Tuesday, January 27, 2009

Elevating Science, Elevating Democracy

Today's NYT features this excellent defense of science by Dennis Overbye. My favorite part:

The knock on science from its cultural and religious critics is that it is arrogant and materialistic. It tells us wondrous things about nature and how to manipulate it, but not what we should do with this knowledge and power. The Big Bang doesn’t tell us how to live, or whether God loves us, or whether there is any God at all. It provides scant counsel on same-sex marriage or eating meat. It is silent on the desirability of mutual assured destruction as a strategy for deterring nuclear war.
Einstein seemed to echo this thought when he said, “I have never obtained any ethical values from my scientific work.” Science teaches facts, not values, the story goes.

Worse, not only does it not provide any values of its own, say its detractors, it also undermines the ones we already have, devaluing anything it can’t measure, reducing sunsets to wavelengths and romance to jiggly hormones. It destroys myths and robs the universe of its magic and mystery.
So the story goes.
But this is balderdash. Science is not a monument of received Truth but something that people do to look for truth.
That endeavor, which has transformed the world in the last few centuries, does indeed teach values. Those values, among others, are honesty, doubt, respect for evidence, openness, accountability and tolerance and indeed hunger for opposing points of view. These are the unabashedly pragmatic working principles that guide the buzzing, testing, poking, probing, argumentative, gossiping, gadgety, joking, dreaming and tendentious cloud of activity — the writer and biologist Lewis Thomas once likened it to an anthill — that is slowly and thoroughly penetrating every nook and cranny of the world.

Nobody appeared in a cloud of smoke and taught scientists these virtues. This behavior simply evolved because it worked.
It requires no metaphysical commitment to a God or any conception of human origin or nature to join in this game, just the hypothesis that nature can be interrogated and that nature is the final arbiter. Jews, Catholics, Muslims, atheists, Buddhists and Hindus have all been working side by side building the Large Hadron Collider and its detectors these last few years.
And indeed there is no leader, no grand plan, for this hive. It is in many ways utopian anarchy, a virtual community that lives as much on the Internet and in airport coffee shops as in any one place or time. Or at least it is as utopian as any community largely dependent on government and corporate financing can be.
Arguably science is the most successful human activity of all time. Which is not to say that life within it is always utopian, as several of my colleagues have pointed out in articles about pharmaceutical industry payments to medical researchers.
But nobody was ever sent to prison for espousing the wrong value for the Hubble constant. There is always room for more data to argue over.
So if you’re going to get gooey about something, that’s not so bad.
It is no coincidence that these are the same qualities that make for democracy and that they arose as a collective behavior about the same time that parliamentary democracies were appearing. If there is anything democracy requires and thrives on, it is the willingness to embrace debate and respect one another and the freedom to shun received wisdom. Science and democracy have always been twins."
Odd as it may seem coming from a proud participant of this "utopian anarchy", I couldn't agree more! The entire essay is well worth reading.

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Monday, January 26, 2009

A graphic novel in time for the bicentennial

Now this might be something to get the kids really excited about:



Doesn't he look dashing, that young field biologist? Says Simon Gurr, the illustrator:



Less than a week now until the printers deliver Darwin: A Graphic Biography, the latest 100-page comic book from Eugene Byrne and me. I’ve seen the proofs and can’t wait to hold the book itself in my hands. The big launch is on 30th Jan, stay tuned for more details and to find out how to get hold of a copy.



And now I can't wait for this week to end...


{Hat-tip: Joe@ForbiddenPlanet]


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A short course on Darwin, his science, and his legacy

Andy Shriver pointed out this University of California Museum of Paleontology short course:



Darwin: the man, his science, and his legacydarwin2009.gif


Charles Darwin was born on February 12, 1809. His birthday is an opportunity to celebrate his contribution to science and its influence in such diverse academic fields as biology, anthropology, and medicine. To kick off the multiple celebrations that will be taking place in the Bay Area, UCMP offers you the opportunity to join historians and evolutionary biologists as they discuss the extraordinary life of Charles Darwin, his contributions, his legacy, and our current understandings of evolutionary theory. Speakers will include Keith Thomson, Kipling Will, Kevin Padian, and Eugenie Scott.


