In Silico

The End of Science In Three Easy Steps

2005-11-28T00:07:00.000-05:00

I must be hallucinating. The Professor double-checked his copy of the Kansas science standards that was approved by the Kansas State Board of Education on November 8, 2005. No, he was not imagining things. The old standards defined science as “a human activity of systematically seeking natural explanations for what we observe in the world around us...”

This year, the board has re-defined science as “a systematic method of continuing investigation that uses observations, hypothesis testing, measurement, experimentation, logical argument and theory building to lead to more adequate explanations of natural phenomena...”

The Professor couldn't believe his eyes. Was it really true? There was no longer a requirement for science to rely on 'natural explanations'? Brilliant! Without these constraints, the Professor thought as he skipped down the University halls like a schoolboy, I can finally make some real progress.

Ten years later, the re-definition of science has taken hold in most parts of the U.S. and has allowed some amazing research to be performed. In fact, our giddy Professor is presenting his latest research to his colleagues. The talk is boldly titled “The Designer Mechanism: Bringing About The End of Science in Three Easy Steps.” Let's take a seat and listen in on this momentous talk.

“...So, as you can now clearly see, gentleman, my observations show that the hypothesis is correct. In order for Mars to revolve around the Earth in 779.96 days, The Designer must intervene to change the 'natural laws' every 25.7 months to briefly place Mars into retrograde motion. Then, after a few months, the Designer re-implements the aforementioned 'natural laws'. This mechanism elegantly reconciles the supposed 'contradiction' of the retrograde orbits with the fact that the Earth is at the very least the center of the solar system, and most likely, the universe.” The Professor anxiously scanned the auditorium, looking for any signs that the logic and simplicity of his arguments was understood and appreciated. The audience members glanced at each other with embarrassment. Good, the Professor thought. They are recognizing the folly of their original ideas and are coming around to the side of Wisdom and Truth.

“Ahem.” The Professor's head turned in the direction of the faux cough, and he saw a raised hand attached to the body of a very skeptical face. The Professor inwardly sighed. These tedious questions would end once they embraced the Designer mechanism, but for now, he decided to humor the audience members.

“Ahem.”

“Yes. You have a question.”

“Indeed. If there is an intelligent designer, as you suppose, then whey doesn't he, she, or it simply change the orbit of Mars once and for all and end the need for intervention? That would seem to be the...'intelligent' thing to do.” There were snickers from the audience at this last remark, but he shrugged off the obvious barb. The fool was simply proving his point for him.

“Precisely. That thought also occurred to me, and wracked with doubt, I almost abandoned the Grand Unifying Designer Theory altogether. But then the solution came to me in a moment of sheer Designer-inspired lucidity and removed the apparent paradox. The Reason that It does not change the orbit of Mars is that It wanted to constantly give us proof that It exists. The Designer purposely left the flaw, and many others in the world I might add, so that It would have to intervene, and we would have Proof of the Designer's existence!” The Professor brought his hand down hard on the podium after this last declaration.

Stunned silence. I have them now, thought the Professor. They couldn't possibly have any questions after that perfect insight into the mind of the Designer. What a Gift he had given to them. Now, for the pièce de résistance.

“So, gentleman, as you can see, even the so-called 'flaws' and 'contradictions' were intentionally placed there so that our less-advanced minds might perceive the presence of the Designer. The Designer mechanism explains everything that we see in the universe. It is the end of questions. It is the end of doubt. For I say to you that the greatest thing has occurred with these revelations. There is nothing left to discover! It is the End of Science!”

Stunned silence.

Mathematical Aphorisms

2005-07-30T12:25:00.000-05:00

Following are just a few funny or insightful quotes that I have recently encountered concerning mathematics.

In mathematics you don't understand things.
You just get used to them.
--Johann von Neumann

Being a mathematician is a bit like being a manic depressive: you spend your life alternating between giddy elation and black despair.
--Steven G. Krantz, A Primer of Mathematical Writing

The basis for poetry and scientific discovery is the ability to comprehend the unlike in the like and the like in the unlike.
--Jacob Bronowski

Problems worthy of attack
prove their worth by hitting back.
--Piet Hein, "Problems," Grooks (1966)

Conquering The Cube

2005-07-12T20:07:00.000-05:00

It was the early 80's, and I was spending the summer at my grandparent's house in Kentucky. My family went up there quite a bit over the holidays and summers when I was a kid and some of my best childhood memories are rooted at that house. And it was there that I was introduced to the most fascinating and infuriating puzzle that I had ever encountered during the course of my short life. Rubik's Cube.

A solved cube was sitting at my grandfather's seat at the kitchen table, and I naively picked it up, thinking that surely I could solve a puzzle that looked so simple. After about an hour of fumbling through permutation after permutation, I looked up at my grandfather in despair. What kind of cruel joke was this? Did he derive pleasure from torturing mere children? It must be impossible to solve, or else I would have been able to figure it out by now. He just chuckled, picked up The Cube, and solved it in under five minutes. He presented The Cube to me and just smiled evilly. My jaw dropped, and I both hated and admired my grandfather at that moment. He had to be the most brilliant man on the planet.

