Saturday, September 25, 2010

I'm in a Pond

Remember The Lonely Island's I'm on a Boat? Of course you do. Here's a geeky scientists version called I'm in a Pond. Yee-ahhhh.


Friday, September 24, 2010

Baba's Word

Tonight I went to see Baba Brinkman's show called The Rap Guide to Evolution. I had a pretty good time so I thought I would post a video of one of the raps he performed. Here's Baba rapping at King's College at the Cambridge Darwin festival.

If you want to find out more and get some downloads then check out his website:

Will Blog for Food

Welcome to the 200th post in my science blog! YAY! (insert confetti cannons here)

To mark this historic event (or just event at least) I've decided to present a story on blogging. Actually, its an editorial that is featured in this month's Nature Neuroscience. The piece centers around the topic of corporate sponsored scientific blogs vs. editorially independent blogs and the need for the disclosure of potential conflicts of interest.

You may, or may not, have heard or seen that PepsiCo sponsored a blog called Food Frontiers on the popular science website The blog was written by PepsiCo's food scientists about the company's research and was then cancelled only 2 days after the launch due to the discontent voiced by independent scientific bloggers. These independent scientific blogs (I'm gonna call them indy-blogs for short) are editorially independent, started as a grass-roots movement, are typically written by scientists and science journalists, are a way to freely share and discuss scientific matters, and are considered by some as an alternative news source. I'm sure you can see where the indy-bloggers are coming from against this whole corporate thing. Add in the fact that the blog platform is hosted by Seed Media Group, a corporation.

Should commercial blogs be allowed to share a blogging platform with these indy-blogs?

Should what are now being called blog conglomerates (, Discovery News, etc) be viewed as legitimate news sources on the web?

As to that second question at least, I do find myself going to such websites to see what kind of stories are gaining media attention. Perhaps the difference, in my case, is that I try to actively seek out the original source material (usually journal article) if I can. And so, perhaps, this is more a question about the reliability of science journalism itself, particularly with the huge cuts many media outlets have given their science journalists and the sources scientifically-untrained journalists are using. The editorial states an interesting stat to this point: "In 2009, 63% of science journalists employed by mainstream media outlets reported to have found 'stories' on a scientist's blog, compared with 15% five years earlier." Granted, the blogosphere has grown enormously in the last 5 years.

What about this growth of the blogosphere? By its very nature it is a medium which can service niche interests, provide alternative news sources, and be an outlet of opinion. But it is also a medium that imposes and regulates its own code of ethics and can be very appealing to the anonymous writer. The casual reader can be easily influenced and even overwhelmed with the information they can find in this sector of the internet. After all, when it comes to fact-checking the casual reader is more likely to just read the blog entry and move on.

Let's loop this argument back to the conglomerates, the corporations, and the PepsiCo example. Because there are so many blogs available and because blogs have assumed the role of science journalism what kinds of lines should be drawn? I mean, one of the main problems with the PepsiCo blog was that Seed Media failed to make it clear that it was corporate sponsored, especially since it was on the same site as indy-blogs. This particular opinion I happen to agree with. I see no problem with corporate blogs designed to highlight corporate sponsored research as long as the blog clearly defines that it is corporate sponsored. Should I say corporate again? Corporate corporate corporate.

Anyway, perhaps the blogosphere will police itself as it has with many other issues. Maybe we just need to give it some time.

This all made great sense in my head, if it made no sense at all to you then I encourage you to read the editorial. Actually, I encourage you to read it either way:
Editorial. (2010) Good blogosphere practices. Nature Neuroscience: 13(9), 1035. (DOI: 10.1038/nn0910-1035)

(image from

Hot and Spicy

When you think of fruit what do you envision? A sweet, juicy treat? That's what I think of, particularly strawberries. Mmmmmm....

This sweet, juicy goodness, evolutionarily speaking, is a reward to animals for the dispersal of the fruits' seeds. In fact, it is considered to be one of the key innovations in the radiation of angiosperms (flowering plants). However, the plants don't receive just the goodly seed-dispersers, they also end up attracting consumers (vertebrates, invertebrates and microbes) that are detrimental to the plants' fitness (put very very simply, how much it reproduces). These detrimental consumers come in the form of seed predators that reduce the likelihood of seed dispersal and viability. The middle ground or balancing factor comes in the form of the fruits' chemistry. The makeup of the fruit can deter seed predators, reduce microbial attack, and/or attract specific seed dispersers, all without compromising seed viability. Generally, this explains the presence of noxious, bitter, and sometimes toxic chemicals in many ripe fruits.

