Darwin and Evolution

Here's another article from the NY Times that's relevant for this blog and any readers out there.

http://www.nytimes.com/2009/02/10/science/10essa.html?partner=permalink&exprod=permalink

Drawing the tree of life

Since I can't seem to find my copy of the Origin of the Species, which is very relevant to the post on Natural Selection that I'm working on, I figured I'd link you to this NY Times articles about visualizing the tree of life.  It's kinda cool when you read an article in the NY Times and you've personally met most of the people mentioned in the article.

Here's the link

http://www.nytimes.com/2009/02/10/science/10tree.html?ex=1391922000&en=7f8374c58013a4f5&ei=5124&partner=digg&exprod=digg

Natural Selection

Ok, here's the biggy.  The thing that everyone seems to argue about.  Charles Darwin's big theory that we're still fighting about almost 200 years later.

Natural selection is based on a couple of simple premises. The main premise is that individuals within a population have heritable differences that result in differential reproduction. The outcome of this is that those heritable differences that relatively increase the number of offspring from a given individual will be found in more and more individuals as time proceeds, as long as those heritable differences continue to have the same effect in response to the environment.

This is best explained by example, and I'm going to use the example of antibiotic resistance. Some bacteria contain genes that make them immune to the effects of certain antibiotics (antibiotics work by disrupting vital activities of bacteria). Let's say you have a strep infection, and some of those streptococcus bacteria in your throat have a gene for antibiotic resistance. You go to the doctor and get a prescription for penicillin. You take your antibiotics, and it kills all the streptococcus bacteria, except the ones that have the gene for antibiotic resistance. Now there are more antibiotic resistant bacteria in the environment. This seems pretty simple, right?

Well, when selective pressure is strong (if you'll die unless you have a certain difference in your DNA), it's easy to see how the concept works. It gets more complicated when the selective pressure isn't as strong. Let's get into that next time.

Taking a random walk

Up front, sorry again for the delay.  Life keeps on interfering with getting things done.

Today I'm going to talk about genetic drift.  And as usual, there's new vocabulary to learn.  So we've talked about genes before and the fact that in most animals, there are two copies of any one gene in any given individual.  Now the sequence of those two copies doesn't have to be exactly the same.  There can be differences.  Slightly different variations of the same gene are called alleles.  A common example is blood type.  ABO blood type is based on a single gene, and there are A, B, and O alleles.  

Now what about genetic drift?  What does it have to do with alleles?  In a field called population genetics, scientists study the genetic makeup of entire populations of organisms, and a common measure of this genetic makeup is allele frequency - how common some alleles are compared to other alleles.  In humans, you can think about this in terms of how common blue eyes are compared to brown eyes, or attached ear lobes versus unattached ear lobes.  On the scale of populations, evolution can be defined as change in allele frequencies over time.  Genetic drift is one explanation scientists have for why allele frequencies change over time.

Genetic drift is why increasing the population size of endangered organisms is important.  Whenever genes are passed from one generation to the next, there is some level of randomness as to which allele in an given individual will be passed on to the next generation (during sexual reproduction, each individual in a mating pair only passes on a single allele for each gene).  So how close allele frequencies stay the same over the course of multiple generations is dependent on the population size.  Why?  Take this completely abiotic example.  You flip a coin.  If you flip the coin only once, then the frequency of tails is either going to be 1 or 0.  If you flip the coin ten times, then the frequency of tails might be something more like .7 or .3.  The more times you flip the coin, the more likely that the frequency of tails will end up to be 0.5.  Genetic drift works the same way - the larger the population, the less variation in allele frequencies from generation to generation.  Conversely, the smaller the population, the more variation in allele frequencies.  If a population is small enough, you can even lose alleles from the population, because they just didn't make it into the next generation.  

Genetic drift is part of neutral theory, because what the allele does is of no consequence to the effect genetic drift has on it.  

If you want to play around with some simulations that illustrate the principle of genetic drift, here are some links:

http://darwin.eed.uconn.edu/simulations/jdk1.0/drift.html

Creating monsters

Sorry for the two week holiday.  Now that the commitments of the holidays are past, I can get back on my weekly posting.

So last time I talked about the meaning of the word evolution, and introduced a couple other topics such as mutation, recombination, genetic drift, natural selection.  So today's topic is mutation.

