Supplemental

A short supplemental to the last post

I was talking to my husband about this last post and I realized I don't understand why people accept these religious explanations of biological phenomena over the scientific explanation. But then I started thinking, and here's a possible thought -

People accept the religious explanation because in their mind it doesn't change - it has stood the test of time. Scientific explanation is always changing - theories are always being adapted to deal with new data. But if you want your explanations to always stay the same, you're essentially saying that we've learned all that we need to know, that there's no real purpose behind science (which in my opinion is to provide increasingly better explanations of the world around us), and that there's no need to learn, to explore, to progress.

That's such a depressing view of the world (that there's only one good explanation for everything and we have it by invoking God). If God really designed us to be the way we are, then I would believe that he would design us to change, to progress. Nothing in this world remains the same, so why would God make us the exception? Even in the Bible, God changes from the vengeful God of the Old Testament to the compassionate and loving God of the New Testament. I really wonder sometimes what these fundamentalist Christians are trying to do. I personally think it's all a ploy to make everyone stupid and to place themselves in power over other people's lives. And if I remember correctly, Jesus never sought power over other people lives.

Sorry for the religious rant. I promise I'll get back to all the good explanations that science has very soon.

"Intelligent" Design

So my mom sent me the following chain letter through e-mail

"This is a pretty neat story and an interesting thing that few of us know. It's brief, so please read. (FROM A DOCTOR)A cou ple of days ago I was running (I use that term very loosely) on my treadmill, watching a DVD sermon by Louie Giglio... And I was BLOWN AWAY! I want to share what I learned.... But I fear not being able to convey it as well as I want. I will share anyway.
He (Louie) was talking about how inconceivably BIG our God is... How He spoke the universe into being... How He breathes stars out of His mouth that are huge raging balls of fire.. . Etc. Then He went on to speak of how this star-breathing, universe creating God ALSO knitted our human bodies together with amazing detail and wonder. At this point I am LOVING it (fascinat ing from a medical standpoint, you know.) .... And I was remembering how I was constantly amazed during medical school as I learned more and more about God's handiwork. I remember so many times thinking.... 'How can ANYONE deny that a Creator did all of this???'
Louie went on to talk about how we can trust that the God who created all this, also has the power to hold it all together when things seem to be falling apart...how our loving Creator is also our sustainer.

And then I lost my breath. And it wasn't because I was running my treadmill, either!!!
It was because he started talking about laminin. I knew about laminin. Here is how Wikipedia describes them: 'Laminins are a family of proteins that are an integral part of the structural scaffolding of basement membranes in almost every animal tissue.' You see.... Laminins are what hold us together.... LITERALLY. They are cell adhesion molecules. They are what holds one cell of our bodies to the next cell. Without them, we would literally fall apart. And I knew all this already. But what I didn't know is what they LOOKED LIKE.
But now I do. And I have thought about it a thousand times since (a lready)....
Here is what the structure of laminin looks like... AND THIS IS NOT a 'Christian portrayal' of it.... If you look up laminin in any scientific/medical piece of literature, this is what you will see...

Now tell me that our God is not the coolest!!! Amazing.The glue that holds us together.... ALL of us.... Is in the shape of the cross.
Immediately Colossians 1:15-17 comes to mind.'He is the image of the invisible God, the firstborn over all creation.
For by him all things were created; things in heaven and on earth, visible And invisible, whether thrones or powers or rulers or authorities;
All things were created by him and for him. He is before all things, and in him All things HOLD TOGETHER. '
Colossians 1:15-17
Call me crazy. I just thin k that is very, very, very cool.
Thousands of years before the world knew anything about laminin,
Paul penned those words. And now we see that from a very LITERAL standpoint,

we are held together... One cell to another... By the cross.


You would never in a quadrillion years convince me that is anything
Other than the mark of a Creator who knew EXACTLY what laminin
'glue' would look like long before Adam breathed his first breath!!

We praise YOU, Lord !!!!!!!!!!!!!!!"

Well, I needed to send an e-mail back to my mom. So here's what I wrote

"Well, I don't think it's that amazing that out of the hundreds of thousands of proteins that are out there, that one of them happens to look like a cross. I did some reading, and it turns out laminin actually looks kinda like a flower when it's in solution (it doesn't stay rigidly shaped like a cross). I am a religious person and I have faith in God, but there is no reason why people need to continue looking for things like this - for intelligent design - for proof that God is so great. To me, the idea that God put together all the rules and set everything into motion is a much more awesome view of God than a God that had to tinker with every set thing in the universe to make it in his vision. Imagine being able to create all the beauty in the universe just by setting down a couple ground rules - the rules that scientists are working every day to understand (and to better know God through those rules). To me that is more amazing than anything anyone who believes in intelligent design comes up as an example of God's "tinkering".

I know there are plenty of doctors who don't believe in evolution, but they use evolution everyday to save lives and to treat sick people. Evolution helps us understand how diseases came to be, and how best to treat diseases. Doctors fight against the effects of evolution everyday when they have to treat someone with a multi-drug resistant bacterial infection. Picking and choosing examples is not "scientific" - it's the realm of science to have to explain everything - all the data. If this one protein (one of the many proteins that help "glue" us together) is in the shape of a cross, why isn't water in the shape of a cross - water is a lot more important to us than this one protein. Water happens to be in the shape of a mickey mouse head - does that have any grander purpose behind it?