Now that we know some general fruit stuff, how do we test something like the variance in microbial pathogen pressure as it is related to the variance in the chemistry of wild, ripe fruits? Well, you would need to start with a fruit species in which you know the chemistry pretty well. You would then need to show that the chemistry of the fruit deters microbial pathogens. Start playing with concentrations of both and you've got yourself an experiment.

Hmmm...what is a fruit that deters things from eating it? If you've looked at the picture above then you can probably guess: Chilies. Chilies belong to the genus Capsicum and were one of the first plants to be domesticated in the New World. They contain what are called capsaicinoids, which produce the spicy/hot capsicum (hotter = more pungent fruit), are unique to this genus, are well characterized, and are broadly antimicrobial. Capsaicinoids also increase in their concentrations during fruit ripening and are limited to the fruit itself (rather than to other parts of the plant). The authors of this paper also rediscovered a polymorphism for capsaicinoid production in wild populations of multiple chili species which allowed them to test the variability of these chemicals in the wild.

The researchers did most of their work with Capsicum chacoense Hunz., which is native to the Chaco region of Bolivia, Argentina, and Paraguay. They used a geographic gradient to study the impact of microbial pathogens on fruit chemistry. The results showed that across all populations the only significant cause of fruit and seed damage was microbial infection, primarily caused by the fungus Fusarium semitectum. This particular fungus enters the fruit by way of the piercing proboscises of hemipteran bugs. On closer inspection they found that the fungal infection of seeds increased with the number of foraging scars on the fruit and that fruits with no insect damage had no fungal infection. This pattern was seen in both pungent and nonpungent fruits, but the slope of the relationship was significantly steeper for nonpungent fruits, the infection rates for nonpungent fruits being almost twice as high. Because pungent and nonpungent fruits are indistinguishable in the wild there must be something else going on. When the scientists created an artificial fruit media that mimicked the nutritional composition of the C. chacoense fruit except for the presence/absense and concentration of capsaicinoid chemicals they found that the inhibition of F. semitectum was dose-dependent. The reduction of infection by F. semitectum was completely accounted for by the capsaicinoid chemicals.

The protection that chilies receive from these chemicals shapes the chemistry of the fruits, provides a selection pressure to the fungus, and explains among-population variation of capsaicinoid production. As fungal pressure increases there will be an increase pungent phenotypes in the chilies. So why not just stay hot and spicy all the time? As with most things there is a trade-off. If the plant puts more into chemical production it puts less into seed coats. That means that pungent plants will protect their seeds from fungal infection but those seeds will not be as well protected when they travel through the digestive system of a seed disperser. You get the idea right?

Being firmly in the medium-salsa crowd I must then ask, why do humans love the hot stuff? Some argue that chilies help lower blood pressure, that the antimicrobial effects also benefit us, and that they increase salivation allowing for better digestion. All good notions, in my opinion, but that's still not gonna make me eat a super-hot chili. No way. According to a NY Times article on this topic, Dr. Rozin (who studies human emotions, likes, and dislikes) says he has evidence for what he calls benign masochism. In the article, Dr. Rozin says that in his experiment he tested chili eaters by gradually increasing the pungency of the chili until they said they could go no further. He then asked what level of heat they liked the best, and they chose the highest level of unbearable pain. Crazy? I think so. I'll stick with bell peppers, thank you.

Here is the paper on chili evolution:
Tewksbury, Joshua J., et al. (2008) Evolutionary ecology of pungency in wild chilies. PNAS: 105(33), 11808-11811. (DOI: 10.1073/pnas.0802691105)

And this is the NY Times article:

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A Meeting of the Minds

 "Sir David Attenborough, 84, is a naturalist and broadcaster. He studied geology and zoology at Cambridge before joining the BBC in 1952 and presenting landmark series including Life On Earth (1979), The Living Planet (1984) and, recently, Life. Richard Dawkins, 69, was educated at Oxford, later lectured there and became its first professor of the public understanding of science. An evolutionary biologist, he is the author of 10 books, including The Selfish Gene (1976), The God Delusion (2006) and The Greatest Show On Earth (2009). He is now working on a children's book, The Magic Of Reality."

What happens when you put them in a room together and ask them questions? Read the interview here:

Thanks for this one Rick!

