Life | Theoretically

Processing!

2008-05-16T17:12:00.001-04:00

So I've been playing with Processing over the past couple days. Needless to say I'm bored. Here's one small applet I've written.

We The Robots

2007-12-30T13:53:00.000-05:00

Here's the first strip of the comic We The Robots. There's no really reason to post it other than the fact that it reminded of a good conversation I had with an old friend about the consciousness of machines. The rest of the strip is quite enjoyable. Have fun clicking.

Conway's Game of Life

2007-11-30T14:12:00.001-05:00

Conway's Game of Life is the perfect example of how a simple rule-set can give birth to a hugely complex and evolvable system. Watch the video below for a wonderful five minute introduction.

See wikipedia for more information.

Mutating Pictures

2007-11-06T00:54:00.000-05:00

I've taken a long hiatus from blogging recently, but luckily I've collected a lot of biological goodies to post over the next few weeks. First up is Mutating Pictures.

Mutating Pictures is attempting to genetically evolve a group of shapes into the form of a face. On the main page, a simple graphic is displayed like the one above. The visitor to the website is asked to rank the image on a scale of one to ten for "faceness." At any one time 1000 faces are in a pool that randomly appear on the mainpage. The most highly rated "faces" are then mated to create the next generation. Overtime you can actually see the random shapes evolve into somewhat face-like projections. [Edit: the website now randomly picks an animal, body, or face for you to rate.]

It's very cool to see just how powerful artificial selection can be: from fruits and vegetables to livestock and pets to computer-generated faces and bodies. It's also interesting to note that the author has switched projects several times: faces to animals to bodies, and yet the final products do not look exactly like the desired form. I'm guessing that the author switched because the the images reached their peak fitness, i.e. they could no longer evolve in the given environment due to some programming constraint. It would be interesting to see if the author can change the code to optimize for selection and variability.

So check out the website and see if you can't help apply some selective pressure, you Darwinian Dogs, you.

Schedule for Next Semester

2007-11-05T17:29:00.001-05:00

If I'm crazy enough to take three bio courses in one semester:

Not the Sum of Adaptations

2007-10-18T04:40:00.000-04:00

Not the Sum of Adaptations

The biological world is replete with diversity of form among individuals of a species. Through this diversity, Darwin saw a mechanism that could drive the creation of new species: natural selection. Natural selection allows for a species to adapt to its environment through the heritable exchange of traits from parents to offspring. Those traits that are best adapted to the environment increase the fitness of an organism so that it may produce more offspring. Coupling natural selection with variation, Darwin argues in The Origin of Species that each and every feature of an organism is an adaptation. His argument runs as follows: assuming that every feature of organisms varies and that every feature is subject to natural selection, then every feature must be an adaptation. Despite Darwin’s elegant argument, the current thinking on the modern evolutionary synthesis serves to prove that his logic and assumptions are incorrect. Firstly, in an organism, some features are subject to structural constraints; secondly, some have no heritable information on which natural selection can act; and thirdly, some are the result of random chance and not natural selection at all. Although he argues that all traits are variable, Darwin is incorrect in assuming that all traits are adaptations because of these three qualifications of his logic.

Darwin claims that all traits have the ability to vary. He does not dare to place a bound on the amount of change that can produce adaptation. To him, nature’s selective power can form any trait. To his opponents who would argue that unity of type prevents variation, Darwin argues that even unity of type can be overcome by selection if the environment of the organism changes. To Darwin unity of type (e.g. all insects have six legs, a head, a thorax, and an abdomen) is the result of similar environmental conditions and a common lineage, not the result of a deeper constraint to the organism. Given a change in a species’ environment, natural selection can overcome the seemingly entrenched body plan of the insect. Because he accepts that natural selection is the only mechanism for evolution and that all features are adaptations, Darwin must believe that all features of organisms vary. Darwin names very many instances of polymorphism to support the idea that traits vary in all organisms including plants, insects, and Brachiopod shells. He also bolsters his claim with examples of variation where dissenters would deem it impossible i.e. the most important traits of a creature. Darwin shows that variation occurs even in the central nervous system of insects despite its importance and unlikelihood to vary. To Darwin all traits must vary because of his observations of widespread variation and because natural selection is the only mechanism to prove all traits adaptive.

