Sunday, February 15, 2009

Epigenetic change during pregnancy

Regular readers of this blog will know that I have commented on epigenetic change before. Epigenetics is rapidly emerging as a significant contributor to our understanding of the ways in which our genes influence both behavior and disease.

Briefly, epigenetic changes to genes do not result in mutations, alterations in the gene sequence, but they do result in changes in the way a gene is translated into protein. In other words, epigenetic changes alter the phenotype (observed characteristic) of the person without changing the genotype (the actual gene they carry).

In a paper out this week researchers from the University of Cincinnati reported that children with in utero exposure to polycyclic aromatic hydrocarbons (PAH – common car pollutants) were more likely to develop early onset asthma (by age 5) and this was linked to epigenetic change in a gene associated with the development of asthma (ACSL3). Living in urban environments has always had certain risks associated with it, but as the earth’s population continues to immigrate into urban centers, we must attempt to anticipate the genetic and epigenetic changes that will result.

Since it was first described, epigenetic change has fascinated me. Certainly its association with disease is important, but even more interesting is its association with behavior. Can exposure to environmental stimulus modify behavioral norms? The early answer appears to be yes, but time will tell. Since exposure to pollutants can affect later disease in children, one wonders whether other behavior in pregnant women can affect disease and behavioral outcomes in their children. In addition, we now believe that epigenetic can be passed on to offspring – do the choices (whether chemical or behavioral) of either parent affect children in epigenetic ways that go beyond and yet reinforce decisions about child-rearing. Perhaps so…

These are profoundly interesting questions both on the personal level and on the level of community and the human race as a whole. One wonders what affect increased urbanization will have on the very structure of the human DNA. Are certain behavioral norms that are more common in cities than in rural communities being reinforced at the epigenetic level? If they are, will these traits become ever more engrained in the fabric of what it is to be human? Then, what affect will new behavioral norms have on our understanding of religious doctrines as expressed through the centuries of church tradition? Is there a genetic underpinning for what many have called the loosening of behavioral standards in some Christian traditions? Though we cannot prove it (yet), the idea is thought provoking.

Friday, February 6, 2009

Want your sequence?

New Scientist is reporting today that the cost of a complete genome sequence has dropped to a mere $5000. This announcement will lead to profound breakthroughs in genetics research - particularly in our understanding of the SNP's genomics scientists say will be necessary for use to design personalized therapies.

We will be able to know - for a relatively modest cost - the exact DNA sequences for thousands of disorders and diseases. Perhaps we will finally be able to understand the contribution of genetics to complex human behaviors.

In addition to complete genomic sequences, at least three more breakthroughs are necessary before we can take full advantage of our genetics:
  1. A computational breakthrough that can not only map the differences between genomes with billions of letters, but also cull out the significant differences in the coding sequences.
  2. A way to map epigenetic modification in genome-wide analysis. Carrying a gene is not enough, it must be expressed to contribute to a person's phenotype.
  3. A database of human disease that contains what is now considered to be private information for comparison to genetic information.
When mapping technology gets down into the $100's of dollars range, look for a push for large scale enrollment in a genetic disease database.

Friday, January 9, 2009

Self-replicating RNA

Yesterday, NPR reported on an interesting experimental system developed at the Scripps institute in La Jolla, CA. The article, published this week in Science describes the creation of a set of self-replicating RNA molecules.

While this may sound a bit bland to the casual observer, it is a significant breakthrough for evolutionary biologists. For many years biologists have theorized that the earliest molecules of "life" must have been RNA rather than DNA. Their speculations were fueled by the fact that RNA molecules make much better enzymes than DNA molecules - therefore, they must have evolved first. It has been postulated by many that the earliest "life-like" molecules must have been self-replicating RNAs of some kind. Interesting theory, but the evidence was lacking. No one had been able to show that simple RNA molecules could be self replicating in the absence of proteins and DNA; until now.

Tracey Lincoln and Gerald Joyce were able to create short, simple RNA molecules that were capable of replicating themselves indefinitely. Are these molecules alive? Do they represent the earliest form of life on planet earth? No, not yet. Single, self-replicating RNA molecules do not display several of the characteristics of life and are therefore not alive. They cannot acquire and process energy and they cannot respond to their environments - Not life.

But Lincoln and Joyce did not stop there. They were able to design about a dozen different self-replicating RNA molecules. The next question - could they compete for limited resources and if they did, would they evolve to be more competitive. The answer - YES! Several of the molecules were more efficient than others at gathering building blocks and they were able to out-compete the others. Even more interesting, some of the molecules were able to mutate to become more competitive and these altered replicators were able to reproduce themselves.

Are these collections of RNA molecules alive - no, at least not in the view of the authors of the paper in Science. They state quite strongly that their self-replicating RNAs are not alive. But they are a step toward that end. Others labs are working hard on creating artificial life and they will learn some significant lessons from the publication of this work. If life can be created in vitro, I suspect that it will be done in 20 years time.

What affect on Christian Faith? As regular readers of this blog will know - that depends on your view of origins.

The young earth folk will quickly point out that of course, created molecules can replicate and mutate... but they were created to do that. This data underscores the idea of a Creator. Of course in saying that they are ignoring their own basic premise that God created all systems complete and perfect. No need to change - change is bad, it leads to disease.

The old earth crowd/evolution will be quick to point out that this "proves" that RNA was at the heart of the earliest forms of life. These experiments demonstrate that RNA could have been there, but they do not definitively prove it is so.

So what should we do with this evidence. The prudent scientist will weigh it, watch it, and withhold judgment for now. The formation of self-replicating, minimally evolving RNA molecules is interesting, but not world-view shattering. This is one more bit of evidence in a long litany of evidence about how things might have happened. One of the maxims of science is that "what the evidence indicates now" may be altered by future experiments. So we wait. If this is another of the "black boxes" or solved mysteries that science is so fond of working at, then we should be careful to build our faith on something other than what we don't know now. Our faith should be built on faith in the living Triune God, and not on the mysteries in the creation that we don't understand.