Southern Saturnian Aurora

Image credit: NASA/JPL/University of Arizona/University of Leicester
I am absolutely fascinated by the planets. In fact, if I had to choose another field of science to go into it might just be planetary science. As such, when I see new data, particularly images, of planets I just jump on the story. I mean, just look at the above picture...its pretty incredible. What you are looking at is a picture of the planet Saturn (in case the rings didn't give it away). Its what's called a false-color composite image. These types of images show colors that differ from what you would see in a true color image, which are how an object appears to the human eye. Usually they either turn up a color aspect, change one color to another to make a feature more visible, or assign colors to particular aspects or features. When NASA's Cassini space craft took some 65 pictures with its visual and infrared mapping spectrometer (VIMS) one of these features to stand out were the glow of auroras in the south polar region. These auroras were seen streaking out about 600 miles from the cloud tops and were clearly visible in the near-infrared wavelengths of light.

In the false-color images scientists usually designate blue to indicate sunlight reflected at a wavelength of 2 microns, green to indicate sunlight reflected at 3 microns, and red to indicate thermal emission at 5 microns. Since the auroral emission appears to be green, this suggests emissions from hydrogen ions of light between 3 and 4 microns in wavelength. You can clearly see the contrast with the rings which appear blue and have a wavelength of 2 microns. The red, 5 micron, wavelengths you see in the southern hemisphere are due to the heat emission from the interior of Saturn.

Image credit: NASA/JPL/University of Arizona/University of Leicester
The auroras were seen to vary over the course of the Saturnian day. This gas giant rotates extremely fast and so a day only lasts 10 hours and 47 minutes. On what is the Saturn's day equivalent to noon and midnight the aurora can be seen to brighten significantly for several hours. This brightening is likely due to the planets angle to the Sun. The auroras are thought to occur in processes similar to those on Earth, where particles from the solar wind are channeled by the magnetic field toward the planet poles. On Saturn you also add in the effects of the electromagnetic waves generated by the moons moving through Saturn's plasma-filled magnetosphere.

And ok, these are not the first pictures of Saturn's aurora. Cassini has returned a number of detailed snapshots in the past. These images are more data scientists can use to understand this phenomena. Not to mention they look pretty bitchin'.

First, I highly recommend watching this short video by NASA/JPL:

And here are some story links:

Monday, September 20, 2010

Sunday, September 19, 2010

Big Bright Jupiter

Jupiter is the largest planet in our solar system, and it is located at 3.95 Astronomical Units (AU) or 368 million miles from the Earth. In our night sky the planet is always bright, but this month it is even brighter than usual as it makes its closes pass by Earth for the year, and closest since 1963 and until 2022. Jupiter's orbit varies in distance about 10-11 million miles over a period of about 60 years, but in terms of brightness to use you have to look at this relatively small variation in terms of magnitude factors. Normally, the brightness varies between -1.6 and -2.94, with the latter being the brightest. But a change as small as 1% can mean a brightness change in either direction of up to 4%. In the current case, we're talking 4% brighter than normal. Tomorrow, Monday, September 20 will be the nearest point to Earth in this near pass. And on Tuesday, September 21, the Earth will pass between Jupiter and the Sun. So grab your telescope and head outside to take a look!

On the topic of looking at the planets through a telescope, Jupiter is one of the largest planets in terms of how much of the telescope's eyepiece it fills up at about 31 arc seconds across. If you have a standard amateur or backyard telescope then that's about a 12th of your field of view, and with this simple of an instrument you can see some good banding around the planet and some moons. Don't have a telescope? Try some binoculars, the view will still be good and you might even see some of Jupiter's moons (hint: keep your arms nice and steady).

If you are in the mid-northern latitudes then look for Jupiter to the lower right of the Great Square of Pegasus. The "celestial trio," Mars, Venus, and the star Spica, will rise at or just after dusk, and as this trio sets you will see Jupiter rise in the east. Or, just look for a bright "star" near the moon. In these, mid-northern latitudes, you'll see it in the early evening and you should be able to see the planet all night long. As you go further north the earlier and longer you'll see Jupiter, and as you go south the later and less you'll see it.

Also, while you are gazing at Jupiter on September 21st move your telescope or binoculars less than a degree to catch sight of the planet Uranus. Its possible that both of the planets will be visible in the same field of view. The planets line up, or are in opposition, on the same night making finding and viewing them easy.

Learn lots more about this event here:

(image from


I found this great story through work about nearsightedness and so went on to the American Optometric Association's website to get a little bit more info first.