Counter to Darwin’s first assumption, not every heritable feature of an organism can vary within a species and thus not every feature can be an adaptation. Surely at an atomic level variation is common, but these traits are not inheritable and thus not subject to natural selection. At the level upon which natural selection can act, some features are subject to constraints. Variation and natural selection cannot produce universally diverse form. Some structures are bound to one another such as the hipbone of the whale and snake. In each case the hipbone is vestigial – owing its existence to a walking ancestor – yet natural selection has not yet acted upon it to remove the seeming waste of resources. The structuralist would argue that the hipbone, once evolved, is now integral to the creature’s body plan. The vestigial hipbone has become locked into the development of the spine and cannot be removed. As such this entrenched trait is not an adaptation. In addition to this argument, constraint can be declared necessary for natural selection to occur. For example, arthropods constrained by a chitin exoskeleton were able to diversify into the varied body plans we see today: spiders, insects, crustaceans, etc. This constraint provided a structure upon which limited variation could occur. Although the exoskeleton can vary in shape and form, the chitin exoskeleton itself as a constraint has now become entrenched into the body plan of the arthropod and cannot be lost. All arthropods maintain this trait and it is arguably invariable to possess an exoskeleton as an arthropod. Because constraints like the hipbone and spine, and the presence of a chitin exoskeleton are locked into the body plan of an organism, these features cannot vary. Without variation, natural selection has nothing on which to act and thus these features cannot be adaptations.

Darwin’s second assumption that every feature is subject to natural selection is also inherently false due to the existence of noninheritable traits. The environment can have a large influence on the development of an organism. A high altitude can stunt the growth of a tree; however, this variation in size does not pass on from parent to offspring. If the seeds of a tall, valley pine tree are planted near the top of a mountain, they will not reach the height of their parents. After a generation or so, if the seeds of the stunted, mountainous pine tree were returned to the valley, they would grow as tall as their grandparents. In this instance the feature of size varies by environment, not by genetics. Because this feature is not heritable it is not subject to natural selection. Because they are unaffected by natural selection, features that are environmentally determined cannot be said to be adaptations.

There is another mechanism through which a species can change over time that Darwin never considers: genetic drift. Some features of a species become fixed from chance, or drift, alone without the effects of natural selection and therefore cannot be said to be adaptations. When a mutation arises, there is a possibility that it will have no measurable change on the fitness of the organism. These mutations are said to be neutral. Despite having the same fitness, not all organisms of a species have the same number of offspring. If by chance alone, the organism with the new mutation were to have more offspring, the neutral trait would begin its random walk between representing zero percent and one-hundred percent of the population. Over time through the laws of probability, there is a small but definite possibility that the new, neutral trait shall become fixed in the population. Through no selection pressure whatsoever, a trait could become representative in all members of a species. Genetic drift occurs without the pressure of natural selection, therefore any trait created from it cannot be said to be an adaptation.

Darwin must argue that all features vary because he believes that every feature of an organism is an adaptation and natural selection is his only mechanism of species change. Despite his best attempts, modern evolutionary theory has discounted Darwin’s assumptions and derailed his conclusions. Some features do not vary due to structural constraints, noninheritable features are not subject to natural selection, and some features are not adaptations at all. From the constrained hip bone of the whale to the environmentally stunted height of the pine tree to the random walk of genetic drift, it does not follow that an organism is just the sum of adaptations.

Archaeoptewho?

2007-10-16T21:02:00.001-04:00

Constraint

2007-10-10T22:43:00.000-04:00

Our world is populated by creatures of every variety, using different adaptations to survive in and even thrive in the habitats they call home. If a species cannot adapt to a changing environment it is doomed to extinction. This flexibility to change is necessary then for survival and thus any hindrance or constraint on flexibility should decrease the specie’s chances of survival. Shocking as it may seem, constraints are not only necessary for adaptations to occur but constraint within reason may actually drive adaptation.

