Sunday, November 23, 2008

Book Review: What is Life?

Anyone who has taken introductory biology is familiar with the stories of Mendel, the discovery of DNA, and Charles Darwin's adventures with evolution and natural selection. What most of these people probably do not realize is why this material is relevant in the modern age of molecular biology.

Ed Regis's book What is Life? Investigating the Nature of Life in the Age of Synthetic Biology takes the reader on the journey from the 1943, and the publication of Erin Schrodinger's What is Life? to the labs of modern day biochemists, cell biologists, and geneticists, who are beginning to unravel some of the fundamental questions about life. The book explores how we, as scientists, have reached the ability to develop life in the lab. This is often called synthetic biology, and it is frequently thought of as being the stuff of science fiction. Several of my blogs have covered topics relating to synthetic life (for example, see Synthetic Life Makes Synthetic Proteins), most because this is going to be a hot topic for society in the next few years. For as Ed Regis points out in his book, the work is already underway, and scientists are getting closer to unlocking some of the secrets of what it means to be "alive".

For those students who are burdened with a heavy reading load, or those non-students with hectic lives, this book is a mere 171 pages in length. Better yet, it is written in a non-technical style that brings to life many of the historical people in the study of the life sciences. It is an easy read, and anyone who has an interest in understanding science should check out this book.

Tuesday, November 18, 2008

The Death of Junk DNA and Birth of the Junkome

Not so long ago, geneticists considered the vast stretches of non-coding regions in DNA to be “junk,” nothing more than the remnants of our evolutionary history. If it wasn’t a traditional gene, and didn’t produce a protein, it wasn’t of interest to most scientists. Luckily, not everyone considered these regions of DNA to be junk. Some considered the junk DNA to be the dark matter of the genome. They believed that it must have some function, but no one had yet determined exactly what that function was.

One of these individuals is Dr Craig Pikaard at Washington University- St Louis. His research group has discovered another use of junk DNA – it acts as a component of the cellular immune system by enhancing the ability of the cell to combat infection by viruses and transposons (also known as “jumping genes”). In a recent manuscript published in the journal Cell (vol 135 #4) Pikaard and associates demonstrate that in Arabidopsis , the fruit fly of plant genetics, the RNA polymerases within the cell use these non-coding regions of DNA to silence viruses and transposons. RNA polymerases are normally active in the process of transcription – the first stage of gene expression. Pikaard’s work suggests that these regions of “junk” DNA may be important in the generation of small interfering RNAs, so siRNAs. siRNAs are known to be involved in the silencing of genes by interfering with the transcription process. The medical community is very interested in the use of siRNAs in the prevention and treatment of diseases. Pikaard’s discovery in Arabidopsis should pave the way for additional studies in animals.

It seems that the time has come to let the term “junk DNA” fade into obscurity. In its place lets use the term “junkome” – those regions of DNA that we have no idea what they do, but agree that they must do something. After all, assuming something does not have a function because we do not understand what it does is not a lesson that we should be teaching young scientists.

WUSTL news release

Wednesday, November 12, 2008

Dr Google

Is there anything that Google can't do?

An article in the NY Times ("Google Uses Searches to Track Flu's Spread") by Miguel Helft reports that Google may be able to detect outbreaks of influenza up to two weeks earlier than the Centers for Disease Control (CDC). According to Google, people who have the symptoms of the flu search for terms such as muscle aches and flu on the search engine, and data-mining of these searches can help pinpoint outbreaks in advance.

There are several alarming items that can be derived from this report.

  • Google is faster at reporting medical events, epecially outbreaks, than the CDC. Maybe we should not be suprised by this since the CDC is a government agency, but one has to wonder what is in this for Google. After all, Google is a for-profit (and big profits!) business, and we may want to be careful about turning over reporting to a private company.
  • People search the internet before seeing their doctors. We all knew that this was the case, and we have all done it. Who wants to sit in a doctor's office for 3-4 hours when they are sick? But this also means that people are using Google as their primary first source of medical information. Anyone who lives on the web knows the amount of garbage that exists in cyberspace.
There is also some good news from this study.

  • We all know that the government is not known for its ability to respond rapidly. The use of the studies by both Google and Yahoo! may help develop a more rapid response plan. Maybe we don't need it for influenza, but other outbreaks, such as SARS and Avian flu, may require a faster response time than the CDC can currently supply.
What would be interesting is if Google informed the medical community on where these people were going to get their information on the web. Is it a reliable source, such as WebMD, or is it Bob's Influenza Shop? Maybe then the medical community can start to use the web effectively to deliver useful information to the public.

Sunday, November 9, 2008

The Return of the Sloth?

Around 10,000 years ago, in the region of the United States now known as the Appalachians, lived one of the most impressive mammals ever to inhabit North American. With a height of over 8 feet, and weighing up to 800 pounds, the giant ground sloth ( Megalonyx jeffersonii to scientists) was a formidable sight. However, the ground sloth, like most large land mammals in North America, went extinct. Why is still a mystery to scientists - some believe that it may have been the result of a change in climate, others suggest that it may have been from predation by humans.

Such is the case for many species, and it is the basis of Darwinian natural selection. Those species that have the genetic variation to adapt to a changing environment do, and those that do not go extinct. Unfortunately, humans have been changing the environment a little faster than most species would like. Many ecologists and biodiversity experts believe that we are experiencing a mass extinction event unlike any in the past 65 million years. And, until recently, we had few choices to prevent the extinction of a species - we could either put it in a zoo, or try to conserve its natural habitat. While both have had some success, most of the news from the conservation front is not good.

Some have asked whether it may be possible to clone extinct animals using the DNA from frozen tissues. Until recently, the majority of attempts to do this have failed - mostly because the DNA was damaged by the process of freezing. DNA is a durable, but also delicate, molecule. Its structure protects it for long periods of time, but even slight damage to its information-containing bases can be troublesome. That may have changed with a discovery by Teruhiko Wakayama, a Japanese developmental biologist. Wakayama has found a way to use frozen DNA in a cloning process. His process appears to reduce the influence of damaged DNA, allowing previosuly unsuitable tissues to be used in the cloning process. Once a cell line is cloned, it could be used to revive an extinct species.

For the ground sloth, passenger pigeon, and the dodo bird, this may be the resurrection that the species needed. Not only could we finally right a terrible wrong in our human history, we may be able to prevent (or at least postpone) the extinction of some species that are currently struggling for survival. Of course, no one is actually (yet) suggesting that we can bring back a giant sloth, but if we can perfect the process, then someday hikers along the Appalachian Trail may have more to deal with than just brown bears.

Additional References:

Wakayama's 2008 paper in PNAS