Intelligent design is just a lazy man's way of making sense of things and makes my job as an evoluutionary biologist harder every day.

Sands in an hourglass

The title comes from my husband, a lovely electrical engineer who has managed to pick up some biology in the almost decade we've known each other.

Imagine each evolutionary change as being like a single grain of sand in an hourglass. Each individual grain seems insignificant, but when they are all amassed together you can start to do amazing things with them, like tell time in the case of the hourglass. In fact, it is possible to tell time using evolutionary changes (the concept of a molecular clock), but that's for another post.

Let's start with a mathematical simulation of natural selection.

http://www.cs.laurentian.ca/badams/evolution/EvolutionApplet102.html

If you have a constant selective pressure, you can infer that over time any small change that improves one's fitness can build on previous changes in order to eventually result in something that seems perfectly adapted to that environment.

So where are all those missing links? All the intermediate organisms between one major type and another? Well, first of all, the fossil record is incredibly incomplete. Everyday paleontologists are discovering new fossils and reinterpreting past fossil discoveries. Also, organisms with similar morphologies can be very different at the molecular level. DNA evidence in many cases has required re-examination of how we thought organisms were related to each other based on morphology (shape, form). So it is unlikely that we will ever be able to completely trace the evolution of a particular lineage. However, with molecular evolution combined with genetics, we can begin to hypothesize what genetic changes may have happened that resulted in the emergence of a group of organisms like flowering plants from organisms that were closely related to some modern day freshwater pond scum.

I personally think many of the best explanations of how radically different organisms evolve from common ancestors is through work in the field of evolutionary developmental biology, also known as evo-devo. There's a lot of cool work being done in evo-devo. Most of the research in evo-devo focuses on regulatory genes - the on/off switches in the genome. A single gene can control entire networks of genes that are responsible for complex machinery such as eyes, wings, and flowers. Mutations in these genes or the stretches of DNA that control when these genes are active can have radical results. These type of mutations are called homeotic mutations. And there are tons of examples. So I'm going to end this post with some examples of homeotic mutations - some are familiar, like domesticated roses with their multiple layers of petals compared to their wild cousins, and some are a little more strange, like fruit flies with additional pairs of wings or legs where antenna should be and various eye mutations (the same gene is implicated in the blind cavefish I talked about last time).

I'd like to think I'm not typing into thin air, so if you have a question about something, feel free to ask it and I'll try to answer it.

Pressure

So I briefly described natural selection and promised to write more about selective pressures. Basically, any element of an organism's surrounding can provide a selective "pressure". By "pressure" I mean something in the environment which provides a reason for change in an organism that would be selected for via natural selection. Now just because there's a selective pressure doesn't mean the change is going to happen. It may be that there is constraint on what type of changes can occur, and of course, just because there's a need for a change to happen, doesn't mean the change is going to happen. The initial change is random, and it could take years, hundreds of years, thousands of years, millions of years etc before a particular random change occurs that actually benefits the organism. In fact, most mutations are deleterious - they actually impair an organism's ability to make the most of its environment. But then again, mutations that could be deleterious in one environment aren't in another environment. Let me explain.

In Mexico, there are blind cavefish. One of my professors at University of Maryland, William Jeffery, studied the blind cavefish, as well as their non-blind relatives. In fact, the blind fish can breed with the seeing relatives - they are the same species. However, at some point a mutation occurred in one of the regulatory genes that controls the development of eyes. Now if this mutation happened in the non-cave dwelling fish, it would be deleterious, and natural selection would most likely result in the elimination of that mutation from the population. But in the cave-dwelling fish, sight isn't very important and therefore the mutation remained in the population because it did not affect the fitness of the fish carrying that mutation. You could say that for the cave-dwelling fish, there was a selective pressure for loss of sight (especially if loss of sight is complemented by an increase in another sensory organ).

Darwin suggested that the cavefish became blind because of disuse, and that elimination of the unnecessary organ increased their fitness. Darwin was wrong on a variety of topics, and this is one of them. Disuse doesn't result in elimination of anything. However, disuse can be a type of selective pressure, or more accurately, a release from a selective pressure. Mutations in genes that are responsible for a particular function, organ, etc can render them useless. Then if they are useless, those mutations will persist in the population, either through genetic drift or natural selection (if those mutations are beneficial in some other way). But just because something isn't used, doesn't mean it will go away. Think of the appendix. Modern humans don't use their appendix because we tend to not eat raw meat and rocks. But we're still born with appendices and our bodies go through all the trouble of making them. Now if someday a mutation occurred that resulted in the appendix not being formed, that mutation would have the chance to spread through the population. It could be that not having an appendix is neither good or bad for you, and the mutation would spread through genetic drift (very slowly given the human population size). Alternatively, not having an appendix could be beneficial (since you remove the risk of dying from appendicitis) and the mutation would be selected for, and it would spread through the population a little faster than if it was just spreading via genetic drift. But eventually, humans might no longer have appendices. Or we might split into two species, humans with appendices (because some group still needed them and not having them was detrimental) and humans without appendices.

I think the hardest part of understanding evolution is understanding how small events, over time, could result in great diversity of life on this planet. I'll work on some examples of this.

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.