In order for species to adapt, the organisms of the species must vary from one another allowing differential reproduction caused by natural selection to favor some traits over others. Those traits that increase the fitness of their organism are thus adaptations. If we took away all constraints there can be no form. Without even the slightest constraints such as base physical laws such as gravity, organisms would be an indiscernible cellular noise. Without form there can be no variation. The molecules of gas in a balloon are as nearly free from constraint. Looking at them, we can describe their state only as a generalization: pressure. There is no form or structure or variation, only average density. Without variation there is nothing on which natural selection can act and thus no adaptations can be formed.

Given too much constraint and a species will fail to adapt to its surroundings, however, given the constraint of body form and structure, small variations can accrue to create adaptations. Arthropods - insects, arachnids, and crustaceans - have become the most successful diversified phyla in the animal kingdom by exploiting the constraint of an exoskeleton. Their building constraint provides a tremendous platform for variation of form and thus makes them highly adaptable to a changing environment.

Cetacean Adaptation

2007-10-08T18:35:00.000-04:00

From the Perry Bible Fellowship:

I Believe in the Stork

2007-09-23T18:35:00.000-04:00

Don't you?

The Great Chain of Being

2007-09-19T12:53:00.000-04:00

“The inhabitants of each successive period in the world’s history have beaten their predecessors in the race for life, and are, in so far, higher in the scale of nature; and this may account for the vague yet ill-defined sentiment felt by many paleontologists, that organization on the whole has progressed” (Darwin, On the Origin of Species, 345).

Not so beautiful a sentence as it is interesting. Darwin continues his theme of offspring beating their less fit parents in the struggle for survival. Now, however, it is infused with the Great Chain of Being, the ordered list of creatures based on their advancement. Oddly rather than abandon the idea, Darwin chooses to maintain the Great Chain of Being – created through natural selection, not the mind God – in an appeal to the order-bent minds of his contemporaries.

It took many more years to give up the idea of biological progression in the academic world, but it persists to this day among most people as a common notion. For one reason or another, we are raised to have that “ill-defined sentiment” to place ourselves at the top of the chain, and order the rest of life below us. We feel we are most advanced. Apes may use tools, but they do not build cities. Ants may form cities but they do not create wonders of technology. Obviously we are the most intelligent. Self-deception is easy when we use anthropic criteria.

Evolution should make no appeal to the scale of nature. A creature’s success is determined by its fitness, the number of children it has or by ratio the amount of genetic material it passes on. Surely we are ashamed of any ordering based on evolution’s only criterion for we are quickly humbled by the modest rodent, the fertile fish, or the lowly bacteria.

We, all creatures of this earth, descend from a common ancestor. We adapt to life’s challenges not progress for them.

Brittle Star

2007-09-16T16:03:00.000-04:00

An order of brittle star known as Phrynophiurida

Spore Release Date Official

2007-09-13T00:35:00.001-04:00

Finding out that Spore finally has a firm release date makes me as awed as this photo. March 3rd, 2008!!! <-- The only time I'll ever use three exclamation points in this blog save for March 3rd, 2008 (link via Amazon, scroll down for release information).

The Wilted Rose and the Common Pebble

2007-09-12T01:15:00.000-04:00

“Slow though the process of selection may be, if feeble can do much by his powers of artificial selection, I can see no limit to the amount of change, to the beauty and infinite complexity of the coadaptations between all organic beings, one with another and with their physical conditions of life, which may be effected in the long course of time by nature’s power of selection” (Darwin, On the Origin of Species, 109).

There is beauty in complexity. We admire the wilting rose more than the common pebble. There is beauty in the delicate balance between structure and disorder. In one sentence, albeit a full one, Darwin cements a structure that embraces both the chaotic and the infinite. At first, chaos would seem to belie order, but in an organic system the two are dependent on one another. A cell must be more chaotic than a crystal to be acted upon evolutionarily, yet it must also have enough order to take energy from its surroundings, grow, and reproduce. Although the father of evolution and a functionalist at heart, Darwin here fiddles with a proto-structuralist view, one in which the underlying “physical conditions of life” dictate organization and change. Darwin recognizes the deep relationships between all things and that this interconnectedness stems from the ideal of limitless change and “infinite complexity.” Given a proper dollop of time, “nature’s power of selection” would populate and speciate the globe.