Nearsightedness is medically termed myopia. It is a vision condition where close objects appear clear but far away objects look blurred. Anatomically, the eyeball is too long or the cornea has too much curvature. Regardless of which one it is the extra length of the eye means that light isn't focused correctly onto the retina. As a condition, myopia is actually pretty common, affecting nearly 30% of the U.S. population. Usually, it first exhibits itself in school-age children, and as the eye grows during childhood until age 20 the condition progresses. Eyeglasses or contact lenses are prescribed to correct nearsighted by bending the incoming light to the eyes. Another option is orthokeratology, or corneal refractive therapy, a non-surgical procedure where a person wears a series of specially designed rigid contact lenses to gradually reshape the curvature of the cornea. Yet another option is laser procedures that reshape the cornea by removing a small amount of eye tissue with a highly focused laser beam.

If you scroll through the advanced online publication of Nature Genetics you will notice an article about the myopia gene. The study conducted a genome-wide association study for refractive error in 4,270 individuals. Basically, they were looking for the gene that causes nearsightedness. The researchers identified SNPs (single nucleotide polymorphisms which occur when a single nucleotide in the genome differs between members of a species or individuals) on 15q25 associated with refractive error. So they replicated the association in six adult cohorts of European ancestry with a total of 13,414 individuals. Actually, these 'individuals' numbers are twins. They found that the locus overlapped a transcription initiation site called RASGRF1. This particular gene is highly expressed in neurons and in the retina and as such is crucial to retinal function and visual memory. Additionally, the scientists found that found a different gene, called CTNDD2, is related to myopia in Chinese and Japanese populations. To be thorough, the researchers also created mice that were missing the gene. These mice showed changes in their eye lenses, adding further evidence to the findings.

Check out the paper:
Hysi, Pirro G., et al. (2010) A genome-wide association study for myopia and refractive error identifies a susceptibility locus at 15q25. Nature Genetics: published online (DOI: 10.1038/ng.664)

Here's a report through Duke Medicine (one of the teams on the paper):

The Australians were also on the team, read an article from there here:

(image from

Wednesday, September 15, 2010

Yummy, Carbonated Light

On the topic of biofuels, solar technology developer Joule Unlimited, Inc. announced yesterday that they have been issued a U.S. patent (#7,794,969, titled "Methods and Compositions for the Recombinant Biosynthesis of n-Alkanes") covering its new energy conversion process. The process converts sunlight and waste carbon dioxide (CO2) into liquid hydrocarbons that the company claims are fungible with conventional diesel fuel. So unlike making traditional biofuels (where you turn sugar or algal or agricultural biomass into alcohol - see story below), this technique is a direct, single-step, continuous process requiring no raw material feedstocks. The company claims that this could be incredibly efficient and cost as little as $30 per barrel equivalent.

Alright. Cool. So what exactly is happening here? Well, Joule has these microorganisms (they don't say what kind) that function as biocatalysts that use only sunlight, waste CO2, and non-fresh water to produce hydrocarbons that are diesel range and chemically distinct from biodiesel. Oh, and they are compatible with the existing infrastructure. Wanna add some more good news? Apparently they are sulfur-free and ultra-clean.

Do I sound a little skeptical? Probably because I am a little skeptical. After all, this info is coming from a company press release. So I looked up the patent number to try to fill in a couple of holes in the story.

One of these holes is the microorganism they are using to convert the light and CO2 into fuel. Apparently they are using an engineered cyanobacterium that "comprises a recombinant acyl ACP reductase (AAR) enzyme and a recombinant alkanal decarboxylative monooxygenase (ADM) enzyme; and exposing said engineered cyanobacterium to light and carbon dioxide, wherein said exposure results in the conversion of said carbon dioxide by said engineered cynanobacterium into n-alkanes, wherein at least one of said n-alkanes is selected from the group consisting of n-tridecane, n-tetradecane, n-pentadecane, n-hexadecane, and n-heptadecane, and wherein the amount of said n-alkanes produced is between 0.1% and 5% dry cell weight and at least two times the amount produced by an otherwise identical cyanobacterium, cultured under identical conditions, but lacking said recombinant AAR and ADM enzymes."

Mmm-hmm, that's a lot of "said's." I would refer to the patent itself (link below) if you are interested in details like the actual amino acid sequences of said (*smile*) enzymes. Another hole is the productivity and/or efficiency of this process, and this is where I would again point you to the patent itself because it is a while lot of numbers. Although there are some figures that help to simplify the information. Based off of what I know of biofuels (which, admittedly, isn't all that much) it seems kinda impressive. That is, of course, if it works.

Another concern, or hole, they left, at least in their press release, was their plans for mass production. In my opinion, on of the problems with biofuel production is not just the efficiency (or lack of) of the process but actually scaling up the process to make an affordable product that anyone can buy anywhere. And that, I think, will be the thing to watch for with a story like this: Will we, average people, ever see this easily available to us?