Saturday, February 7, 2009


2050 Valley Life Sciences Building, UC Berkeley


9:00 am to 4:00 pm (registration opens at 8:15 am)


As an added bonus, a teacher workshop on evolution presented by UCMP, California Academy of Sciences, Human Evolution Research Center, KQED QUEST, SETI, and the National Center for Science Education will be held the following day on Sunday, February 8, 9:30 am to 3:00 pm (registration opens at 9:00 am). The workshop, held in 2063 VLSB, will include behind-the-scenes tours of the Human Evolution Research Center and lunch. More information is available here.


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Tuesday, January 20, 2009

Science: the metaphysical party-pooper!

And we now have a president who likes to have this designated driver along? Should be fun times at the upcoming parties...


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Monday, December 22, 2008

Phylogenomics suggest ratites lost flight multiple times

ResearchBlogging.orgRebekah Wukits discusses recent findings about ratite evolution for Bio 135.


Ratite evolution has been debated for centuries. Some of the earliest evolutionary biologists questioned whether or not ratites had a linear evolution or if the major groups had had independent origins. Richard Owen proposed that living ratites had much more in common with other flight capable groups while being united by the “arrested development of wings unfitting them for flight”. In 1951, two ornithologists, Mayr and Amadon, stated that, “the present consensus is that the main groups of these birds are of independent origins”.


Traditionally, ratites have been considered to be monophyletic, or ascending from a common ancestor. They are placed in the major group Noegnathae, with the flight-capable tinamous as a sister group. Since the extinct tinamous were capable of flight, it has been thought that the ratites lost flight once in their history, then diversified. Unfortunately, simple geography contradicted this theory. All living ratites (rheas, cassowaries, emus, ostriches and kiwis) are isolated on different southern continents.  Rheas are found in South America. Ostriches reside in Africa. Emus and cassowaries are found only in Australia and kiwis can be found in New Zealand. Extinct species of ratites follow the same pattern. Moas were also found in New Zealand, and elephant birds lived in Madagascar. The question became that if flight was lost once early in ratite evolution, how did they become so spread out and isolated? The perfect answer seemed to reside in the theory of continental drift. Ratites came from a single ancestor, lost flight and were then isolated when Gondwana broke up.


Though most of the recent studies of morphological and molecular ratite characteristics have supported the monophyletic theory, many still debate it. Rarely challenged is the fact that adaptations to a cursorial lifestyle, one that is adapted to running, can lead to convergent evolution, and can be misleading when basing phylogeny on morphology. This led scientists to do further phylogenomic studies in order to test the prevailing theories. These studies include data taken from genetic loci that represent the entire avian genome. In this particular study, data was taken from 20 loci that are dispersed widely throughout the avian genome. The data set included all living ratites and eight outgroup taxa. Previously done similar genetic tests have supported ratite monophyly, however these tests were more sophisticated and advanced and supported a different conclusion.


The results are as follows: analysis of the data strongly supports placing the flight capable tinamous within ratites and ostriches as the sister group. If this new phylogeny is correct, the single loss of flight in ratites is unlikely. In order for all ratites to have lost flight in a common ancestor, the tinamous would have had to regain flight at a later time. It is much more likely that flight was lost multiple times do to convergent evolution than to have gained flight in the earliest ancestors, lost flight in the common ancestor of ratites, than gain flight again in tinamous.


It seems more likely that ratites descended from a single ancestor, than diversified when gondwana broke up. Flight was lost in each family and convergent evolution occurred due to similar environmental conditions. Flight is very costly both energetically and morphologically. Ratites had little pressure to fly and since these features are costly to maintain, they became reduced over time.  The theories of this paper seem concrete however more study is needed. Their own genetic studies produced conflicting results. Placing tinamous within ratites has great implications for their evolution and dispersal. This idea needs to be further developed and supported.


Reference:


J. Harshman, E. L. Braun, M. J. Braun, C. J. Huddleston, R. C. K. Bowie, J. L. Chojnowski, S. J. Hackett, K.-L. Han, R. T. Kimball, B. D. Marks, K. J. Miglia, W. S. Moore, S. Reddy, F. H. Sheldon, D. W. Steadman, S. J. Steppan, C. C. Witt, T. Yuri (2008). Phylogenomic evidence for multiple losses of flight in ratite birds Proceedings of the National Academy of Sciences, 105 (36), 13462-13467 DOI: 10.1073/pnas.0803242105

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Wednesday, December 10, 2008

Studying the Flamenco Dance of the Jumping Spider

If you were intrigued by the video you saw in class of the mating dance of jumping spiders, this will show you a bit more about how one can go about studying such fascinating complex behaviors.