The genetic material within a cell is composed of DNA - deoxyribonucleic acid.  In eukaryotic cells like ours and other animals, DNA is found wrapped around a protein scaffold and forms chromosomes.  Chromosomes are typically found in matching pairs (except for sex chromosomes).  Genetic material is compartmentalized in eukaryotic cells - most of the genetic material is located in the nucleus, where chromosomes reside.  All of the genetic material belonging to a given compartment is called a genome.  In most eukaryotes, there are two genomes - the nuclear genome and the mitochondrial genome.  I'm just going to focus on the nuclear genome, because the mitochondrial genome is special (as well as the chloroplast genome in plants).  The nuclear genome in most eukaryotes is diploid, meaning that each chromosome is a member of a paired set.  In gametes (specialized cells for sexual reproduction such as eggs and sperm), only a single member from each paired set is present. So back to this whole mutation thing.  There are variety of different ways mutations can occur.  A mutation is basically a change in the genetic material.

DNA is a double helix - this means that simply put, it consists of two strings of individual "letters" running in opposite directions and additionally those strings are complementary in such a way that if you know the sequence of one string, you can deduce the sequence of the other string.  These letters are nucleotides, and there are only four of them - A (Adenine), T (Thymine), G (Guanine), and C (Cytosine).  A and T are paired together in a complementary set, and G and C make up the other complementary set.  

There are several types of mutations.  I am going to discuss the following types: 1) point mutations; 2) insertions/deletions; 3) duplications; and 4) rearrangements.

A point mutation describes a change in one of the letters to one of the other letters.  Sometimes this makes a difference in what the DNA codes for, and sometimes it has no effect at all.  In a protein-coding region (typically known as a gene), mutations that change the protein the gene codes for are called nonsynonymous mutations and mutations that don't change the protein are called synonymous mutations.  An example of a point mutation is the disease sickle cell anemia, which is caused by a single point mutation.  This point mutation changes the hemoglobin protein, which carries oxygen in red blood cells.  The mutation causes the hemoglobin proteins to attach to one another, changing the shape of the red blood cells, and causing them to create traffic jams in certain parts of the body.  Point mutations may also cause changes in when a gene is turned on (the protein is made) or turned off (the protein isn't made).

Insertions/deletions (commonly referred to as indels) are simply instances in which a single letter or a series of letters have been either inserted or deleted from the DNA.  Indels will always change the makeup of the protein that a gene codes for if the indel occurs in a gene.  Since DNA is written in a three-letter code, indels of three, or multiples of three letters, usually have the least impact since they will disrupt the rest of the code minimally.  However indels of other sizes will change essentially what every letter downstream of that indel means.  But these are generalities.  

Duplications come in a wide variety of sizes and mechanisms by which they occur.  Basically a duplication means that some pre-existing piece of DNA is copied and added to the genome.  Duplications can involve a single letter, large segments of DNA, entire chromosomes, and even entire genomes.  Excessive duplications of a three letter segment of the huntingtin gene causes Huntington's disease.  Extra copies of chromosomes in humans usually causes miscarriage, but Trisomy 21 (having three copies of chromosome 21 instead of 2) causes Down's syndrome.  Whole genome duplication is rare in animals, but we can detect episodes of whole genome duplication in fish and frogs.  Whole genome duplication is a very important part of the evolution of flowering plants (a lot of my PhD dissertation was on this topic).  Duplication basically enables other mutations to occur that change expression and function, while still maintaining what's needed to keep things running.  We'll talk more about duplication at another time.

And there's rearrangement - you don't change anything about the DNA except where it's located and maybe what direction it's in.  The most common type of rearrangement is recombination.  During meiosis (the process during which haploid (single set of chromosomes) cells are formed), chromosomes interact with their partner and swap some genetic material.  On average, one part of the chromosome is swapped with its partner during meiosis.  This only happens when sex is involved (meiosis).  But it means that there's a chance for new genetic combinations to form when the next generation is formed.

So there's a listing of all the changes that can occur.  When it comes to evolution, the only mutations that matter are those that occur in sex cells (for sexually reproducing organisms) since those are the only changes that will be passed onto the next generation and are heritable changes.  Now how mutations spread throughout a population of organisms will be the next thing I discuss - natural selection and genetic drift.  