Look up the patent using the U.S. Patent Number 7,794,969 at this website:

This is the press release from Joule:

This is where I originally found the story, but it says basically the same things as the press release:

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A colony of the fungus Neurospora crassa (left) growing on cellulose and the yeast Saccharomyces cerevisiae. Sugar transporters from Neurospora that have been inserted into the yeast are tagged with green fluorescent protein. (Image: Jamie Cate and Susan Jenkins, UC Berkeley & EBI)
Reseachers at the University of California, Berkeley have been working on how and what yeast can digest. They have taken genes from a grass-eating fungi (Neurospora crassa) and put them into yeast. This new set of genes allows the yeast to produce alcohol from cellulose, a material that is normally indigestible. N. crassa is one of the rare yeasts that can digest cellulose because its preferred diet is fire-damaged plants. The genes were located by doing a genome-wide systems analysis to see which genes are turned on when the fungus grows on cellulose. The researchers were able to locate a family of genes which produces proteins that transport sugars into the Neurospora cell to be used a fuel and some transporters, in particular, that allow the cell to import a few types of cellodextrins (specifically cellobiose, cellotriose, and cellotetraose), simple-ish sugars.

Why should we care what yeast are able to digest? The biofuels industry has been struggling to make cellulosic ethanol economically feasible. Right now the industry is using brewers yeast, the single-celled fungus (Saccharomyces cerevisiae) to turn sugar or other simple carbohydrates into alcohol. So far cellulose has been a bit of a problem as it is a pretty tough molecule; it is composed of glucose (simple sugar) molecules all linked together into long chains. Its a molecule that you can find in abundance in various materials such as corn stalks, leaves and cobs (and the US uses a whole lotta corn!) as well as paper waste or any other plant material. Normally these long chains have to be broken up into smaller cellodextrins by enzymes called cellulases using a method called saccharification. Then another enzyme called beta-glucosidase is added to break down the cellodextrins into their simple sugar components. That's all before the yeast even get introduced to the system! If the N. crassa genes (cellodextrin transporters) can be inserted into the industrial strains of yeast that are currently being used for ethanol production the efficiency of the fermentation process can be greatly improved.

The paper appeared in this weeks ScienceExpress:
Galazka, Jonathan M., et al. (2010) Cellodextrin transport in yeast for improved biofuel production. Science: published online. (DOI: 10.1126/science.1192838)

Here is UC Berkeley's new article about the paper:

Monday, September 13, 2010

Biodiversity Soapbox

This week Science magazine had a nice focus on biodiversity in their ecology section. It seems to me that biodiversity was a much hotter topic in the past than it is today. I don't think I've heard many mainstream news stories on it recently. Today its all about the economy and energy consumption. Don't get me wrong, those are very good topics to be concerned about, but as a society that is attempting a green movement I'm not so sure we should be so choosy in what we conserve.

In relation to the topic of conserving biodiversity you are going to hear a few terms that you may or may not know the actual, or scientific, meaning of, so lets take a sec and define a few things. We'll start big and work to small. First, biodiversity (short for biological diversity) is the range of variation found among microorganisms, plants, fungi, and animals. An ecosystem includes a geographic area including the living and nonliving components. A species is a group of populations of organisms that reproduce among themselves (although you can find many other definitions). A community is composed of the populations of different species that interact with each other. A population is a group of individuals belonging to a single species living in a particular area. An organism is an individual living thing. And finally, a gene is a unit of inherited material which as a collection determines the look and behavior of an organism. When you talk about biodiversity you can mean genetic diversity, species diversity, or ecosystem diversity. Or some combination of these.

The biggest threats to biodiversity worldwide include habitat loss and destruction, the introduction of exotic (non-native) species, pollution and contamination, alterations to ecosystem composition, over-exploitation of (a) species, and global climate change. Many people don't like to see animal and plant populations decline or go extinct, but they also don't think such a thing could affect their lives. But in fact, it has been shown to directly affect our basic needs for food, shelter, and health. Think about it. The food can be pretty obvious in that we eat plants and animals, but also consider that things like greater genetic diversity allowing species to adapt to changing environmental conditions and pressures placed upon them by  competitors, predators and diseases. The shelter part includes many material goods such as timber and fibers, but it can also include underpinning functions such as nutrient cycling, flood control, and climate regulation. Then there is health. Many medicines, traditional and synthetic, have a biological source. Not to mention the simplicities of everyday life which contribute to overall mental health, something as simple as taking a walk or going camping.