What is most striking is Darwin’s universality. He abandons his pigeons, his finches, and his beetles and applies this beauty of adaptation to all forms. There are no longer any needs for specific anecdotes of variety and speciation. Darwin pans back effortlessly for the reader to gasp at the vista of his theory, universal in scope and replete in form. There is beauty in the structure of a theory that can bind the chaos of our organic world. There is beauty in this complexity.

Diatoms

2007-09-11T17:04:00.000-04:00

Diatoms are microscopic organisms, or more specifically, eukaryotic algae that encase their single cell in a shell of silica called a frustule. It is estimated that by weight they make up one-fourth of the world's lifeforms.

Honeybee Disappearance Explained

2007-09-09T22:45:00.000-04:00

Remember how all those honeybees were disappearing, and doomsayers were forecasting the collapse of agriculture and the economy? Well it turns out the problem wasn't as serious as most had thought. And now a group of scientists has linked the "colony collapse disorder" to the rare Israeli acute paralysis virus. (link via Scientific American).

I wonder if I could still make a stock portfolio to play off of this? Eh.

Great Moments in Biological Mixups

2007-09-08T11:47:00.001-04:00

Is it a butterfly, a moth, or a horse? You decide, dear reader!

Sphincter for an eye?

2007-09-01T02:05:00.000-04:00

Sorry for falling off the horse. I'll try to get back on it in the next couple of days. I've accrued a lot to write about, but for now: the one, the only, the Vampyroteuthis.

The scariest squid in the whole ocean. The Vampire Squid's ancient eye does not have eyelids like yours or mine. It instead must constrict its skin around its eye in a sphincter-like movement. Disgustingly fun.

Originally found on Pharyngula.

Evolutionist up a tree

2007-08-27T17:10:00.001-04:00

Creationism and Evolution

2007-08-24T13:07:00.001-04:00

Spore!

2007-08-23T13:09:00.000-04:00

Spore is finally finished, but we'll have to wait another six long months until it ships. Read a recent review here. Don't worry; I'm excited too.

Recipe for Artificial Life

2007-08-21T20:20:00.000-04:00

The Recipe

A container
A storage of genetic information
A metabolism

ETA: 3-10 years according to the AP. Let's hope they do a little more research. (link)

Schrodinger's LOLcat

2007-08-20T13:05:00.000-04:00

Duke

2007-08-19T20:22:00.000-04:00

I'm finally back at Duke and am finally settled in. Finally. Finally? Yes.

Sometimes I just get caught on a word.

I'll be updating more frequently and with more worldly content in the next few days.

Biltmore Commercialism

2007-08-16T23:41:00.000-04:00

Continuing our meandering vacation, my family stopped at the Biltmore Estate nestled in the mountains near Asheville, NC.

Biltmore House is a French Renaissance-inspired chateau near Asheville, North Carolina, built by George Washington Vanderbilt II between 1888 and 1895. It is the largest privately-owned home in the United States, at 175,000 square feet. Still owned by Vanderbilt's descendants, it stands today as one of the most prominent remaining examples of the Gilded Age. (wikipedia)

The whole experience is overwhelmed by a condescending commercialism. The estate is currently owned by a private corporation, not a trust or non-profit of any kind. Admission is 45$, more than twice the price of the Metropolitan Museum of Art, and contains half the culture. There is a point along the unguided tour at which you must stop and have your photo taken where you can pick it up later for fee a la Disney World attractions. After finishing our tour of the house, we wandered outside near the stables which have been converted to series of elaborate giftshops which boast memorabilia printed with "Biltmore House, largest house in America (tm)." If I'm ever wealthy enough to build a larger home and do so, I'm going to sue them over their trademark. And last but not least, Lowe's is the official home improvement store of Biltmore Estates.

What a lovely little diddy of American commercialism's overreach.

The Luray Caverns

2007-08-15T23:23:00.000-04:00

Well, the lighting conditions inside the Luray Caverns were very hard to navigate with a camera. I wasn't able to take any pictures I was happy with. Please, take this professional shot I found online in lieu of any awful photos I took.

