The Power of Comparison

It's always a little awkward to describe what it is I do to people I meet, or people that I'm related to.  Sometimes, when I'm feeling brave (or when I just want to stump someone because I don't want to talk about it), I say I have a Ph.D. in Molecular Evolution, studying the evolution of single copy genes in flowering plants (or angiosperms) if I'm feeling particularly crabby.  It is a guarantee that the conversation will end.

Let's see if I can actually explain the basics of my interests without putting you to sleep or you walking away with the thought that I work in cloning (somehow this is how my parents described what I did to countless people throughout undergrad, I'm not even sure how they would describe it now, but then again, now they can just tell people I'm a stay at home mom).

At the very core of it, molecular evolution is generally the study of how genetic material changes over time.  Usually, studies of molecular evolution are based on DNA sequences - long strings of A/T/G/C - the four nucleotide components of DNA.  You can retrieve some basic information from a single DNA sequence - such as the amino acid sequence of the protein it encodes (if it's a gene), but the greatest amount of information is obtained when you can compare one DNA sequence to another that represent DNA sequences that have a common ancestor (imagine a fork in the road - the two sequences are the two different paths and the single path represents the common ancestor).  When you start comparing related sequences (aka homologous DNA) across different species, then you're in the realm of comparative genomics, utilizing the tools developed to understand molecular evolution.

Remember those compare and contrast essays you had to do in high school English?  By comparing and contrasting sequences, you can identify commonalities and differences at the genetic level that might relate to commonalities and differences at the physical/behavioral level.  You can also use this information to figure out how organisms are related to each other.

Why is this useful? Well, I'll talk about a project that first led me down the path into studying molecular evolution.  There are nematodes (small, worm-like creatures) that chew on banana roots, causing agricultural damage.  Well in some of these nematodes (about 50 years ago) a mutation occurred that meant they would now attack citrus roots.  The banana attacking nematodes were common, but the citrus attacking ones were rare.  But to prevent the spread of the citrus attacking nematodes, rootstock containing the banana attacking or citrus attacking nematodes couldn't be transported to new citrus growing regions since they both looked alike.  We were trying to identify genetic markers to be able to ID the citrus parasitic nematodes, so you could tell them apart. I never reached that endpoint, but we were using comparisons of rudimentary genetic assays to try to identify markers.  I was also able to use those comparisons to investigate how these nematodes were related to each other and from what population the citrus parasitic nematodes likely evolved from.

So yeah, my scientific life is comprised of really complicated ways to compare and contrast - and it's pretty cool what we can figure out doing just that.

Renewal

I had abandoned this blog years ago.  Life got busy, I didn't think anyone was paying attention.  Seems like some people have.

I still have my toes in the research arena - working on the utility and evolution of shared single copy genes in flowering plants.

I'll try to get back to paying some attention here - and coming up with new examples of evolution that help explain what can be a very complex and difficult subject without the necessary background information.

Dinoflagellates

I couldn't have said it better myself.

http://opinionator.blogs.nytimes.com/2010/01/05/a-tale-of-two-flagella/?

When I was an undergrad in the Delwiche lab, I learned a little about dinoflagellates (the Delwiche lab is now working on a tree of life project for dinoflagellates). They are extremely adaptable, versatile and complex creatures. Proof that complexity is not just a matter of how big you are or how many cells are required.

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.