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Why Sex?

Apropos of the recent steamy discussions in class about sex and evolution, Sonica Sangha shares this video she found on the PBS website:



[via Evolution: Library: Why Sex?]


And as a bonus, here's a behind-the-scenes video podcast accompanying the wonderful PBS Nature series "What Females Want and Males Will Do" which aired last spring. Click on the show titles for more fun video clips and information from the PBS Nature website.




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Wednesday, December 3, 2008

Modeling the emergence of multi-drug resistant TB hot zones

ResearchBlogging.orgRebecca Freeman submitted this essay for the Evolution class.



According to the World Health Organization (WHO), a “hot zone” is an area with >5% prevalence (or incidence) of Multi-Drug Resistant Tuberculosis (MDRtb). Sally M Blower and Tom Chou have been using a mathematical method to track the emergence and evolution of multiple strains of drug resistant tuberculosis, but they have now developed a new, more complex mathematical model. Before this model, there was only a two strain model, meaning it was only relevant to individuals that can be infected with a wild type pansensitive strain or a drug resistant strain, but there are many more strains then this. There are a resistant strains only to one drug and some resistant to multiple drugs. This means there is a multitude of strains in these hot zones and there was a need for a better way to track this (Blower and Chou 2004). Blower and Chou realized that a more complex mathematical model is necessary to capture the complexity of the epidemiology of the hot zones, and the evolution of hot zones was very unclear



Understanding drug resistance is important to understanding the, and Blower and Chou explain the evolving of resistance very well. They give three processes that are involved in generating drug resistance: Transmission of drug resistant strains to uninfected individuals, which is transmitted resistance; Conversion of wild pansensitive cases to drug resistant cases, which is acquired resistance; finally, cases where they have drug resistant strains and it becomes resistant to more antibiotics during treatment, which is amplified resistance. What everyone has had to do in the past is just study acquired and transmitted resistance, and now with the new model, they can incorporate amplification resistance. This was a big problem because it has been shown that inadequate treatment of DRtb can result in the amplification of drug resistant strains, which may be an important process of MDR epidemics (Blower and Chou 2004). So this is where Blower and Chou came in. They created a model, the call the amplifier model, that enables the tracking of emergence and evolution of MDR strains, the transmission of these strains and the amplification of these strains during repeated episodes of treatment.


Blower and Chou are really studying the effects of inadequate treatment programs, and how this may lead to a higher prevalence in MDRtb. One problem that this research cannot completely take into account yet is the transmittance ability of MDRtb compared to pansensitive tuberculosis. This is an area that is hazy right now, and so this cannot completely be incorporated into the model. Amazingly, they have measured a general fitness of MDRtb vs. pansensitive tuberculosis, by calculating the treatment fail rates and treatment cure rates of the each category of strains.



The authors were very clear with the purpose of the model. Even though the mathematical model is very complex, the idea and how they explain it is easily understandable. They use R0 to stand for the average number of secondary cases caused by one infectious case in a population where treatments are available. Their model breaks this up into four categories of strains: The wild type pansensitive [R0(1)], which is sensitive to all drugs; Pre-MDR [R0(2)], which is sensitive to one of the main drugs used to treat tuberculosis; MDR [R0(3)], which is resistant to both of the main treatment drugs; and post-MDR [R0(4)], which is resistant to both of the main antibiotics and others as well (Blower and Chou 2004). With the information gathered from over 30 years of date they constructed likely evolutionary trajectories of hot zones, and with this they also took into account low cure rates vs. high amplification probabilities in many areas. They also tried to incorporate which strains are more transmissible, but as I said before this was not really possible with their model and there was a large degree of uncertainty.



The results of their model matched the WHO predictions well, but there were some distinct differences, and I think these differences are what make this research so important. By using all for types (R01-4) they found great variability in incidence and prevalence. When treatments were originally started strains of pre-MDR strains emerged quickly, so incidence and prevalence of pre-MDR strains increased, and this subsequently led to possible amplification of resistance and MDRtb epidemics in certain areas. The question is: Why certain areas and not others? This question is explained by Blower and Chou. Interestingly, areas with bad treatment programs do not necessarily have a really high incidence of MDRtb, it has stayed pretty steady at a 5%-14% (Blower and Chou 2004). This to me seems like an argument that MDRtb is not as easily transmissible, because its rates overall have stayed pretty low, but there was no significant evidence for this. The WHO predictions state that a >5% prevalence OR incidence in MDRtb equals a hot zone. Blower and Chou found the mathematical relationship between MDR prevalence and incidence. MDR prevalence can be three times greater then MDR incidence. They used the results to evaluate the hot zones on prevalence or incidence. If it is by incidence then only 20% of those areas would be considered hot zones and 51% if criterion is prevalence (Blower and Chou 2004). I see this as an argument for the fitness of MDRtb to be very high and transmissible ability to be lower, because there are less new cases, and more cases that have just become more resistant.