Let me take a sec to step down from my mini-soapbox...

On the topic of conservation, specifically reducing human impacts on biodiversity, there has been wide political recognition. In 1992 there was a UN Conference on Environment and Development where the United Nations Convention on Biological Diversity (CBD) was agreed upon. Since 2002, 193 parties to the CBD committed themselves to substantially reducing biodiversity loss by the year 2010. This commitment was also endorsed by the World Summit on Sustainable Development and later incorporated into the UN Millennium Development goals in 2005. Other organisations around the world are also actively supporting this conservation effort. Organisations such as the Nature Conservancy, the Royal Society for the Protection of Birds, and the World Wide Fund for Nature (WWF). We're talking millions of members per organisation!

News bulletin: Its 2010. Did you know that it is the International Year of Biodiversity? So how are we doing?

As with most conservation efforts, we are doing a good job but it just isn't enough. The CBD failed to meet its lofty goal and is planning to meet again to adopt a new strategic plan. This plan will include revisions to several of the 21 previous subtargets. The news focus in Science took a look at 6 of these subtargets.

1. Degradation of Habitat - The 2010 goal was to decrease the rate of loss and degradation of natural habitats, but many regions continue to lose habitat. The new goal is to halve or nearly eliminate the rate of loss, degradation, and fragmentation of habitat.
2. Conservation Status of Species - The 2010 goal was to restore, maintain, or reduce the decline of species in selected taxonomic groups. This has worked in some countries but overall, not so much. The new goal is to prevent the decline of known threatened species and improve the conservation status of at least 10% of them.
3. Funding for Conservation - The 2010 goal was to transfer new funding to CBD participants. It kinda worked, but the monetary focus has switched to climate change over the last few years. The new goal is to increase the human resources and financing by 10-fold.
4. Consumption of Biological Resources - The 2010 goal was to reduce biologically unsustainable or consumption. Basically, there was no real progress on this one. So sad. The new goal is to continue to reduce consumption with a specific goal to end overfishing and destructive fishing practices.
5. Protected Areas - The 2010 goal was to effectively conserve at least 10% of each of the world's ecological regions. This one was actually pretty successful, the target being reached for more than half of the terrestrial ecoregions. The new goal is to protect 15-20% of land, with no coastal/marine in the plan as of yet.
6. Invasive Species - The 2010 goal was to establish management plans and control invasive species pathways. Some of this has been met but species are still spreading and many countries still don't have management plans. The new goal will be to prioritize control efforts.

Let's look at it this way: Biodiversity worldwide is still declining even though the conservation efforts are increasing. Why is this? Perhaps it is due to the varying success of different organizations and the practices and policies they employ. Traditional approaches such as the formation of national parks (and other protected areas) and ecological restoration (habitat management, invasive removal, captive breeding, etc) have had some success. Additional success has been seen in those conservation approaches that have economic benefits such as secotourism. Based on your knowledge, are you seeing some gaps in our conservation efforts? Maybe some more funding and conservation effort into the pressures and underlying drivers that cause biodiversity decline and better ecosystem management and restoration techniques?

Here are the references:

Stokstad, Erik. (2010) Despite Progress, Biodiversity Declines. Science: 329 (5997), 1272. (DOI: 10.1126/science.329.5997.1272)

Rands, Michael R. W., et al. (2010) Biodiversity Conservation: Challenges Beyond 2010. Science: 329(5997), 1298 - 1303. (DOI: 10.1126/science.1189138)

In addition to the in-text links, also take a look at:
The CBD's complete revised and updated strategic plan

The UN Millenium Project goals:

A short pamphlet by the Ecological Society of America on biodiversity:

And these related sources:
Pennisi, Elizabeth. (2010) Tending the Global Garden. Science: 329 (5997), 1274. (DOI: 10.1126/science.329.5997.1274)

Normile, Dennis. (2010) Saving Forests to Save Biodiversity. Science: 329 (5997), 1278. (DOI: 10.1126/science.329.5997.1278)

(image from

Sunday, September 12, 2010

Be Flexible

Engineers have published in Nature Materials about artifical electronic skins that may help robots and/or prosthetic limbs to feel. These skins can detect the gentlest of touches by sensing pressure changes. How gentle? You may ask. Less than a kilopascal, about the pressure you use when typing for picking up a pen.

There is actually more than one paper published on this topic this week. The papers describe similar devices that work in different ways. One of the devices uses six square centimeters of an elastic polymer called ppolydimethylsiloxane (PDMS) that has pyramid-shaped chunks cut out of it at regular intervals. When the material is compressed the chunks, which were previously filled with air, become filled with PDMS and change the material's ability to hold an electric charge. Put this little square onto an organic transistor (reads differences as a change in current) and you can track pressure changes across the material. This little device can detect pressure changes as light as a fly or butterfly landing on it.