The meaning of the word

I guess that before I start telling tales, I should make sure people understand what I'm talking about.  Like any field, biology is full of jargon - specialized terms used to describe what's going on.  Biologists spend an inordinate amount of time debating what those words actually mean.  So here's my disclaimer:  any jargon I attempt to define in this blog is my own interpretation of what a particular word or phrase means.  There may exist alternative interpretations.  I'm not a lawyer, I'm a biologist.

So let's start with the obvious - evolution.  Simply put, evolution is change over time in the DNA of a population of interbreeding individuals.  I tend to favor talking about evolution in terms of changes at the DNA level, because I'm a molecular evolutionary biologist, and I think it's easier to understand that way.  Now there are a couple things that evolution is NOT.  

Evolution is NOT:

- directed.  There is no goal, no plan.  Evolution is like taking a random walk without a map.  You don't know where you're going and you might have a faint idea of where you came from.

- progressive.  All organisms are equally advanced.  There are not higher plants and lower plants.  Flowering plants, because they are more recently derived, are not "better" than algae, which share a common ancestor with flowering plants.  It is only fair to describe things in terms of increasing complexity.  

So to me, if you say you don't believe in evolution - then what you're telling me is that you think that the DNA of every organism on this planet is the same as it was at the beginning of time.  Now, I ask you - do your children have the exact same DNA as you, with absolutely no changes?  If your answer is yes, well then I'm afraid males shouldn't exist in your world.  The basic idea behind evolution is random change in the genetic material that is passed from one generation to the next.

Now I think the only world people would disagree with in that statement is the word random.  If you think all change is directed and progressive, then you don't agree that the process is random.  I guess my challenge is to supply evidence for the random nature of evolution.

There are a lot of different processes that result in evolution, starting from the mechanisms of mutation and recombination to evolutionary forces such as natural selection and genetic drift.  So that's what I'll talk about in my next posts.

Frozen accidents

There's a term used in evolutionary biology - "frozen accidents".  Generally it means that the state of something in biology is the way it is just because it's the way it is - that there is no overall purpose or benefit for something being done a certain way.  It's an accident of evolution, and it's just stuck, or frozen, because we're so far down the line that changing it would be near impossible - that natural selection, or any of the evolutionary forces are not sufficient to make it any better.  

The first example of this I was introduced to was the genetic code.  The genetic code is a series of 3 letter "words" or strings of individual bases of DNA that are translated into a particular amino acid (the building blocks of proteins).  Throughout life on earth, the genetic code is the same for the vast majority of organisms (mitochondria and a few organisms have different codes, but they're very close to the "universal" genetic code).  The genetic code is redundant - multiple words translate to the same amino acid.  However, there didn't seem to be any explanation for why certain DNA words stood for particular amino acids.  This was a frozen accident - the vast majority of life on earth has the same genetic code because we have a common ancestor that had this code, and since it's such a vital part of how things work, it's hard to change it.  If you change the code in any one organism, you would end up changing the makeup of all the proteins in the cell, and they most likely wouldn't function properly anymore.  So we're stuck with a genetic code from a couple of billion years ago.  Fortunately, research hypothesizes that this code is actually fairly optimal - it minimizes the impact of the most common mutations.  Amino acids have basic chemical properties - some like water, some stay away from water (like fats), some are basic, some are acidic, etc.  The genetic code is such that a common mutation in the DNA is more likely to change the amino acid that's coded for to another amino acid that acts kinda like the original amino acid.  But researchers found that if this is the reason for the genetic code being the way it is, it isn't the best it could be.  

And that's kinda the point of this blog - to discuss topics in biology in sync with their evolutionary origins and how those origins aren't really founded in "intelligent design" because if there was a designer and that designer was intelligent, that designer would have done a better job.

As far as I'm concerned, I hold a Ph.D. in Biology, specializing in Molecular Evolutionary Biology.  I'm a practicing Roman Catholic and I manage to believe in God and still think that evolution exists.  My purpose is education - because if people are going to spread the word that evolution doesn't exist, I'm going to fight back by teaching people how evolution does exist and why it's really the best explanation anyone has for the beauty and diversity of the life that surrounds us.