Monday, July 4, 2011

Fracking, What You Need to Know

Recently, I tweeted about the French instituting a fracking ban while Governor Cuomo partially lifted New York’s ban. What is fracking you might ask? Properly known as hydraulic fracturing it is a process whereby a hole is bored into subterranean layers of shale (a sedimentary rock) and an undisclosed mixture of water and chemicals is injected at high pressures to crack the shale open and release the natural gas.

The process of fracking is highly controversial, and was featured at length in the 2010 documentary Gasland (IMDB). The release of chemicals which naturally occur in hydrocarbon deposits is a potential source of water contamination. These chemicals include volatile organic compounds which can potentially cause kidney damage and benzene which is a carcinogen. Additionally, there is concern that the chemicals used for fracking might leach into the water table as well. The level of exposure to these chemicals in areas which have been fracked has not yet been quantified and it is not known to what extent leaching may occur.

An examination of the map of major shale deposits in the United States shows 3 major shale gas deposits in the Appalachian Mountains between the Mohawk River Valley and northern Kentucky. One of these, the Marcellus Shale formation is estimated to hold up to 14 trillion cubic meters (TCM) of natural gas. To put that in perspective currently the US consumes 646 TCM of natural gas per day and produces 593 TCM of natural gas per day. Dr Gary Lash of SUNY Fredonia estimates that only 10% (or 1.4 TCM) of these deposits are recoverable using current techniques.

About half of New York City's drinking water comes from the Catskills watershed which lies above the Marcellus formation. Any fracking which  threatened the drinking water of 8 million New Yorkers and the reserve drinking water of 2.8 million Nassau and Suffolk county residents is a political non starter. Predictably, early reports seem to indicate that Cuomo will not allow fracking in the NYC or Syracuse watersheds or within 500 feet of a drinking water source. Thus it appears the new rules will lead to the development of fracking in the western third of the state.

So what do I think about fracking? First off, clean potable water is a precious resource, more precious than energy. After all, you need water to live. Fracking has been utilized for many years in other states and in time cleaner and more environmentally sound techniques will be developed. New York should consider allowing fracking when such techniques have been perfected, not now.

Wednesday, June 29, 2011

Hemophilia Cured in Mice

Gene therapy involves substituting or introducing a therapeutic gene to replace or accompany the defective one. Many previous attempts at gene therapy have utilized retroviruses, however the main pitfall of retroviruses is that scientists cannot control where the therapeutic gene will be inserted. This is a huge drawback as the therapeutic gene might be inserted in a potentially useful or necessary part of the genome, which could lead to even more genetic mutation.

Recently, a team of scientists led by Dr Holmes and Dr High used a zinc finger nuclease to repair hemophilia in mice. Zinc finger nucleases don’t actually exist in nature and are engineered from a fusion of a Zinc finger domain and a nuclease. Zinc Finger domains are typically found in transcription factors (proteins which help to control the rate of transcription of RNA from DNA) because they recognize and interact with very specific sections of DNA. Nucleases on the other hand as their name implies are involved in cutting the Nucleic acids. 

Typically, scientists have used the ZFNs to specifically induce a double stranded break in the DNA, this in turn recruits the DNA repair mechanisms. The Holmes/High team co-delivered a gene targeting vector which allowed them to replace the broken hemophilia gene with a good one. This is amazing, and raises the possibility of targeted gene-editing as a therapy for genetic diseases.

Saturday, June 18, 2011

Cellulosic Ethanol, One Step Closer to Practical

The fermentation of the natural sugars (and starches) in grains and grapes yields beer and wine, and this has remained essentially unchanged for almost 10,000 years.  Distilling these products yields pure ethanol.

Recently, there's been much ado about Ethanol subsidies in Congress. Corn producers are very keen on keeping these subsidies intact, of course. However, utilizing a good portion of our food grain for fuel production probably isn't a long term solution as it will serve to increase food prices.

In the production of our food crops, we have several tons of secondary material - such as corn stalks, which essentially go to waste. This material, is indigestible by yeast because it mostly consists of lignin. Furthermore, plants like switchgrass cannot be used for large scale ethanol production because most of the carbohydrate it contains is in lignin. (Switchgrass can grow on land unfit for food production making it an ideal biofuel crop.)

For many years, scientists have been trying to develop methods of breaking down lignin to produce fermentable sugars. Fungi which can break down lignins have been known for a quarter century, but scientists have been unable to develop that into an industrial technology. Recently, however, a potentially revolutionary discovery was made. The soil bacterium Rhodococcus jostii was discovered to contain a gene (dypB) which has lignin peroxidase activity. Bacterial genes are inherently easier to manipulate than fungal genes 

In their discussion, the authors state that they suspect that they have identified just one of a host of enzymes which make lignin digestion possible. In the future, scientists may be able to engineer a bacteria which overexpresses these genes and that might lead to industrial scale production of cellulosic ethanol.

Friday, June 17, 2011

Major Advancement in Hydrogen Production

Recently, I read about two major scientific advancements in the field of alternative fuels. The first involved the production of hydrogen, and the other is a major breakthrough in the production of cellulosic Ethanol. In this post, I’ll talk about the hydrogen production breakthrough.

Others have already demonstrated “artificial photosynthesis” where light is used to cleave water into hydrogen from oxygen. A so called hydrogen economy would be ideal because its main byproduct would be the production of water vapor as opposed to carbon dioxide or particulate pollution. Artificial photosynthesis would allow for the cheap production of hydrogen and is one part of many missing parts in converting into a hydrogen based economy. (Other problems include how to store hydrogen effectively, how to transport it and how to retrofit the existing infrastructure, including gas stations and cars.)

