- Monday, February 8, 2010: The Problem with Chickens on the Moon
- Tuesday, December 22, 2009: Evangelism Evasion: How to Fake the Possession of Your Eternal Soul by Demonic Forces
- Tuesday, December 8, 2009: Just in Time for XXXmas!
- Tuesday, December 8, 2009: Let's Clarify, Shall We?
- Saturday, December 5, 2009: The Reason for the Season
- Thursday, July 23, 2009: For the Children
- Thursday, July 23, 2009: Growing up fundie
- Monday, July 13, 2009: Perspective
- Tuesday, July 7, 2009: Wal-Mart Has Comforters, Right?
- Friday, June 12, 2009: Masturbation: Doctor's Orders! (Part 2)
Understanding Evolution, Part 2
Change is constant.
This is a simple yet encompassing statement. No matter what, no single moment in time is like the other. Every day is composed of 24 hours, but each of those is undeniably different. Each Monday is so inherently unlike the other, and some are even good ones. The same is true on the molecular level. To understand how, you’ll need the following far-to-brief crash-course in biochemistry (further research is highly encouraged!):
Inside of the nuclei of each cell that contains one (some cells do not), billions of nucleotides arrange themselves linearly and in base pairs in a sequence. The sequence may seem random, but in reality it is the famous DNA double-helix. The central dogma of biochemistry states that DNA codes for RNA (a type of messenger and primordial genetic and catalytic molecule), which in turn codes for proteins. Proteins, in turn, are made up of amino acids. This is a very clever molecular bureaucracy because it allows for stringent regulation of processes. Tight regulation is a good thing. Imagine not knowing exactly if you will have to get a haircut 5 minutes after you just got one!
The four nucleotides which code for the animal genome (and plant as well) are aligned in groups of three, called codons. Each codon in DNA can be transcribed to a corresponding set in RNA, and in turn translated into one of the 20 amino acids. Even though there are only 20 commonly occurring amino acids, there are 64 codons. The more specialized amino acids have fewer codons and the less functionally important amino acids have more codons; the system is therefore degenerate, yielding a sort of flexibility in coding. A good comparison is a chess set where there are more pawns than knights and so on.
Billions of these codons make up our DNA. With each passing generation and through the variation in population migration patterns and our choices in mating partners, the chromosomes of each offspring become slightly different. Scientists can measure this mutation rate (how often changes in codons or just in any base pair happen), and we know that the rate is constant, much like we know there are 60 seconds in one minute. However not all mutations cause changes in our morphology or physiology, in other words, not all changes are visible. Remember that the genetic code is degenerate, so there is room for error. One thing to keep in mind is that no machine is perfect; all of them malfunction. This is where natural selection comes in.
Thursday, May 28, 2009 at 11:47
You refer to “errors” and “malfunctions” in DNA/RNA transcription and replication. Both of those words assume goals established in a top-down fashion: these base are SUPPOSED to combine with those others; this gene is SUPPOSED to code that protein; this genome is SUPPOSED to lead to this species. However, at the molecular level, there is no imposed end goal; things just happen. Certainly, guanine is far more LIKELY to pair with cytosine, and viable offspring are more likely when this happens. If it pairs with adenine or thymine instead, though, it is not a mistake. Rather, it is just a (very much) less likely molecular event. It only looks like an error to us because it does not result in the same end product we were expecting. Molecules, even DNA, do not have the end goal of producing living things (for example, humans), they just bond to each other. We happen to be the product of that bonding writ large.
Like I said, this is just a minor point on the use of language, but it seems useful to me to reinforce the idea that these are chance molecular events happening without guidance, one way or another. Also, I should be clear that this is not my original idea by a long shot. Unfortunately, though, I cannot find the source where I first came across it to give proper credit.
Keep up the good blogging!
Thursday, May 28, 2009 at 05:23
Hi Todd, thanks for the response. You are correct that mismatches in Watson-Crick base pairing do happen, however thermodynamically speaking is much more likely for that to happen in RNA than DNA, and they can be functionally relevant to the structure of rybozymes and such. DNA actually has a proof-reading machinery dedicated to fixing these mismatches since DNA polymerase is a processive enzyme. It would be mind boggling to the average non-science major reader to imagine chemical equilibrium for example; even though chemical bonds exist, there is a temperature and pH dependent on-off rate. Nothing is constant.
You are also correct in saying that the existence of DNA/RNA/proteins are not necessarily indicative that life may develop. However, until science discovers alternative life forms that do not use the same materials (likely non-carbon based), the top-down approach cannot be disregarded, however I would like to think of it as more of a probabilty-guided fashion. We know for certain that those are needed materials for life. The uniqueness of Earth thus far as compared to the rest of the Universe hints at that probabilty-guided view. The point is, I cannot design an experiment to prove what came first, the chicken or the egg! I think the issue goes back to thermodynamics and equilibrium. and the chemical evolution of biomolecules which requires stability or a regulation thereof in first principles.
The text is really supposed to be an entry level into further research and by no means could I have covered all of the nuances of DNA structure/function. I will keep posting more material on biochemistry since this preliminary entry already got a response, and a great one at that! Once again, thank you and keep reading!
Thursday, May 28, 2009 at 05:26
one of the arguments creation “scientists” like to use is that any time there is a mutation in the species, that mutation often leads to disastrous consequences - http://www.angelfire.com/mi/dinosaurs/mutations.html - any mutation, therefore, is due to the degeneration of our species (which began in a pure form as Adam and Eve) or because of radiation (we read! er, comic books).
on the surface (to someone who knows NOTHING of actual molecular biology) that seems logical - the only “mutations” we know of are some type of affliction or other.
while the language here may muddy the waters a bit as far as suggesting intention, i think that it speaks directly to the creationists “but mutations are BAD!” argument.
however, pointing out that there is no point, no goal to evolution is also really important to understand.