A Matter of Perspective

In molecular biology, it's all about scale. The size of a tissue inside your body, the size of a cell, the size of a protein inside of a cell, the size of a small piece of DNA, the size of a small signaling molecule...the range is pretty impressive. Traditional biology was done by amateurs, if you will; people with a curiosity for the world around them who simply observed the way things work. Biology today is surprisingly not that different, since our goal is still to figure out how things work. However, because of the increasingly minute scale of the systems we study, the issue becomes how can we be an observer?

Much of the work that I do on a day to day basis involves manipulating biological molecules in such a way that I can "see" them. For instance, I can look at my cells under a microscope, but I can't see their DNA. How do I know that it's there? What does one have to do to actually "look" at DNA? Several cute tricks that exploit the properties of DNA have been developed over the years which, when combined, allow me to examine DNA (Sorry biologists, this is sort of a rundown for people who have no idea what we do). For instance, DNA has an overall negative charge which is proportional to the length of the DNA itself. Therefore, you can expose DNA molecules to an electric field and they will separate based on the length of the molecule. By putting the DNA into a gel matrix, I can isolate DNAs of different sizes. This is a good separation technique, but it still doesn't allow me to "see" DNA. However, I can take the gel and expose it to a chemical called ethidium bromide which fluoresces under UV light. The chemical will seep into the DNA and then when a picture of the gel is taken with UV light exposure, the DNA will fluoresce brightly! Hooray, I can see! The gel in the post is a very pretty picture of an enzyme titration that I use to get mononucleosome DNA.

Even the boring stuff that I do everyday is pretty amazing when I stop and think about what it allows me to accomplish. However, one of the next big areas in biology is using all of the imaging technology that we've developed over the past half century and using it to actually observe molecular biology. Tricks are cool and everything, but seeing is believing, or so they say. Instead of isolating proteins in massive amounts and testing their interactions in a test tube with other purified proteins, wouldn't it be much more informative to track different proteins in a living cell? And if I wanted to see how a transcription factor finds a piece of DNA, instead of crosslinking the two and purifying them, wouldn't it be great if I could watch that transcription factor scanning DNA in real time? With improved fluorescent microscopy techniques, this is becoming possible. It's definitely the future of biology and exciting, especially for those of us who are observational biologists at heart.

1.2 million year evolution experiment!

This post is about an amazing ongoing experiment in evolution. Over its course, there are populations that have been controlled and observed for over 40,000 cycles of reproduction. This would correspond to 1.2 million years of human evolution! However, the actual experiment takes place in E. coli bacteria and has taken 20 years thus far. It is a perfect system to study how mutations occur in populations, how these changes take hold in populations and how changes lead to evolution over long periods of time.

This is definitely a relevant topic in science discussion today, considering the prevalence of religious-based arguments against evolution. While these experiments do not address evolution into new species, it does share some important insights that connect changes at the molecular biology level to changes in broad population characteristics. Once this connection is established, it isn't quite as difficult to imagine broad population changes leading into species divergence and evolution. It's also important to remember that this time course in bacteria is definitely not long enough to capture the estimated time, for example, of divergence between humans and chimpanzees. If carried out long enough, however, maybe the next generation of scientists will have realized this evolution experiment to that time scale.

Anyway, to the science! One of the big questions that this experiment is trying to address is the question of how mutations actually accumulate within a species. The current thought is that there is a certain probability of your cells making an error in DNA replication; this would correspond to a linear rate of mutation over time. This is known as genetic drift and this principle is used to estimate age and divergence of species, fossils, etc. Over the course of the experiment, the scientists expected to see a certain number of mutations accumulate between the starting bacteria and the bacteria that had been growing for 20 years. What they found was that the bacteria accumulated significantly fewer mutations than expected. This means that species have unexpected mechanisms for selecting against mutations.

The main question the authors wanted to ask, however, was how do mutations actually get established within a population versus an individual. To answer this, scientists looked at the DNA sequences from a population at various time courses. What they found was that mutations seem to sweep one at a time through a population. Once a mutation is established, it encourages a different mutation to develop and likewise sweep through the population. They did not observe several mutations being established at one time.

Some of the important conclusions that the scientists found were that there weren't any neutral mutations, only beneficial ones. This led to slower accumulations of mutations over time than expected. Finally, the stabilization of a mutation within a population is the result of two things: fitness and evolvability. All mutations confer some increase in fitness; those with higher fitness levels will "win" in a population of different mutations. However, the other way a mutation can "win" is if it provides the organism with increased evolvability. In other words, it provides a genetic background that allows for even more beneficial mutations in the future.

Most of the actual mutations the bacteria accumulated weren't especially interesting. The bacteria were grown in very minimal media, which means they grew really slowly and didn't have much food. However, one group of bacteria evolved over the twenty years to "eat" one of the chemical chealators found in the media. With this mutation they were able to grow at least 1000 fold faster than the original bacteria. Incredible! Take that evolution naysayers.

If you're interested in reading the work, it was done by Jeffrey Barrick and Rich Lenski at Michigan State University. "Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature. 2009 Oct 29;461(7268):1243-7"

For serious, this time.

I have decided, after working on compiling a 5 page summary of a 4 day long Keystone Conference on Chromatin, that scientific writing is indeed a useful skill. Also, it is a skill that I feel I don't practice enough. Since practice makes perfect, I am recommitting myself to writing this blog. I'll be complaining and posting my science fails on my other blog, Disaster in the Microcentrifuge!, so this will primarily be focused on summarizing talks, papers and generally interesting science that I've heard about or read. I promise it won't be too heavy and hopefully we can generate some interesting science discussion! Hooray!

Stay tuned for an awesome evolution experiment...