And this is when I learned the meaning of obsession.

When I saw that it was possible, I had to discover the solution. I worked feverishly for hours and hours and hours, but I could not see a clear path to the solution. The more I worked at it, the more confused I became. I thought that this is what Hell must be: being confronted with a problem, seeing that it is possible to solve, and not being able to find a solution yourself. I didn't solve The Cube during that visit, and although I tried for many years afterwards to solve it, my efforts were for naught. Finally, I just gave up.

Fast forward to the present. I can now conquer The Cube in under 5 minutes! From where did this newfound wisdom originate? I was recently at my grandparent's house, and my my 14-year-old cousin picked up my grandfather's cube and solved it in under 3 minutes. I was stunned and annoyed, and I asked him to lead lead me down the path of enlightment. He is a very, very smart lad, and it apparently became a fad with the young geeks at his school to solve The Cube. He showed to me the method in the madness, and after solving it myself for the first time, I felt momentary elation and then utter disappointment. Why, you may ask? Because solving The Cube is simply a matter of memorizing certain patterns to move a piece from one location to another and then stringing those patterns into a particular order. So, with alot of time, patience, and obsession, it is possible to solve the puzzle by memorization alone.

I'm still happy that I can conquer The Cube, but it's not enough to solve it now. I need to understand why the patterns work the way that they do. As I have come to find out, the mathematical discipline of Group Theory has even tackled the problem of finding solutions to The Cube, and this will most likely be my next destination in trying to understand this deceptively difficult puzzle.

Recent Reading List

2005-06-22T13:45:00.000-05:00

The following is a list of books that I have read in the past 6 months or that I am currently reading. My assessment of these books range from abject horror that someone would have consented to publish the book to paradigm-shifts in thinking to childish wonder. I will only spoil the neutral nature of the lists with a single judgment: Bioinformatics - Sequence and Genome Analysis has to be one of the worst scientific books that I have ever read! Avoid it like you would a pack of rabid sewer rats that are carrying 20 strains of the Black Death! Hope you find something in here that you will enjoy.

Free-Time Books (Not Very Much of That)

Girl in Landscape by Jonathan Lethem
Startdust (Graphic Novel) by Neil Gaiman
The Sandman: Preludes & Nocturnes by Neil Gaiman
The Spiderwick Chronicles by Tony Diterlizzi and Holly Black
Banner of Souls by Liz Williams
Nine Layers of Sky by Liz Williams
Shadows of Myth by Rachel Lee
The Black Magician Trilogy by Trudi Canavan
The Briar King by Greg Keyes
Emergence by Steven Johnson
The Time Traveler's Wife by Audrey Niffenegger (Currently Reading)
The Roald Dahl Omnibus (Currently Reading)

School Books

Computational Molecular Biology - An Introduction by Peter Clote adn Rolf Backofen
Biological sequence analysis - Probabilistic models of proteins and nucleic acid by R. Durbin, S. Eddy, A. Krogh, and G. Mitchison
Bioinformatics - Sequence and Genome Analysis by David W. Mount
Exploration and Analysis of DNA micorarray and protein array data by D. Amaratunga and J. Cabrera
Analyzing Microarray Gene Expression Data by G.J. McLachlan, K-A Do, and C. Ambroise
Microarray Bioinformatics by D. Stekel
Graph Theory and Its Applications by Jonathan Gross and Jay Yellen (Currently Reading)
Evolution of Networks - From Biological Nets to the Internet and WWW by S.N. Dorogovtsev and J.F.F. Mendes (Currently Reading)
Principles of Biochemistry by H. Robert Horton, Laurence A. Moran, Raymond S. Ochs, David J. Rawn, K. Gray Scrimgeour, H Robert Horton (Currently Reading)

Reproductive Contingency Plan

2005-06-06T00:05:00.000-05:00

Preface

In a biological context, the evolutionary success of an individual organism (including humans) is solely determined by the number of viable offspring that the organism produces. At a molecular level, this means that at least parts of the organism's reproductive material (DNA or RNA) has been transmitted to a new organism. It is a common misconception that the success of an organism can be quantified by traits such as speed, strength, agility, and intelligence. Although these traits may contribute to the reproductive success of an individual, they are not in and of themselves the measure of said success. So, in a nutshell, the more offspring that one produces, the more successful is the individual from a biological perspective.

I recognize that there is also cultural/social evolution in human populations and that culture plays a vital role in the propagation of the human species (and to some extent, other species). However, human culture is just another trait, similar to strength or speed, that may increase the reproductive success of an individual, but is itself also not a measure of success.

The Plan

Keeping the previous concept in mind, here's my very simple reproductive contingency plan:

If I have not produced any offspring by the time that I am 35 and it does not appear that I will produce offspring in the foreseeable future, I will hop into my car, drive across the country for a month or two, and donate at every sperm bank that I can find during that time.