When looking at the four strains the hot zones had a much lower R0 for pansensitive strains (median=.82), which suggests that the wild type strain should be slowly eradicated. The R0 for the pansensitive strains in non-hot zones were all above 1 (median=1.39) Looking at the rate of detection of cases and treatment rates in hot zones versus non-hot zones it is 55% to 25% (Blower and Chou 2004). This shows that places where they have control programs were successful at fighting pansensitive strains but ironically it created more MDRtb strains, making it more likely to become a hot zone.



The importance of this research is that they have figured out that the difference between incidence and prevalence rates is significant enough to change the view of an area as being a hot zone or not. Their research looks at many factors that go into the evolution of these hot zones. Out of the many factors they actually saw that case detection and treatment rates were the most important factors. They came to this conclusion because if case detection and treatment rates were low, and the amplification was high, it still did not generate a hot zone. Vise versa, if the case detection and treatment rates were high and the amplification rates were low; it was likely to become a hot zone. The point is that these areas with high case detection and treatment rates should not increase these rates unless high cure rates are achieved first. Blower and Chou have created a model that has multiple dimensions and can help the WHO in the future to prevent hot zones from popping up in high risk regions. The WHO already had a model for this but it was nowhere complex enough to correctly calculate prevalence and incidence of MDRtb, and how their mathematical relationship.


Reference:



Sally M Blower, Tom Chou (2004). Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance Nature Medicine, 10 (10), 1111-1116 DOI: 10.1038/nm1102




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On Hormonal and environmental control of neuroplasticity

Andrew Mora review's Christy Strand's seminar on neuroplasticity.



Nueroplasticity is an interesting concept that deals with changes in the brain due to experiences. In order to study neuroplasticity better, Dr. Christy Strand used hormonal and environmental cues to see how they would affect the brain. The specific region of the brain that Strand was interested in was called HVC (high vocal center in birds) and the size of this region of the brain was recorded before and after experiments. According to Strand, this region in birds is important in motoring song output, and is also involved in song learning. She asserted that testosterone, an important steroid that affects the brain, did in fact increase HVC volume, but was uncertain as to how the region got bigger. Did individual neurons get bigger? Was the density decreased? Or were there simply more neurons from new cells?



In order to test for the size of the HVC, Strand used bromodeoxyuridine (BrdU) which is a cell birth marker. She used house finches because they are very common throughout the US and they are great song birds to test for the HVC region. Besides using testosterone treatment for the birds, she also wanted to know the role of the photoperiod in increasing HVC growth. Her results indicated that testosterone treatment does affect HVC growth, that photoperiod alone might affect HVC growth, and that testosterone treatment does not affect the number of new HVC neurons, despite an increase in total neuron number. Her reasoning for this might be because of a natural turnover; that is, there is no new neurons being created, but there is a decrease in cell death. Corticosterone (a stress hormone) had no affect on HVC growth.



In another related experiment, Strand used rufus-winged sparrows to test environmental cues on HVC. She used these birds because they have a unique characteristic of beginning their breeding season after the first monsoon in southern Arizona and northern Mexico. Breeding season is important for HVC size because the birds are singing frequently when they are looking for a mate. According to strand, the testes of these birds are big in March, but only used in July when the first rain falls. Her results found that during breeding of these sparrows, HVC neuron number does not increase, and testosterone levels were not different on sampling dates. She did find that singing behavior increases during the breeding season, but was still unsure whether or not HVC affects singing behavior or if the reverse was true.



I particularly enjoyed the area of future research being done by Dr. Strand. She discussed that she will be experimenting with hormonal factors affecting neurogenesis and neuroplasticity in adult snakes and lizards. She will look at the affects of captivity on neurogenesis and affects of sex on neurogenesis. Instead of the HVC region she will look at the size of the medial cortex in adult rattlesnakes. I like this integration because it attempts to compare research done on birds with similar research done on reptiles. Hopefully we will see this work published soon.


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