Calculus Cookie and Road Trip

2007-08-14T23:02:00.001-04:00

If you chuckle at this miracle of shelving, you obviously paid attention in calculus class.

So this week I'm returning to Duke University. My family and I are taking a road trip through Pennsylvania, West Virginia (yes we made it out alive - thank you for your concern), Virginia, and North Carolina, maybe even Tennessee somewhere in between. Our first stop is the Luray caverns which we will see tomorrow, and then we will visit all the wonderful sites and sights of Asheville, NC.

We ate in Red Robin. Insteresting. They had two televisions on either side of the restaurant so that our family didn't have to waste time communicating while we ate. Instead we could watch the Simpsons and Everyone Loves Raymond. In he bathroom there was a television also opposite from the urinals. To my surprise there was a mirror above each urinal angled to face the television screen. I normally micturate for less than 30 seconds so the mirror had little utility, but I can see how impressed men with prostate problems must be with the installation.
Please, pardon this blog's first instance of scatological humor.

Tomorrow, look forward to my first batch of cavern photos.

This week in originality

2007-08-13T15:21:00.000-04:00

From CuringDeath.com:

"A promising new line in anti-cancer therapy by blocking the molecular motors involved in copying genetic information during cell division is being pursued by young Dutch researcher Dr. Nynke Dekker in one of this year's EURYI award winning projects sponsored by the European Science Foundation (ESF) and the European Heads of Research Councils (EuroHORCS). Dekker and her team are trying to stop tumor development by interfering with the molecular motors that copy DNA during cell division. This will cut off the genetic information flow that tumours need to grow, and could complement existing cancer therapies, while in the longer term bringing the promise of improved outcomes with greatly reduced side effects."

Remembers kids, part 2

2007-08-11T02:32:00.001-04:00

Sandy Hook at Night

2007-08-09T23:49:00.000-04:00

Ladies?

2007-08-08T23:44:00.001-04:00

The one, the only: xkcd.

Out of Asia?

2007-08-08T18:59:00.000-04:00

Out of Africa, the theory that modern humans evolved in Africa before leaving, has been the mantra of anthropologists for nigh a decade now. That idea might need some qualification though. After analyzing nearly 5,000 ancient tooth samples from the genus Homo (Humans are Homo sapiens), researchers led by Maria Martinón-Torres at the National Research Center on Human Evolution in Burgos, Spain cast doubt on the second great migration out of Africa. Their article, published this week in the Proceedings of the National Academy of Sciences USA, stresses the importance of early humanity's move across Eurasia. (link via Scientific American)

Let's hope the media realizes there was still a great deal of genetic drift and gene flow. We're still one people.

Up and down

2007-08-08T17:23:00.000-04:00

Very crazy day. Market up, market up, market down, market up. I'm visiting today with my uncle who works at Morgan Stanley in algorithmic trading. It's amazing how their product is a self-fulfilling prophecy: create more information for the customer, the customer will make more trades, make more commissions. That seems like a perfectly sound business plan to me.

Are there any other ways you can do that?

Pharmaseuticals? Create drugs that solve one problem, cause others in the general population when their excreted, create new drugs to fix all the new problems you inadvertently created? It can't seriously work that way though.

Remember kids

2007-08-07T23:49:00.000-04:00

New/Old Bacteria from Melting Ice

2007-08-07T11:13:00.000-04:00

Organisms always get trapped in an ice cap as it is forming. The unwitting bacterium can be locked away for aeons never to be heard from again. Or not. A group of scientists with an ice sample over 8 million years old were able to find one type of bacterium in it that they were able to thaw out and grow in a culture. The bacteria exhibited extremely sluggish reproductive behavior, doubling once every seventy days. (In contrast, the cancer cells I worked with this summer double every day.) They attribute the slow growth to the cosmic radiation that was able to scramble the microbe's DNA for so long a period. (link via New Scientist).

Now imagine the thinning ice caps, and the fact that more microbes like this one will be spilling into the sea. Seems like the earth created another unwitting compensatory mechanism to deal with warming periods. And if not, atleast it's pretty cool to see the old become new again.

