involved.

July 5, 2006

Seeding North America with Large Vertebrates; Erudition #9

Conservationists have been debating about whether or not they know enough to begin rebuilding long-lost ecosystems by replacing extinct large vertebrates with analogues from other areas.

From "Restoring Nature's Backbone" by Henry Nicholls for PLoS Biology:
Rather than trying to simply ring-fence what wildlife remains, conservationists need to be restoring whole ecologies to something of their former glory, says Josh Donlan, an ecologist at Cornell University (Ithaca, New York, United States). Last year, he and a long list of high-profile conservation biologists penned a controversial commentary in Nature in which they laid out the case for rewilding North America seeding the continent with suitable stand-ins for species that went extinct thousands of years ago [2].

Donlan's world would see carefully chosen slivers of North America grazed by giant tortoises, horses, and camels; the stamping ground of elephants in place of five species of mammoth; and African lions in lieu of the extinct American lion that once stalked the continent.

The benefits, they argued, are obvious. It would restore ecological processes that have gone by the wayside, mend broken evolutionary relationships, create a back-up population of some of the planet's most endangered species, and raise huge awareness for the conservation cause. The obstacles are substantial and the risks are not trivial, but we can no longer accept a hands-off approach to wilderness preservation, they wrote of their optimistic vision.

Optimistic is an appropriate term. I can see the attraction of a program like this; conservation biologists are often ignored, and seem to be relegated to passive measures of protection. This seeding method is an active approach, where they can use their knowledge to manipulate ecological systems in order to save certain environments.

But is there enough knowledge of these systems to be able to manipulate these environments effectively? Ecosystems are incredibly complex, and if their data are incomplete, if
one organism or mechanism in the system is missing from ecological models, manipulation enters a dangerous zone.

In other words, do we know enough about nature to rebuild it?

The same question can be asked of drug companies. How many pharmaceuticals are pulled from the market because of unforeseen consequences? And this comes after years of research and testing.

Administering drugs to the body is an inelegant process, like tossing a wrench into a car engine and hoping it will fix itself. I'm exaggerating of course, the body automatically distributes chemicals along certain paths, but the paths themselves are not fully understood.

My point is, there are trillions of chemical factors extant in one human being, and one person's chemical environment is sometimes drastically different from the next.

The same can be said of ecosystems. Each one runs analogous to another in certain ways, with different organisms filling certain niches, but there are certain distinctions that need to be fully understood before administering new organisms that never existed in that particular system before.

All I'm saying is this: Ecologists need to make sure that the African lion is truly analogous to the extinct American lion before the animal is introduced to the North American landscape, and the system that exists now, thousands of years after the American lion's extinction, can support such a predator.

July 4, 2006

Happy Indepedence Day!

Despite all of America's problems, I'm still proud to be able to discuss them freely.

Happy 4th, everyone. Check out RocketScience, the science of fireworks, from Drexel University.

I'll be back in a few days (maybe this evening, maybe Friday...); Heather and I have been touring the family holiday circuit. :-)