The Gates of Academe

The Daily Lesson From Biology Class

One of the small pleasures of going to biology class is the expectation of a good quote...the professor likes to quote a learned figure to create context for the day's lecture, and it's been very informative.

So, a few weeks ago, when we were beginning the last part of the course, we walked into the auditorium and saw this projected on the wall:

Animals have these advantages over man: they never hear the clock strike, they die without any idea of death, they have no theologians to instruct them, their last moments are not disturbed by unwelcome and unpleasant ceremonies, their funerals cost them nothing, and no one starts lawsuits over their wills.

Voltaire
French author, humanist, rationalist, & satirist (1694 - 1778)

Seems kinda harsh...

Darwin Week

February 9 - 15 will mark the annual celebration of Charles Darwin. Here is a link to the College of Charleston's Darwin webpage.

Here is a link to the wikipedia site for the "Great One". According to wikipedia, Darwin is credited as being the first person...

who realised and demonstrated that all species of life have evolved over time from common ancestors through the process he called natural selection. The fact that evolution occurs became accepted by the scientific community and much of the general public in his lifetime, while his theory of natural selection came to be widely seen as the primary explanation of the process of evolution in the 1930s,^[1] and now forms the basis of modern evolutionary theory. In modified form, Darwin’s scientific discovery remains the foundation of biology, as it provides a unifying logical explanation for the diversity of life.^[2]

As we have come to understand in class, his ideas moved biology from a process of collecting to a scientific method; biology joined mathematics, physics, chemistry, and other sciences as a method of explaining the world that humans occupied.

A great man.

Great Quotes....

Our biology professor likes to start each class with an inspiring quotation as the first slide of her power-point lectures. Today's quote was, at least for me, particularly insightful:

I have learned throughout my life as a composer chiefly through my mistakes and pursuits of false assumptions, not by my exposure to founts of wisdom and knowledge - Igor Stravinsky

The point seems to be that knowledge is best acquired through experience, mixed with a little education. This is a strange truism for a bunch of college kids in their first or second year of school; for me it's a statement of fact. Time is a great explainer.

And yet, in the grand scheme, I approached this educational opportunity as a way to acquire knowledge that I did not possess. The practical side of the equation.

Have I got it backwards?

Altruism - A Dying Concept?

Some quotes from my current reading in Biology:

It is also tempting to think that evolution by natural selection is progressive - meaning organisms have gotten better" over time.(In this context, better usually means more complex.)...In fact, complex traits are routinely lost or simplified over time as a result of evolution by natural selection. Populations that become parasitic are particularly prone to this trend...

Individuals (in this case organisms....my comment) with self-sacrificing alleles die and do not produce offspring. But individuals with selfish, cheater alleles survive and produce offspring.As a result, selfish alleles increase in frequency while self-sacrificing alleles decrease in frequency. Thus, it is not possible for individuals to sacrifice themselves for the good of the species. No instance of purely self-sacrificing behavior - where the individual received no fitness benefit in return, has ever been recorded in nature.

Hmmmmmm.....

Hello Its Me

...working late Friday night on a programming lab. Wondering why the damn javascript won't work, even though I have minutely examined every line of code for the last 2 hours. All I want to do is generate an alert box for empty fields when it's time to submit the form. I suspect either a logic bomb so simple and plain that my tired brain overlooks it (kinda like I don't notice the grey in my hair after seeing it in the mirror every day for the last 10 years), or an equally simple syntax error is raising it's ugly head and Lord, I am blind to see.

Making this process bearable are the pleasing notes of Pandora Radio filling my ears through an old set of headphones (so as to not disturb You Know Who). 

Appropriately enough, I discovered Pandora Radio when I walked into my biology lab and immediately heard DeBussy playing on the desktop computer's speakers. The lab instructor (a tight, smart, 20-something grad student with a perpetual tan and achingly white teeth) gave me the 5 minute tour. By that afternoon I was up and running.