Sugar more addictive than cocaine

2007-08-06T01:09:00.000-04:00

First spotted on Dr. Joan Bushwell's Chimpanzee Refuge of ScienceBlogs:

This PLoS paper from researchers at the University Bordeaux shows that when rats where given a mutually exclusive choice between saccharin and heroine, they overwhelmingly chose saccharin, a common sugar substitute.

First sentence of the conclusions:
"Our findings clearly demonstrate that intense sweetness can surpass cocaine reward, even in drug-sensitized and -addicted individuals."

The researchers hypothesize further that the relatively sugar-poor diets of our ancestors sensitized the brain to trace amounts of sweet tastants. In our modern day society, where sugar-rich diets are common, the "supranormal reward signal in the brain [has] the potential to override self-control mechanisms and thus to lead to addiction."

Sorry Caroline. You're addicted to cotton candy.

Did I hear that right?

2007-08-04T12:41:00.000-04:00

Steps to understand the McGurk effect:

watch this video. Ask yourself if you heard that right? Chances are you didn't.
play this video again with your eyes shut
say "holy shit."

The McGurk effect highlights the combination of both auditory and visual cues in speech recognition. This clip was produced by overlaying the sound of "ba" over a video of someone saying "ga." The perceived speech should sound like a combination somewhere between the two: "da." If you close your eyes, there is no incorrectly matched video to confuse your brain and only the spoken "ba" can be heard. Cool, no?

The End of an Era

2007-08-03T19:58:00.000-04:00

Goodnight lab bench.
Goodnight so soon?
Goodnight oxidative stress.
Goodnight moon.

Wee planets

2007-08-02T14:06:00.000-04:00

My new favorite group on flickr is Wee planets. The group take 360 degree panoramas and skews them to look like small planets, more like dwarf planets. The fictitious planets look much closer in size to those of Le Petit Prince than any true dwarf planet. No baobabs so far, but I'm still looking.

This Week in Celebrating Original Minds

2007-07-31T07:51:00.000-04:00

The Fosbury Flop revolutionized the sport of high jumping. A clever thought and a graceful twist catapulted Fosbury to fame in the 1968 games where he took gold.

Guess whose middle finger

2007-07-28T19:08:00.001-04:00

See if you can guess whose middle finger this is. Because the website is under a Creative Commons Attribution-ShareAlike License I'll atleast have to point you in the direction of this. (which is the answer by the way.)

Throw your cameras in the air

2007-07-28T18:42:00.000-04:00

Clickykbd continues his excellent photography over at flickr. Recently, he has created some programs in Processing to display colorful polygons of which he takes time-lapsed photographs. To add to the excitement he's been throwing his camera though the air to create some stunningly abstract swathes of color. Unfortunately he broke his camera in a toss before finishing all his experiments. Let's hope he makes a full and fast recovery.

Documented Computer Defenstration

2007-07-26T23:19:00.000-04:00

de·fen·es·tra·tion - (dē-fěn'ĭ-strā'shən) - n. - An act of throwing someone or something out of a window. [From de- + Latin fenestra, window.]

(link).

Scientific Literacy: Drafting Plans

2007-07-26T21:21:00.000-04:00

Earlier this week I addressed my disgust over the rates of scientific literacy around the world as well as here in the United States. They are appalling low, so much so that I'm stirred to action.

My first small scale idea: starting a program/club at Duke University, where I currently attend, to advocate scientific literacy. The club would sponsor talks directed at the layman. Know of anyone particularly good at explaining complex topics in simple and enlightening terms? Also, we are committed to inspiring the generations to come to find science both exciting and inspiring. Enter Durham public schools. Oh, the moldable masses.

Steps:

Club formation
Mission statement
Fund raising
Advocacy
Work the media

Let me know if I missed anything or if you have any lovely suggestions.

Man vs. Wild Faked?

2007-07-26T21:07:00.001-04:00

Apparently Bear Grylls, professional badass, still enjoys a comfortable stay at a hotel over the wet interior of a cave. Oh, the humanity! (link)

LOLCats + LOLGeenomz

2007-07-25T10:30:00.000-04:00

First spotted on Mike the Mad Biologist:

P.S. Still working on that plan of action. No need to worry.

