Monday, September 1, 2008

The DNA Network

The DNA Network

Darwin’s impact on our place in the world [HENRY » genetics]

Posted: 01 Sep 2008 06:36 PM CDT

As part of the 150th anniversary celebrations of a certain Charles Darwin, Radio New Zealand is getting a whole bunch of New Zealand scientists to give public lectures about Darwin’s impact on our place in the world. They’re recording them, broadcasting them over the radio, and you can listen to them on the internet here (the first two are online already).

Lecture 1 - Darwin and the Evolution of an Idea (Professor Lloyd Spencer Davis, University of Otago)

In the last 2000 years there has been one idea, above all else, that has altered the way we view the world and our place in it. That idea is evolution by natural selection and the originator of the idea was Charles Darwin

Lecture 2 - The Evolution of Biological Complexity (Professor Paul Rainey FRSNZ, Massey University).

Professor Rainey paints a picture of life’s evolution from the perspective of major evolutionary transitions, including that from solitary organisms to societies.

Lecture 3. The Principle of Evolution: Absolute Simplicity (Professor David Penny CNZM FRSNZ, Research Director, Allan Wilson Centre for Molecular Ecology and Evolution, Massey University)

Can we find anything in biology that is not understandable, or not explainable, by the things we can observe and measure in the present? Evolution is, by far, the simplest possible way of understanding ourselves, our past, and our future.

Lecture 4. The fossil record (Professor Alan Cooper, Director, Australian Centre for Ancient DNA, The University of Adelaide)

How should we interpret what the fossil record tells us about evolution - both in general, and with regard to how New Zealand has ended up as it is today?

5. Evolutionary Psychology (Professor Russell Gray, The University of Auckland)

Attempts to explain human behaviour in evolutionary terms have a mixed history. Today, crude social Darwinian and socio-biological explanations are increasingly being replaced by richer, more complex theories.

6. The Storytelling Ape: Evolution, Art, Story, Culture (Professor Brian Boyd, The University of Auckland)

Brian Boyd will focus on art, perhaps the feature of human behavior that might seem to have least to do with a struggle for existence. Can biology explain why art (music, dance, visual art, storytelling and verse) is a human universal? Why do we so compulsively invent and engage with stories we know to be untrue?

Online presence is multidimensional [business|bytes|genes|molecules]

Posted: 01 Sep 2008 03:52 PM CDT

This is an atypical bbgm post. I am going to talk about “scientific blogging” in light of various recent events and discussions on the web on the subject.

I started blogging over two and a half years ago, mostly as a way to write about material in my head. I used to label myself a “blogger”, but since I also dabble in video/screencasts, podcasts, maintain a wiki, etc, that label is one of convenience. The point is, that by painting blogging, including scienceblogging, with one big brush, we are selling ourselves short.

Some people use a blog as a diary of observations. Others talk about specific scientific experiments (which might also go up on a wiki). Some record screencasts of their work, while some might choose to go with putting up material on slideshare, or increasingly on Nature Precedings. Others use their blogs to report news, provide commentary on issues of the day, write essays, and many other uses. Note that I haven’t even talked about Tumblelogs, Twitter or Friendfeed yet.

In other words, we need to look at online presence in two dimensions at the very least; the choice of medium, and the nature of the content. That’s one reason I was very pleased to see that Scienceblogging is changing titles to ScienceOnline in 2009. It’s much more inclusive and a better approach.

The other thing that galls me on occasion is the “are bloggers journalists?” discussion. People take things much too seriously sometimes, and just love using broad brush strokes. There is enough place for online communication and presence of multiple types, so once again a gentle reminder. Don’t think of online presence in one dimension. You need at least the two described earlier, and discussions around citability, value, etc need to take that into account

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Where does life hide when the meteor strikes? [Bayblab]

Posted: 01 Sep 2008 12:30 PM CDT

Deep trenches in the ocean? Underground cave systems? Amazing...

Cool Plant Comparative Genomics Resource: Phytozome [The Tree of Life]

Posted: 01 Sep 2008 12:04 PM CDT

I spent the last few days at a "retreat" for the Joint Genome Institute and heard about a few things there worth sharing with everyone. I will try and post about some of them in the next few days. Here is one. The JGI and the Center for Integrative Genomics have made a pretty cool tool for comparative analyses of plant genomes. It is called Phytozome and has a variety of simple and nice features. JGI is doing more and more work on plant genomes as part of their energy research and I think Phytozome could turn into a good place to go to get the latest plant genome information. Go to to see the real thing.

