My TEDxCincy Xperience

October 24, 2010

On October 7, 2010 I was proud to take part in the first TEDxCincy Conference at the Aronoff Center for the Arts in downtown Cincinnati. I joined 18 other speakers talking about everything from corporate culture to new media to inner city violence to personal encounters with wildlife to high tech tools in the study of Cincinnati's history. I spoke about the revolution in the life sciences created by the widening availability of next generation DNA sequencing. Now that a little time is past and I've got some other things out of the way in the lab I can sit back and reflect on the experience.

A leg up, and a neck up, on the competition

September 10, 2010

Giraffe (Giraffa camelopardalis) at the the Cincinnati ZooOK, let’s face it giraffes (Giraffa camelopardalis) are just plain cool. Tall and lanky Manute Bols of the animal world covered in spots. In addition to being high on the list of must-see animals on an African safari, giraffes have served as poster children for evolution. Long before Darwin, that other evolutionist, the French naturalist Jean-Baptiste Lamarck, speculated that the long-necked giraffe was descended from shorter-necked ancestors. According to Lamarck, all that stretching to get to juicy, tree-top leaves changed their necks in ways that they then passed on to their offspring.

“The giraffe lives in dry, desert places, without herbage, so that it is obliged to browse on the leaves of trees, and is continually forced to reach up to them. It results from this habit, continued for a long time in all the individuals of its species, that its fore limbs have become so elongated that the giraffe, without raising itself erect on its hind legs, raises its head and reaches six meters high (almost twenty feet).” Lamarck on giraffes taken from Alpheus Spring Packard. 1901. Lamarck, the founder of evolution: his life and work with translations of his writings on organic evolution. Longmans, Green and Co.

Along comes Darwin who bought into the idea that living things can change over time but didn’t buy into Lamarck’s mechanism for evolution. For Darwin the evolution of the giraffe’s elongated neck was due to selection. From the standpoint of Darwin’s natural selection individuals in ancestral giraffe populations varied in some intrinsic and immutable way, at least immutable in the lifetime of an individual. These ancestral giraffes not only varied in leg and neck length but they also varied in their propensity to survive and contribute offspring to the population. Variation in survival and reproduction was in turn correlated to some variation in physical traits. Proto-giraffes that survived and successfully bred (one usually is necessary for the other) then passed on their intrinsic “legginess” and “neckiness” to their progeny and the population changed over time, generation-by-generation getting a little taller and necks a little longer as selection sieved through that variation in the population that can be passed from parent to offspring. It’s remarkable that Darwin came up with natural selection while knowing next to nothing about exactly how traits were passed from parent to offspring. It wasn’t until nearly a century after Darwin that natural selection was reconciled with the viable model of biological inheritance we call genetics.

But where are we then left with giraffes? Clearly neck and leg length evolved and likely by some sort of Darwinian selection in giraffes. Giraffes’ closest living relatives, the equally cool, West-African forest dwellers, the Okapi (Okapia johnstoni), have comparatively short necks and the fossil record reveals many giraffes with short necks. Modern giraffes are nested in a family tree that therefore points to short-necked ancestors. But, if selection plays a role then what is the agent of that selection? Darwin posed two models of selection; good-ole-fashioned natural selection where predators, the physical environment, competition for food, parasites or some other agent act on survival and reproduction and sexual selection where the agent of selection lies in a species’ own gene pool. In sexual selection the variance in individuals contribution to the population stems from competition for mates, either competition with members of your own sex to access the opposite sex or competition imposed by a choosy opposite sex. These forms of selection, natural and sexual, are basically the same, both involve filtering through available variation to change the population, but in sexual selection the agent of selection lies specifically in competition for mates. Competition for mates can lead some some crazy characteristics, everything from a moose’s antlers to the gaudy flowers of orchids, and maybe giraffes necks?

Why we get cancer

July 12, 2010

The short of it...

Creationists often put physicians on a pedestal as the scientists doing the real work in biology, useful work of improving human health and well-being as opposed to the pontificating, abstract work of the evolutionists. But, can we really understand human aliments outside of the light of evolution? Well worn examples of antibiotic resistance vividly illustrate the folly of ignoring evolutionary processes in medicine. Cancer however is another example of evolution in action. Tomislav Domazet-Loso and Diethard Tautz of the Max Planck Institute for Evolutionary Biology in the journal BMC Biology used a technique called phylostratigraphy to trace the origin of the genes associated with cancer to the origins of the cell and the first multicellular animals. The evolution of the first multicellular organisms necessitated a fine balance between the reproduction of individual cells and the evolutionary interests of the multicellular organism. The role of genes involved in cancer is to keep the peace and limit the ability of particular cells to go rogue, curtailing the reproductive success of individual cells in favor of the group. Understanding the evolutionary origin of these ancient genes sheds light on why we get cancer and can light the way to new treatments.

Back on the horse...

May 17, 2010

OK, after months of ignoring this web site I'm committing to building it back up. Lots of things have happened since the last update way back in June 09. Trips to Taiwan and China, teaching undergraduate classes from general biology to molecular genetics at local colleges, lots of ongoing collaborative projects in the lab, a new paper published in BMC Evolutionary Biology by my collaborators and I as well as the many new developments across the field of evolutionary biology. Maybe after a few posts I can build a modest audience back up again and start some discussion about the ever developing world of evolutionary biology. Stay tuned...