One of the major drawbacks with producing hydrogen from water is up till recently, these processes required fresh water. Unfortunately, we live in an era where there are many competing demands for an increasingly limited supply of fresh water. An increasing human population, the challenges of feeding that population and improving standards of living have all increased demands for fresh water. The ability to use relatively unlimited supplies of sea water would reduce growing pressures on fresh water supplies.

A team led by Dr Daniel Nocera of MIT previously showed that they could utilize a Cobalt-Phosphate (Co-Pi) catalyst to function similarly to the Oxygen Evolving Complex of plants, and that they could use this in both fresh and sea water. Furthermore the deposition of Co-Pi on various semiconductor materials increases the efficiency of the system.

Silicon is one of the most abundant elements on earth, and as anyone with a solar panel on their roof can tell you, silicon is effective at absorbing light energy. In fact, the artificial leaf has shown that silicon immersed in water and exposed to sunlight will split water. However, until recently the main problem with using silicon to split water has been that the very oxygen released by water splitting would react with the silicon and over time the silicon would lose its effectiveness.

In a paper published in the Proceedings of the National Academy of Sciences, Dr Nocera reports that by combining the CoPi catalyst and a silicon based solar cell he was able to make hydrogen and reduce silicon oxidation using sea water. The next challenge is to scale this up. Dr Nocera has previously announced a deal with the Indian mega corporation Tata Group to build a large proof of concept reactor.

Thursday, June 9, 2011

An Interdisciplinary Discussion on Climate Change

Recently I attended “Climate Change, Science and Society: A Multidisciplinary Discussion” hosted by the New York Academy of Sciences and arranged by Wiley WIRES Climate Change.

The speakers were: Stephen Rose, an economist with the Electric Power Research Institute , Lauren Chamblis of the Cornell University Agricultural Experiment Station a science communications specialist and a former journalist, and David Rind, a NASA/GISS climate scientist emeritus. The interdisciplinary aspect of the talk was unique and this talk was well worth attending.

The climate scientist David Rind, spoke about climate change in a way I hadn’t considered before. New models are now predicting an increase in temperature of 4 degrees. That may not seem like much he said, “But global temperatures were only 4 degrees lower when there was a 3 kilometer thick glacier where we sit right now” (downtown Manhattan). Interestingly, he first showed the early models which showed areas of increased/decreased precipitation and areas of increased/decreased evaporation. Then he showed a revamped model which combined these two data sets to give a drought prediction model. A four degree increase in global temperature showed a world engulfed by drought conditions by 2100, clearly beyond society’s ability to provide for itself.

I’ve seen many predictions that dealt with climate change in terms of potential economic change - flooded and abandoned cities, lost ways of life etc. However, Steven Roses’s presentation was the first time a talk really boiled down the approaches to climate change in an economist's terms. Obviously, no one intends to release greenhouse gases; rather, we produce these gases as a result of our primary economic activities – i.e. traveling or making widgets. Economists separate the activities (or intentions) and the unintended consequences (or the externalities) which can be either positive or negative. So for an economist the production of greenhouse gasses, aerosol or particulate pollution, and eventual global climate change are externalities which are a consequence of our economic activities. It’s helpful to separate what we want to do (which is get where we want to go and make the widgets and gizmos) from the greenhouse gases that they produce. That is, we want to maximize the good while reducing the bad - none of us want to return to the preindustrial world. I always find how economists approach a problem particularly fascinating which is why I enjoyed reading Freakonomics.

Later in his talk, Steven presented a number of statistical climate forecast models that were compared to examine the effects of a global strategy to reduce greenhouse gases. Essentially, the models predict that if all nations agreed to limit the production of greenhouse gasses then there is still time to avert a climatic catastrophe. However, all the models are in agreement that if policies aren’t implemented soon then more drastic changes will need to be made. Furthermore, and perhaps more disturbingly, if the BRIC countries (Brazil, Russia, India and China) don’t participate, any hope of changing global CO2 levels is infeasible. Yet, the BRIC countries are unanimous in their desire to hold off any greenhouse emissions treaties. To them it’s an issue of fairness - the west after all was able to pollute with impunity for more than a hundred years. Of course, it doesn’t really matter what’s fair or not. If temperatures rise as much as predicted, it will adversely affect all four countries. This of course is a very timely discussion given the current rancor about developing countries cutting back on CO2 emissions at the current talks to extend the Kyoto protocol.

Lauren Chamblis, spoke about how scientists must communicate more effectively about climate change, and how the public is not as antagonistic towards climate science as is commonly believed, and that people honestly would like to do something about climate change. This is a fact well worth remembering given the trouble Mitt Romney seems to have gotten into for suggesting he was for combating global warming.

We know much about global climate change and yet there is so much more we don’t know and it is what we don’t know that will undoubtedly influence the accuracy of climate models. However, there are two things to keep in mind here. As Steven said in economic terms, the longer we wait to see how bad this thing will be the more drastic the changes we will need to make in our lives and societies to stave off the worst global climate change. Essentially, we are taking less drastic options off the table with each passing year. Secondly, thus far every climate model out there has widely underestimated the effect of climate change on the Antarctic and arctic ice sheets, so clearly there is way more going on here, but what we know so far seems to indicate that things are getting real worse real fast.