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Friday, June 27, 2008

One advantage developmental biologists have over paleontologists is that they can experiment on the development of these animals. Most of the genes in

I live in a very windy area. Pretty much every afternoon as I ride my bike home directly into the full-force wind, I wonder how I could set up some sort of sail system so that I don’t have to pedal as hard as possible only to go about 2 miles an hour. I also think about how I can be capturing all this wind so I can power my home. In other words, because of where I live, wind is on my mind a lot. So, over the weekend I was glad to read about the WINDPOWER 2008 conference. It was the first time I’d heard about the annual conference and tradeshow and it sounded like something I’d love to attend. Well, clearly not knowing about it in the first place made attending a little difficult, but luckily the folks at Clean Tech were there and posted some video and interesting info on vertical wind turbines.

Vertical turbines have a few one-ups on the traditional three-blade turbines for urban areas like where I live. They’re quieter, blend in with a rooftop more seamlessly, take up less space, can produce 50% more electricity per year, can produce energy at lower wind speeds, and are safer for wildlife such as birds and bats.

Considering the amount of thought going in to urban turbines, I’m curious as to why vertical turbines aren’t gaining more popularity. It seems like there are myriad ways to utilize them. For instance, many cities are installing solar panels on streetlamps to generate electricity to power the lamp…but not as many are combining solar and wind. Seems like the more logical thing to do since the odds of getting enough electricity go way up. “Gus” (shown in the above image) is a turbine from Tangarie, and it has been combined with solar for streetlamps. But, I suppose when you look at the price tag, my “why” question is answered – the package runs about $7,000 and that doesn’t include the cost of installation. “Gus” creators have thought about aesthetics, and have utilized a reflective coating to reduce glare. It’s the little things like this that will help turbines gain popularity as the aesthetics are boosted and innovation is amped up.

The video below shows a design from Energy in which light metal bands surround the turbine to give it a low start-up wind speed, which allows users with a less substantial wind resource to get at least a little power from local winds. With designs like these helping people even in soft breezy environments to utilize wind, I just can’t help but wonder why not more…

Apparently vertical wind turbines are expected to grow in popularity in urban settings, but I’m surprised that it hasn’t taken off more quickly. I know I’m already geared up for how to retrofit my house to be powered by some pretty rooftop vertical axis turbines!

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Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift


Corrections Appended

Is Darwin due for an upgrade? There are growing calls among some evolutionary biologists for just such a revision, although they differ about what form this might take. But those calls could also be exaggerated. There is nothing scientists enjoy more than the prospect of a good paradigm shift.

Paradigm shifts are the stuff of scientific revolutions. They change how we view the world, the sorts of questions that scientists consider worth asking, and even how we do science. The discovery of DNA marked one such shift, the theory of plate tectonics another.

Many scientists suffer from a kind of split personality. We believe that this is the most exciting time to be working while yearning for the excitement of a revolution. What ambitious scientist would not want to be part of a paradigm shift? Not surprisingly, this yearning occasionally manifests itself in proclamations that a revolution is at hand.

To understand the current tumult it helps to understand how our evolutionary framework developed. It was constructed from the 1930s to 1950s by early geneticists, paleontologists and others, who disagreed about the efficacy of natural selection in driving evolutionary change (Darwin’s big idea) and about the nature of the underlying genetic variation upon which natural selection could act. What they came to agree on was called the modern synthesis, and it established an intellectual zeitgeist that continues today, and has been continually adapted, in the best evolutionary fashion, to encompass new discoveries.

That synthesis holds that mutations to DNA create new variants of existing genes within a species. Natural selection, driven by competition for resources, allows the best-adapted individuals to produce the most surviving offspring. So adaptive variants of genes become more common. Although selection is often seen, even by biologists who should know better, as primarily negative, removing poorly adapted individuals, Charles Darwin understood that it was a powerful creative tool.

It is the primary agent in shaping new adaptations. Analytical studies have shown how selection can produce a complex eye from a simple eyespot in just a few hundred thousand years.

In the past few years every element of this paradigm has been attacked. Concerns about the sources of evolutionary innovation and discoveries about how DNA evolves have led some to propose that mutations, not selection, drive much of evolution, or at least the main episodes of innovation, like the origin of major animal groups, including vertebrates.

Comparative studies of development have illuminated how genes operate, and evolve, and this places less emphasis on the gradual accumulation of small genetic changes emphasized by the modern synthesis. Work in ecology has emphasized the role organisms play in building their own environments, and studies of the fossil record raise questions about the role of competition. The last major challenge to the modern synthesis came in the 1970s and 1980s as my paleontological colleagues, including the late Stephen Jay Gould, argued for a hierarchical view of evolution, with selection occurring at many levels, including between species.

Transitions between species documented by the fossil record seemed to be abrupt, perhaps too abrupt to be explained by the modern synthesis. If this were generally true, it could render irrelevant much of natural selection occurring within species, because just as mutations are produced randomly with respect to the needs of a species, with selection shaping these into new adaptations, new species might evolve randomly with species selection shaping them into evolutionary trends. This challenge was greeted with less than fulsome praise by evolutionary biologists studying changes within species. The resulting hubbub has yet to fully die down. But the newer work cuts closer to the core of the modern synthesis, and is potentially more revolutionary, because it addresses the fundamental question of how really new things happen in the history of life. What brought about the origin of animals, or the invasion of land?