Plush accommodations

June 11, 2009

Debate is bouncing around the evolution blogs. The extreme poles in the evolution-creationism debate agree on one thing; namely that one can not be a Christian and accept the modern scientific consensus on biological evolution. However, in recent years several prominent scientists of faith including Ken Miller and Francis Collins have spoken out about their own personal experience in reconciling science and religious convictions. Even agnostic participants in the debate like Florida State University philosopher of science Michael Ruse have taken a position against these polarizing views that evolution necessarily equals atheism. Science and science education organizations such as the National Academy of Sciences (NAS) and the National Center for Science Education (NCSE) have gone to great lengths to counter the creationist claim that evolution is somehow antichristian by frequently emphasizing the views of religious scientists like Collins and Miller, philosophers like Ruse sympathetic to the idea that both faith and science can coexist and religious leaders like Pope John Paul II who see no fundamental conflict between evolution and the central tenets of the Christian faith. These organizations do this for one key reason; to counter the claim by creationists that evolution necessarily leads to atheism.

Heads or Tails

March 10, 2009

Transitionals are a hot topic in evolutionary biology because they provide clear evidence of common ancestry. In linking two seemingly unrelated groups in a shared genetic heritage one looks for evidence of organisms that display a moasic of characteristics, some characters defining one group and some another. Transitional forms are those organisms that display this mix of traits from two seemingly desperate groups. Contrary to denials of creationists transitionals are indeed found throughout the fossil record.

The evolutionary transition from land mammals to cetaceans (whales, porpoises and dolphins) is one of these well documented transitions. For many years the origin of whales was a mystery. Whales were obviously mammals but where they fit in the mammal family tree was unknown. Comparing the genes of cetaceans and other mammals lead to the conclusion that cetaceans arose from within a group of hoofed mammals called artiodactyls, but, this conclusion disagreed with the fossil evidence. This disagreement largely ended in 2001 when University of Michigan paleontologist Phillip Gingerich and colleagues published an account of new species of proto-whales from Pakistan, Artiocetus clavis and Rodhocetus balochistanensis. These fossils had skulls with the characteristic features of whales but unlike modern whales had hind limbs. But these early whales, protocetids, didn't just have any hind limbs but hind limbs with ankle bones only found in the artiodactyls, exactly as the genetic data predicted.

Gingerich and colleagues describe another protocetid from Pakistan in the journal Public Library of Science ONE. The two new fossils are typical of early whales with four well-developed limbs and a cetacean-like skull.

Pygmy origins

March 1, 2009

Human populations vary genetically, however, much of this variation is not divided into discrete groups but rather is distributed as a cline, or gradually, with one population smoothly transitioning into another. Genetic isolation in most human populations is therefore primarily dictated by distance. Also, the human propensity for roaming and spreading into new environments means that humans spread their genes widely and tend to genetically homogenize populations. However, there are some exceptions to these general patterns. Some human populations have experienced relatively long periods of genetic isolation.

Pygmies of West and Central Africa are known for their comparatively short stature. Pygmies do not comprise a single group but rather approximately two dozen groups with a diverse array of different languages. While on average adult male height is about 5 feet, comparatively small for most human populations, mean height can vary by as much as 8 inches among different pygmy groups. Pygmies are among the last groups in Sub-Saharan Africa to practice the hunter-gatherer lifestyle typical of our earliest human ancestors and as such understanding their evolutionary history can provide important clues to the history and diversification of our species.

Please stimulate my research!

February 18, 2009

The American Recovery and Reinvestment Act, otherwise known as the Economic Stimulus bill, includes 2.5 billion in additional funds for the National Science Foundation (NSF) specifically for "research and related activities". To help build scientific infrastructure 300 million of these funds are reserved for the NSF's Major Research Instrumentation program. An additional 502 million, of which 400 million will go to research equipment and facilities and 100 million to education and human resources, will go to other NSF activities. Incidentally NSF's Major Research Instrumentation program provided funds for Cincinnati Museum Center's (CMC) new Molecular Ecology and Systematics Laboratory. Hopes are this will push the US towards increased innovation in basic science. New proposals to the NSF, if funded, will help CMC grow as a research institution, spread scientific literacy and train students at every level in the high tech skills required for a modern economy. Wish me luck!

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Happy Birthday Chuck!

February 12, 2009

Today is the 200th anniversary of Charles Darwin's birth. The notion that life changes over time and the idea that species share a common ancestry both predate Darwin, but, Darwin was the first to provide a viable mechanism by which biological evolution occurs, namely evolution by natural selection. Darwin solidified the idea of evolution and this idea rapidly spread in acceptance among scientists after the publication of Origin of Species.

Evolution's importance can not be overstated. Today evolution is the central organizing principle in the life sciences. To date, it is our only viable explanation for the diversity of life on earth. Data from paleontology, ecology, anatomy and most recently, modern molecular genetics and comparative genomics continue to support the conclusion that life shares a common genetic heritage.

Darwin is a model of how science should work and how scientists should conduct themselves. He was careful, thorough, curious, and dedicated to the details and all the while humble and considerate of his colleagues. Darwin did not have the computational mind of a Newton nor was he capable of the abstraction of an Einstein. Darwin's genius was simply as a clear thinker, ever mindful of the evidence and ready to follow that evidence where it leads. At the center of Darwin's ideas was a broad knowledge of natural history all to be brought to bear on big questions in science.

Darwin and Abraham Lincoln were born on exactly the same day. Both played key roles in building the world we live in today. The bicentenial of their births should be a time to reflect on their accomplishments and follow their example to move society forward.

Happy birthday Chuck!

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Origins blog at Science website

February 3, 2009

With 2009 as the 200th anniversary of Darwin's birth and the 150th anniversary the publication of the Origin of Species evolution is spreading across the web faster than a large bill in a drought-ridden finch population. The American Association for the Advancement of Science's Science Magazine has a new blog all about origins. Inspired by Darwin, AAAS will spread news on all things evolution from anthropology to genomics to the origin of life. So check in regularly as part of Darwin year 2009!

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