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.