I say appropriate because the Pandora website says "Radio from the Music Genome Project", a snippet which explains some of it...

The Music Genome Project, created in January 2000, is an effort founded by Will Glaser, Jon Kraft, and Tim Westergren to "capture the essence of music at the fundamental level" using over 400 attributes to describe songs and a complex mathematical algorithm to organize them. The company Savage Beast Technologies was formed to run the project.

A given song is represented by a vector (a list of attributes) containing approximately 150 "genes" (analagous to trait-determining genes for organisms in the field of genetics). Each gene corresponds to a characteristic of the music, for example, gender of lead vocalist, level of distortion on the electric guitar, type of background vocals, etc. Rock and pop songs have 150 genes, rap songs have 350, and jazz songs have approximately 400. Other genres of music, such as world and classical, have 300–500 genes. The system depends on a sufficient number of genes to render useful results. Each gene is assigned a number between 1 and 5, and fractional values are allowed but are limited to half integers.^[1]

Given the vector of one or more songs, a list of other similar songs is constructed using a distance function.

To create a song's genome, it is analyzed by a musician in a process that takes 20 to 30 minutes per song. Ten percent of songs are analyzed by more than one technician to ensure conformity with the standards, i.e., reliability.

And understanding cell structure, cell division, meiosis, mitosis, genes, DNA (et al), genetics, and inheritance are the main objective of this biology class as we approach the end of the term. Given that the Human Genome Project is very nearly complete, isn't it to be expected that we will turn our attention to our pleasures as the next step?

And, having learned what science has been able to achieve in terms of understanding the form and structure of life, I cannot be surprised that Man can apply the same tools and techniques to one of our most precious pleasures.....music.

Photosynthesis

It seems so simple. 6 molecules of carbon dioxide from the atmosphere, 6 molecules of water, sunlight, a little chemical interaction, and suddenly there exists glucose, the food of life.

6 CO₂ + 6 H₂O + photons of light (2,870 kJ) → C₆H₁₂O₆ + 6 O₂

"This process is one of the most important biochemical pathways,^[1] since nearly all life on Earth either directly or indirectly depends on it as a source of energy"...Wikipedia

It highlights, for me, the breathtaking complexity of our existence. The result of a few billion years of natural selection, even a non-creationist like me wonders about the enormous intersections of probability that must have taken place for our planet to arrive at this place in time.

And this comes from a subject that I studiously avoided in my earlier academic life. This only confirms my belief that we do and can change our ideas and beliefs as we learn from the experiences of our life.

This is a very rich time.....

Surprises

In what seems the blink of an eye we have reached the mid-point of the semester. Having a few days off marks a chance to reflect on the last 7 weeks, as well as giving oneself a moment to bask in the warmth of a (so far) successful term. Some things have been very difficult, and a brutal schedule had to be modified so as to provide time to eat, study, and simply get from one class to another without inducing a cardiac episode. But all in all, not a bad start.

The biggest surprise has been biology. It's the first of a two semester sequence required of all science majors (unless they place out based on their AP tests in high school), a sequence that had me shivering in contemplation of its difficulty, given its reputation as the destroyer of med school dreams for the hundreds of freshmen that sign up. I have, instead, found a class so fascinating that I wonder how many more biology classes I can sign up for. The professor is wonderful, the textbook thick with study aids (website, study guide) and supplemental instruction there for the taking. It requires time, for sure, but the concepts, at least at this level, are not the abstract nightmares of Java, replete with objects, methods, classes, loops, boolean logic,....you get the drift.

This stuff is just plain fun to study! Who knew the beauty of enzymes and transition states and catalytic reactions, or the mystery of chemical reactions between oxygen, carbon, hydrogen, and nitrogen, or the power of water? The cytoplasmic exoskeleton........monotubules as a transport mechanism for transport vesicles?

Are you kidding me? I feel like I'm in a transition state, a compound being catalyzed, yet not sure what my next state will be........