The Achilles’ heel of the modern synthesis, as noted by the philosopher Ron Amundson, is that it deals primarily with the transmission of genes from one generation to the next, but not how genes produce bodies. The recent discoveries in the new field of evolutionary developmental biology, or evo-devo, that the gene Pax-6 controls the formation of eyes in mice and humans, Nkx2.5 heart formation, and a suite of other genes the formation of the nervous system, has provided a means to investigate the genetic and developmental mechanisms influencing how the form of organisms has evolved, not just their genes. Perhaps the most exciting area in evolution is in exploring how rewiring the circuitry of genes produces different arthropod appendages, or wingspots on butterflies.

Eric H. Davidson, a colleague of mine at CalTech, has dissected the network of interactions between the genes that build the gut of sea urchins and starfish during development. When he compares these gene networks, there is a core of about five genes whose interactions are essential to forming the gut, and which have been preserved for some 500 million years.

One advantage developmental biologists have over paleontologists is that they can experiment on the development of these animals. Most of the genes in this network can be removed, and the developing embryo finds a way to compensate. But these five core genes, which form what Davidson calls a kernel, cannot be modified: change any one of them and no embryo forms at all. There is no reason to think that there was anything unusual about how this kernel first evolved some 500 million years ago (before sea urchins and starfish split into different groups), but once the kernel formed it locked development onto a certain path. These events, small and large, limit the range of possibilities on which natural selection can act. These questions about mechanism were not even being asked under the modern synthesis.

The failure to consider how biodiversity grows reflects an even more troubling flaw in the modern synthesis: it lacks any real sense of history. This may sound odd, as evolution is about history. A geologist would describe evolutionary theory as uniformitarian: “The present is the key to the past.” This is the principle we use that by understanding how processes operate today we can understand past events. Evolutionary theory assumes that the processes we can study among fruit flies disporting themselves in a laboratory capture the broad sweep of evolutionary change.

But just as the erosive power of a river changes the future options for the course of the river, so evolution itself changes future evolutionary possibilities. This can happen in simple ways, as termites construct their own environment by building termite mounds. These mounds may last for dozens or hundreds of years and provide a sort of ecological inheritance for generations of termites.

The first cyanobacteria turned carbon dioxide into oxygen and set off a revolution that completely changed the chemistry of the oceans and atmosphere. Most species modify their environment and this often changes how selection affects them: they construct, at least in part, their own environment. As evolutionary biologists we have little understanding of what these processes mean for evolution.

Does all this add up to a new modern synthesis? There is certainly no consensus among evolutionary biologists, but development, ecology, genetics and paleontology all provide new perspectives on how evolution operates, and how we should study it. None of these concerns provide a scintilla of hope for creationists, as scientific investigations are already providing new insights into these issues. The foundations for a paradigm shift may be in place, but it may be some time before we see whether a truly novel perspective develops or these tensions are accommodated within an expanded modern synthesis.


Project to reveal choc's DNA code


Cocoa pod (Mars)
The work will take about five years to complete

The chocolate company Mars has announced that it is to decode the genetic structure of the cacao tree.

The research project, which is to be done in collaboration with the US Department of Agriculture and IT firm IBM, aims to improve cocoa production.

Scientists hope the Chocolate Genome Project can assist breeding programmes.

Understanding the tree's DNA could make crop production more resistant to pests, diseases, and water shortages that may come from a warming climate.

Howard-Yana Shapiro, Mars' global director of plant science, said African farmers stood to benefit the most as they accounted for nearly two-thirds of world cocoa production.

The research would "ultimately improve cacao trees, yield higher quality cocoa and increase income for farmers", he told BBC News.

Dr Shapiro would not be drawn on whether the research might lead to genetically modified chocolate.

"Researchers worldwide will have access to our work, the cacao genome. What they do with it, I can't control," he explained.

It is likely to take approximately five years to sequence, assemble, annotate and analyse the cacao genome.

But information will be available before then, as it is gathered, through the Public Intellectual Property Resource for Agriculture (PIPRA)

DNA sequence information will be publicly available for no charge and no information will be patented.

Dr Jane Rodgers, of the John Innes Centre in Norwich, UK, welcomed the fact that the research results would be put in a public database.

"This kind of approach is the norm," she said. "The results of the project will underpin all research in the field and stimulate its application to the greater benefit of all."

Dr John Orchard, of the Natural Resources Institute in Kent, said that it was essential to develop hardier varieties regardless of climate change.

"The cocoa crop is particularly vulnerable to disease. Sixty percent of the Brazilian harvest was wiped out by a disease called witches recently and this kind of impact is not uncommon," he told BBC News.

The research is similar to the sequencing of the rice genome five years ago.

That project has already led to "huge strides" in the basic understanding of the food crop, according to Dr Hugh Jones of the Institute of Arable Crop Research in Harpenden in Hertfordshire.

"This study should lead to similar benefits," he said.

Project workers at IBM's TJ Watson Research Centre in New York will use their experience of computational biology to create a detailed genetic map of cacao.
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