And check out The Aethernauts. It looks like it's finally getting going.

Scientific Literacy

2007-07-23T23:13:00.000-04:00

I'm becoming a strong advocate of scientific literacy for all Americans. The problem is much more serious than I had thought. The theories that describe the inner workings of the world fascinate me but the majority of the population has disconnected from a scientifically accurate world view. Referred through More Coffee, Please, I found a New York Times article that shares some shocking statistics (from the Center for Biomedical Communications at Northwestern University Medical School):

"American adults in general do not understand what molecules are (other than that they are really small). Fewer than a third can identify DNA as a key to heredity. Only about 10 percent know what radiation is. One adult American in five thinks the Sun revolves around the Earth, an idea science had abandoned by the 17th century" (Cornelia Dean, Scientific Savvy?).

This is appalling, not only from a scientist's perspective, but also from a citizen's. Technological advances and scientific theories are ever entering into the political domain: climate change, evolution, stem cell research. From the previous statistics it appears that an American's education is largely inadequate for responsible citizenship on scientific issues.

Perhaps less important, but equally pressing: the re-emergence of magical thinking. We all succumb to it in one way or another. (Don't say you've never crossed your fingers before hoping for better luck.) The foreseeable problem occurs when an individual sees a piece of technology and accepts a magical explanation for its properties just as well as a scientific one. I am worried that a remote control might just as well work by telepathically communicating button presses to a television instead of using infrared light pulses. And from the above statistic, only one in ten people might know of the radiated infrared light from their remote control.

Tomorrow's work: a plan of action.

Reading to relax

2007-07-22T21:39:00.000-04:00

Time to take a sizable chunk out of The Best of Enemies: Race & Redemption in the New South by Osha Gray Davidson. Duke University has selected this book as summer reading for its freshman class. As an orientation adviser I'll to read it too.

I've heard that the summer book committee had selected this book without knowing that it was out of print. We've all received freshly printed books with custom covers for Duke Class of 2011. Looks like a good way to share at least one common intellectual experience besides complaining about freshman writing.

Star Wars Episode I: Racer

2007-07-22T01:47:00.000-04:00

I dug up my old N64 today and proceeded to play video games for several hours. Best video game memories from childhood: Star Wars Episode I Racer. For some reason I always played as Toy Dampner. No real idea why. I had some pretty serious nostalgia for boosting, dodging, turning, all with cat-like reflexes might I add. Not sure why I ever stopped playing video games. Maybe it was the ladies.

My thougts exactly

2007-07-20T13:41:00.000-04:00

Randall Munroe of xkcd.com delivers a knock-out blow to any overblown pomposity,
unless, of course, that pomposity was born by caesarian section.

What I haven't been reading

2007-07-19T22:33:00.000-04:00

In honor of Marginal Revolution's "What I haven't been reading."

At Home In the Universe, by Stuart Kauffman, 10 of 304 pp.

The Structure of Evolutionary Theory, Stephen Jay Gould, 1 of 1343 pp.

Revolutionary Wealth, Alvin and Heidi Toffler, 63 of 391 pp.

The Best of Enemies, Osha Gray Davidson, 1 of 298 pp.

What is Life?, Erwin Schrodinger, 1 of 184 pp.

The Aethernauts

2007-07-18T22:58:00.000-04:00

Some friends and I are starting a blog named the Aethernauts. We're all very interesting; I promise. No one has posted anything yet, but you should probably check it out. C'est fantastique, non?

Influence?

2007-07-17T21:01:00.000-04:00

Today is National Show-a-Blogger-You-Care Day. It's a lot harder to write for an audience when you don't think they're there.

Don't get down; someone is not getting up

2007-07-16T21:48:00.001-04:00

Sadly today was the first day I actually ducked against my bedroom wall because I thought a plane flying overhead was going to drop a bomb. In retrospect my own behavior scares me more than the perceived threat from which I hid.