This seems like a perfectly reasonable plan to me, given the above definition of biological success, and I mentioned it to some of my friends some time ago while we were sitting around and talking. I'm not sure exactly how it played into the conversation, but it was relevant at the time. To my surprise, it sparked a somewhat heated debate and the idea was promptly labeled as being weird. The idea has since gone through at least two rounds of debate and the consensus amongst my friends is that the idea is bizarre. So I leave it to you, dear readers. Is the plan sound, or am I a crackhead? If you think that it is a bad idea, please explain why you think so. Let the debate begin!

Grad School (Year 1) - Thank the Gods, It's Over!

2005-05-23T23:07:00.000-05:00

It's been a week since I took my last exam, and I only now feel like I've recovered sufficiently to write about it. The horror, the horror! It actually wasn't that bad, but I definitely lost any semblance of a social life and nearly lost my mind several times. I think I need a bit more time to gain any sort of appreciation for how much I learned this year, but I can already say that I feel both smarter and stupider all at the same time. I suppose that's the curse of education. So, here's the final results for the year (drumroll please):

Fall Semester

Research Methods: A+
Numerical Methods for Bioinformatics: A
Molecular Cell Biology: A

Spring Semester

Gene Expression Analysis: A
Biological Sequence Analysis: A
Numerical Sequence Analysis: A+

And you too can have these grades for the small price of your social life! And yes, I did post them on my refrigerator.

It's funny. I used to be a slacker and didn't care at all about doing well in school when good grades mattered. Now that grades don't matter much, I manage to pull good grades. It would appear that timing may never be my strong suit. However, the first year is done, and I am very happy to get a break.

Adventures In Geocaching

2005-02-10T11:07:00.000-05:00

In case anyone is actually reading these posts, I just wanted to let everyone know that Daedalux and I have started a new blog called Team Geocache. As the name implies, we will use this forum to write about our adventures in geocaching (both together and separately). Hope you enjoy.

In Case You're Feeling Like a Loser

2005-02-05T17:40:00.000-05:00

I was recently in a bookstore with Daedalux and came across the following book:

The Complete Idiot's Guide to Enhancing Self-Esteem

Need I say more?

Geocaching Demystified

2005-02-05T17:33:00.000-05:00

My friend, Daedalux, introduced the sport of geocaching to me several months ago. At first, I was somewhat blase about the whole thing, but a couple of weeks ago I started reading about it. After going to the geocaching.com website and reading the book Geocaching for Dummies, I became hooked on the idea.

Essentially, geocaching is a poor man's version of high-tech treasure hunting. A "cache" is a collection of relatively inexpensive items that are stored in containers ranging in size from something as large as an ammo box to something as small as a pill bottle. The cache owner initially fills the cache with "treasure", hides it in either a woodland or urban setting, records the coordinates of the cache, and then posts the coordinates and a brief description of the cache on a site such as geocaching.com. Then an intrepid geocacher, armed only with a set of coordinates and a GPS device, can attempt to find the hidden cache. If the geocacher is lucky enough to find the cache (which is really the fun part anyways), the finder can take an item from the cache. However, if an item is taken, it is expected that the geocacher will replace the item with a new item that is of equal or greater value. Taking and replacing an item from the cache is completely optional. Also, the cache usually contains a logbook that the geocacher can sign and then peruse to see who else has found the cache.

Admittedly, this is a somewhat nerd-centric pasttime, but it is a lot of fun and if nothing else, is a great excuse to get outside and exercise.

NIH Working Definition of Bioinformatics and Computational Biology (July 17, 2000)

2005-01-27T11:14:00.000-05:00

The NIH Biomedical Information Science and Technology Initiative Consortium agreed on the following definitions of bioinformatics and computational biology recognizing that no definition could completely eliminate overlap with other activities or preclude variations in interpretation by different individuals and organizations. The original document can be found at http://www.bisti.nih.gov/CompuBioDef.pdf.

Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.

Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems.

A Random Thought

2005-01-14T00:35:00.000-05:00

The lottery is the new opiate of the masses.

Haiku for Central Dogma of Molecular Biology

2005-01-09T13:13:00.000-05:00

from DNA source
code passes to RNA,
a protein is born

In Silico - An Introduction

2004-12-21T17:01:00.000-05:00

In Vivo - Within a living organism.
In Vitro - Within an artificial environment e.g. test tube.
In Silico - Within a computer (digital) environment.

I have recently started a Ph.D. program in Bioinformatics/Computational Biology and will spend the next few years of my life learning techniques to understand the natural world "in silico." One of the main, underlying threads of this blog will be to chronicle the whole Ph.D. process in general and the field of bioinformatics/computational biology specifically. The wealth of information available to biologists, not the least of which is the sequencing of the human genome, is staggering, and computer analysis of this information will be crucial to our understanding of biological systems during this century.

Since my studies will take up a significant portion of my time, I will naturally write much about them. However, my writings will not be limited to the academic process and my own specific field. Rather, I will most likely write about a number of random things, including:

Books that I am reading
Philosophy and religion
Other scientific disciplines and how they relate to what I am doing
Story ideas and/or short stories
In general, any bizarre or random thought that pops into my head and that I think would be worthwhile to print