Invisible Fishnets and Baby Boomer Pain [Sciencebase Science Blog]

Posted: 01 Sep 2008 09:21 AM CDT

fishnetsIt’s that time of the month again, so here’s the latest round-up from my column over on SpectroscopyNOW, covering a whole range of science and medical news with a spectral twist from magnetic resonance to Raman by way of fishnets and infra-red.

Fishnet invisibility cloak - It is what fans of science fiction and technologists have been waiting for since HG Wells’ Invisible Man first came into view - or not, as the case may be. Scientists at the University of California, Berkeley, have engineered three-dimensional meta materials that can reverse the natural direction of visible and near-infrared light, which could one day lead to an invisibility device.

Bending MRI to diagnose joint disease - Osteoarthritis has turned out to be the bane of the Baby Boom generation, causing joint pain and disability for millions of people, more than half of those over the age of 65 in fact. Unfortunately, current approaches to diagnosing the disease cannot provide definitive results until the disease is in the advanced stages. This is often when symptoms have become severe and irreversible joint damage may already have occurred. Magnetic resonance imaging could provide an early diagnosis of osteoarthritis (OA), the most common form of arthritis, according to scientists speaking at the recent ACS meeting.

Universal detector - A team in Japan has used UV spectroscopy and microscopy to study the interaction between liposome clusters and endocrine-disrupting chemicals (EDCs) as a model of how living cell plasma membranes might be affected. The work could lead to the development of a universal detector for EDCs

Dance of the xenons - An NMR study of xenon atoms has demonstrated a fundamental new property - what appears to be chaotic behaviour in a quantum system ? in the magnetic spin of these frozen atoms. The work could lead to improvements in our understanding of matter as well as in magnetic resonance imaging.

Handling chirality with X-rays - X-rays are rather useful in determining the structure of materials and biomolecules, but are relatively insensitive to chirality. Now, a team of scientists in Japan has shown that circularly polarized X-rays at an appropriate wavelength can distinguish ‘left’ from ‘right’ in alpha-quartz. The work could have implications for studies of other inorganic organometallic materials, including industrial catalysts, liquid crystals, biomolecules, and pharmaceutical products.

Hybrid technology - Surface-Enhanced Raman Scattering (SERS) was first used in 1977 and since the has proven itself as an extremely sensitive analytical technique requiring only small volumes of sample and with wide application. Researchers have suggested that it is so sensitive that it could be used as a new tool in single molecule detection to augment or even displace techniques such as laser-induced fluorescence, frequency-modulated optical absorption at low temperature, and electrochemical detection of redox-active species. SERS of silicon nanostructures coated with a gold-silver substrate can be used to detect DNA hybridisation for taxonomic, biomedical and medical diagnostics purposes, according to a new study by researchers in Singapore.

Oh, and speaking of fishnets…anyone been thinking about the modelling career of John McCain’s running mate Sarah Palin?


Invisible Fishnets and Baby Boomer Pain

Long term cultural selection for male dominance traits? [Yann Klimentidis' Weblog]

Posted: 01 Sep 2008 09:19 AM CDT

Male dominance rarely skews the frequency distribution of Y chromosome haplotypes in human populations
J. Stephen Lansing, Joseph C. Watkins, Brian Hallmark, Murray P. Cox, Tatiana M. Karafet, Herawati Sudoyo, and Michael F. Hammer
PNAS August 19, 2008 vol. 105 no. 33 11645-11650
Abstract: A central tenet of evolutionary social science holds that behaviors, such as those associated with social dominance, produce fitness effects that are subject to cultural selection. However, evidence for such selection is inconclusive because it is based on short-term statistical associations between behavior and fertility. Here, we show that the evolutionary effects of dominance at the population level can be detected using noncoding regions of DNA. Highly variable polymorphisms on the nonrecombining portion of the Y chromosome can be used to trace lines of descent from a common male ancestor. Thus, it is possible to test for the persistence of differential fertility among patrilines. We examine haplotype distributions defined by 12 short tandem repeats in a sample of 1269 men from 41 Indonesian communities and test for departures from neutral mutation-drift equilibrium based on the Ewens sampling formula. Our tests reject the neutral model in only 5 communities. Analysis and simulations show that we have sufficient power to detect such departures under varying demographic conditions, including founder effects, bottlenecks, and migration, and at varying levels of social dominance. We conclude that patrilines seldom are dominant for more than a few generations, and thus traits or behaviors that are strictly paternally inherited are unlikely to be under strong cultural selection.