The other skin uses semiconductor nanowires pulled into the shape of a 7-centimeter-square grid using a method called contact printing. They then put this grid on a flexible pressure-sensitive rubber. The nanowires operate using low voltages while the rubber changes its electrical resistance under pressure. Because of the rubber this device is much bendier than the first one, allowing it to shape around various objects.

You look at these together and you see that they each have their pluses. The first detects very very small pressure differences while the second is very flexible. Obviously there is much more research to be done to get these skins working like actual skin. But it is definately a step, or a touch, closer.

Read the papers for more:
Mannsfeld, Stefan C. B., et al. (2010) Highly sensitive flexible pressure sensors with microstructured rubber dielectric layers. Nature Materials: published online. (DOI: 10.1038/nmat2834)

Takei, Kuniharu. (2010) Nanowire active-matrix circuitry for low-voltage macroscale artificial skin. Nature Materials: published online. (DOI: 10.1038/nmat2835)

Boland, John J. (2010) Flexible electronics: Within touch of artificial skin. Nature Materials: published online. (DOI: 10.1038/nmat2861)

Story Links:

(image credit Linda Cicero, Stanford University News Report)

Wednesday, September 8, 2010

Dance Dance Evolution

 Perhaps I should create a "Picture This" category/label for some of these stories because that's what I'm going to ask you to do once again. Ok, so picture this: You're a guy, you've gotten all gussied up (do guys 'gussie up'?), you get in your I'm-compensating-for-something-car, you drive to your local dance club, you grab a drink and check out all of the available singles mingling and flirting, you strut out to the dance floor to show off your moves and you choose....

(I suggest reading both options before clicking)

Dance Option 1: You have large, variable movements, keep your torso moving (bending forwards and/or backwards), make wide (but not flailing) gestures with your arms, nod your head while also turning it side to side (video demonstration)

Dance Option 2: Keep your movements relatively contained, move your torso but with no big bending movements, move your arms but keep them below the shoulder and closer to the body, move your head in subtle ways/directions rather than nodding (video demonstration)

Which style of dance do you chose? Which of these styles makes you more attractive to the ladies?

Based off a new study in the journal Biology Letters, I'm hoping you picked the first option. In this study, psychologists from Northumbria University have taken a look at what kinds of male dance moves catch the eyes of the ladies. They stuck 38 reflective markers to the joints and other body parts of volunteer male students, and they asked them to dance to a thumping drum beat for 30 seconds as if they were in a nightclub. Twelve video cameras recorded the dancing, and using 3D motion-capture technology, uniform avatar figures were created. Examples are the video links from above. Next, they had heterosexual women watch the avatar videos and rate them according to whether the man was a good dancer or a bad dancer (note that pilot studies showed that women equate good dancer to more attractive). Using the avatar videos and the ratings from the women, the researchers were able to identify the key movement areas of the dancers' bodies that influenced female perception.

What kinds of moves make you stand-out, or I guess dance-out, to the ladies? Moves very much like those from Dance Option 1. Eight movement variables made a difference when females rated men as either good or bad dancers: the size of movement of the neck, trunk, left shoulder and wrist, the variability of movement size of the neck, trunk and left wrist, and the speed of movement of the right knee (probably because most volunteers are right handed and movement is dominated on this side of the body). The movements that were perceived as best were those that were influenced most greatly by large and varied movements involving the neck and torso.

Is there an evolutionary explanation for this? Not a tested one that I know of, at least in humans. The authors suggest that human male movements may act as honest signals of traits such as health, fitness, genetic quality, and developmental history. I don't know. I'm not an archaeologist or anthropologist but I do know that dancing is not exactly a new human behavior. Perhaps in the past it acted as these subconscious signals while also very consciously showing strength, coordination, creativity, and hunting prowess. Too bad the dancing you see in clubs today doesn't tell you things like job security, family man abilities, degree of commitmentphobia, or his ability to put the toilet seat down after use. 'Course that might just be the jaded single part of me talking.

You can read the actual paper here:
Neave, Nick, et al. (2010) Male dance moves that catch a woman's eye. Biology Letters: published online. (DOI:

Monday, September 6, 2010

Sunday, September 5, 2010

Pale is Pretty

Let's see, how to make South Beach scientific....hmmmm...