I have become an adamant admirer of non-zero-sum games. That probably comes from my penchant for the economy as a complex system. A non-zero-sum game describes a situation in which the sum of the of loss and gain of each participating party does not equal zero. In contrast, a zero-sum game occurs when the benefit of the winner exactly equals the loss of the loser. For example, in a game of soccer, at the end of the match, one team has lost, the other won. The utility of each result is equal and opposite. In contrast, in a non-zero-sum game such as economy, both parties can gain. When you sacrifice your leisure time to work for your company, you benefit the company and are in turn rewarded with a paycheck.

Why doesn't any national political move in the last few years reflect this world view? I have never taken a political science or public policy class so please correct me if I sound naive. If only we understood our neighbors' utility to directly benefit our own. Man's inability to recognize his negative and positive externalities just might be his second fundamental depravity.

Atleast some people are thinking about the world in a non-zero-sum way, and some of them are even optimistic about the world's future! Meet Robert Wright, best-selling author of Nonzero and The Moral Animal. Catch a video of his inspiring talk to the TED conference at ted.com and realize that everything might not be so bad afterall if we just learn to lend a helping hand.

Investigations - Stuart Kauffman

2007-07-16T01:02:00.000-04:00

For the past two weeks I have been inching through Investigations by Stuart Kauffman. I am only half way through the work that some have called as influential as Schrodinger's What is Life?, but already I can see for what Kauffman lacks in answers he makes up for in scope. Investigations is a declaration of a journey just begun, one to define a theory of the living organism.

Most simply, Kauffman describes life as any system able to perform autocatalysis and perform a thermodynamic work cycle, that is - a system able to split itself in two and able to extract energy from its surrounding system. On earth all living things possess DNA, the blueprint of the cell; RNA, the cell's messengers of instructions; and proteins, the cell's doers. Kauffman elevates his discussion of a theory of life by positing that these might not be necessary in all forms of life. The current facts presented in a General Biology textbook are merely the rules of Earth Biology, and may not be as pervasive as we have thought. Life is out there, but without a proper theory can we ever truly define it?

Seeing a video by Kauffman on edge.org when I was 17 years old firmly cemented me to a path in biology, be it theoretical or otherwise. His views of a theoretical biology have been just as large an influence on this blog as my own dreams.

To discover the true stuff of life...
If only, if only...

Jared Tarbell and Seed Magazine

2007-07-14T17:56:00.000-04:00

Something that really made me smile today: seeing Jared Tarbell of complexification.net fame team up with Seed Magazine's Carl Zimmer. Tarbell's old art project Bone Piles complemented Zimmer's endeavor to describe the modern problems facing a standard definition of life. I might delve a little deeper on that some other time.

Organic Photographs

2007-07-13T00:50:00.000-04:00

Sarcasm

2007-07-12T00:46:00.001-04:00

Did you know that sarcasm doesn't exist on the internet? It's all too true.

Memorial Sloan-Kettering Cancer Center

2007-07-11T23:43:00.000-04:00

This summer I am researching oxidative stress at a lab owned and operated by Sloan-Kettering in New York City. When I'm not commuting, I divide my time between doing productive work and waiting.

Lab work requires its own form of patience. Cells never quite grow as quickly as you would like and experiments unavoidably incur periods of waiting. Rushing a procedure or juggling two experiments never seems to work out as planned; it's best to work with a patient trepidation to avoid losing a day's data.

The work is good. I'm trying to figure out a way to reverse the resistance that most cancer lines build up to chemotherapeutics. After chemo does its initial damage, the drug is often broken down into reactive oxygen species, as a secondary effect, that can cause the same if not more damage to the cell. Because of the high mutability of cancer cells, they can often have a natural immunity to this oxidative stress. If only one cell of a tumor survives the damage from chemo because of this resistance, the tumor will regrow with an unfortunate immunity to the same drug.

Goals (from easiest to hardest):
Must figure out how immunity develops.
Must figure out how to reverse immunity.
Must create drug to enhance existing cancer treatments.
Must cure cancer.

The Rules

2007-07-11T23:34:00.000-04:00

Author's rules for posting:

1. Don't over do it.
2. Make this a habit.
3. Write for yourself (because no one else is reading this, yet).
4. Always in permanent marker.
5. It's theory! Be brash! You're not wrong until you figure you are or others prove you are.