See no evil []

Posted: 01 Sep 2008 08:11 AM CDT

If you don’t want to look at Alzheimer’s because you’re afraid that you would be unable to face the fact that you’re likely to lose the little God gave you, then you just don’t click on it.

- Kari Stefansson, DISCOVER magazine, September 2008

Teaching Genetics Without the Mumbo Jumbo [Eye on DNA]

Posted: 01 Sep 2008 06:40 AM CDT

A study in the Journal of Research in Science Teaching suggests that primary school students should be introduced to scientific concepts in “everyday English” first before being forced to memorize vocabulary.

The results reveal that although learning the language of science remains a primary hurdle, students taught using our content-first approach demonstrated an improved conceptual and linguistic understanding of science. would this apply to teaching genetics? My son’s current favorite series of books is Geronimo Stilton and in Geronimo and the Gold Medal Mystery, a professor conducts “extremely secret experiments in genetics.” Genetics was explained as:

…the science that deals with the hereditary characteristics of species in the plant and animal world.

Not quite everyday English. How might this be rephrased?

Genetics is the science that looks at how parents pass along certain traits to their children.

Is that too simplistic? How would you explain genetics in one sentence?

via Stanford News Service

Nourishing Innovation: Open Science and Federal Support [Bitesize Bio]

Posted: 01 Sep 2008 05:46 AM CDT

Following on last week’s post about the NIH and English as the Language of Science, I have another selection from Arthur Kornberg’s book For the Love of Enzymes to highlight.

Essentially, Kornberg is describing the critical elements in the relationship between scientists, industry, and innovation (page 294):

One critical ingredient must be provided by industrial management if it wishes to capture and retain creative and productive scientists. It must provide an open atmosphere which encourages the scientist to discuss ideas, progress, and failures with colleagues in and out of his organization and to publish without restraint. Such an atmosphere is conductive to a flow of students, postdoctoral fellows, and visiting professors through the company.

Medium ImageHe explicitly argues that innovation and discovery depend upon open access to ideas. Many will react by suggesting that private industries will lose money from the competition by sharing secrets. That would be my gut reaction as well. Scientists however, [should] keep laboratory notebooks documenting the progress of their discoveries, just as companies retain patent attorneys to ensure fair compensation for work done.

That this reminds me of the Open Access publication is of course no coincidence. What promotes innovation in one setting promotes innovation in all, generally speaking.

Innovation in industry cannot maintain itself on its own however. Kornberg continues:

One often hears that the private philanthropy and corporate contributions will fill the gap left by reduced federal support. This is utter nonsense. The gap in question is billions of dollars a year. Such private philanthropic resources are not available, nor are there equitable mechanisms for obtaining and distributing such sums except through federal taxation and administration. Will biotechnology companies, having obtained their science and scientists from the universities, share their fortunes with their academic parents and benefactors?

Kornberg’s points are plainly obvious to anyone familiar with how research is financed. The success of American science is singularly the result of impressive government support. Continue reducing that support, and innovation will come to a screeching halt over the course of the next generation.

Basal expression from inducible transgenes [Reportergene]

Posted: 01 Sep 2008 12:25 AM CDT

Of course, a critical drawback of inducible transgene expression is the amount of basal expression (leakage) responsible to making noise in the discrimination of specific transgene patterns analysis (and even, to reduce potentially harmful effects of transgene).

The Australian team of from Stuart M Pitson (University of Adelaide) by incorporating AU-rich mRNA destabilizing elements (ARE) into the 3′ untranslated region (UTR) of inducible constructs, demonstrated that this modification minimized sphingosine kinase 1 (SK1) basal expression from a Tet-inducible vector with only a slight decrease in the maximum level of fully induced SK1. This approach, might improve signal-to-noise ratio and should also be applicable to other inducible expression systems.

On the other hand, if your transgene is a reporter gene, sometimes a minimal basal level expression would be appealing to monitor physiological patterns that could be increased or decreased by your treatments. Isn't it?

This short technical report was published on the August issue of BioTechniques (sorry, I did not find a DOI for

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