Processing!

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

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

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

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

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

Not the Sum of Adaptations

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?

Constraint

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

From the Perry Bible Fellowship:

I Believe in the Stork

Don't you?