You know I found a paper. It has a pretty amazing title too: "Bronze is beautiful but pale can be pretty: The effects of appearance standards and mortality salience on sun-tanning outcomes." *Grin* See I told ya.

Ok, seriously. A huge number of people expose themselves to harmful amounts of ultraviolet (UV) radiation in an effort to tan their skin. Such exposure can heighten the risk of skin cancer. Why do this? I think we all know. Tanned skin is perceived as physically attractive. I, for one, have been exposed to enough UV radiation and the resulting sunburns (including earlier this summer) to last me a lifetime. This trip, though, the three of us went through three bottles of sunscreen in four days. Sun and skin conscious? Oh yeah.

The introduction of this paper introduces terror management theory (TMT) which argues that "individuals are motivated to live up to culturally derived standards because doing so confers self-esteem, which helps manage the potential for anxiety inherent in the awareness of personal mortality." Translated: People do things they know are not necessarily good or safe in order to live up to society's standards and in doing so it makes them feel better about themselves. Also, there is the terror management health model (TMHM) which "posits that when thoughts of mortality are accessible in the context of health decisions, outcomes should reflect motives oriented toward self-esteem rather than health protection." Translated: Decisions are influenced by how people perceive the behavior to be attractive. Now let's relate that to sun-tanning.

The paper actually consists of two studies:

Study 1 tested whether telling people that a tan is more attractive would increase tanning intentions and whether telling people that "pale is pretty" would reduce tanning intentions. First, they "reminded" 101 female (because they are more likely to report investing self-esteem in their appearance than males are) psychology students of their mortality  Did you pick up on the same bit I did? The reminded of their mortality part? How exactly do you do that anyway? The researchers here used the "Fear of Death Scale" where participants responded either "true" or "false" to 15 items about the extent to which they fear death. Lovely. Next, they had the participants read articles ostensibly taken from a fashion magazine reporting on the appeal of tanned or pale skin. These articles came in three varieties: "Bronze is Beautiful,"  "Style: The Fair-Skinned, Natural Look Is In," and "Style: The Simple Natural Look Is In" (the control group). They featured headshot photographs of tan and fair-skinned celebrities, respectively, along with text on the subject. Afterwards, the participants were asked to complete a five-item assessment of sun-tanning intentions. Study 1 concluded that the effect of mortality salience varied as a function of the article. Women reading articles about how bronze is beautiful showed an increase in their tanning intentions. Similar results occurred with the pale is pretty group. It appears that awareness of what society considers to be attractive greatly influences people's behavior even as it relates to their health, positively or negatively.

Study 2 was conducted on a public beach and tested whether mortality reminders and the "pale is pretty" would increase the desire for sunscreen with a higher SPF and the intention to use it. This study was designed to test Study 1 in a real world setting. The test was conducted at a public beach in South Florida during Spring Break. They recruited 53 Caucasian women to fill out a short survey consisting of a packet of questionnaires containing similar questions to those in Study 1 including the fashion articles. After reading an article the participants were given a questionnaire divided by a line. Above the line was a set of instructions explaining that as a token of appreciation they were to be given a sun product of their choosing upon filling out the below-line portion. After tearing off and handing in the top half they were to fill out the below-line portion which asked them to check a box next to 1 of 10 different skin products characterized by their SPF (50, 45, 30, 15, 10) and whether they were described as sun block or tanning lotion. The participants' sunscreen intentions were also measured by questionnaire. Study 2 concluded that reminders of death increased the level of SPF chosen, and the association between attractiveness and fair skin increased the level of SPF chosen. Also, after people were primed to associate fair skin with attractiveness the reminders of death increased sunscreen use intentions and intentions to use it in the future.

Alright, so how should we start out the letter to the fashion magazines? "Dear Promoters of Skin Cancer..." Well, perhaps we should work on that one.

ResearchBlogging.orgCox, C., Cooper, D., Vess, M., Arndt, J., Goldenberg, J., & Routledge, C. (2009). Bronze is beautiful but pale can be pretty: The effects of appearance standards and mortality salience on sun-tanning outcomes. Health Psychology, 28 (6), 746-752 DOI: 10.1037/a0016388

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Tales from the Road: South Beach

I'll bet that you've heard of South Beach, right? It is a "neighborhood" located in the city of Miami, Florida. Technically it is the southernmost 23 blocks of the main barrier island that separates the Atlantic Ocean from Biscayne Bay. It is known for its amazing beaches, art deco, and nightlife. Art deco is an eclectic design style that is often described as elegant, lavish, functional, and modern. You typically see materials such as stainless steel, lacquer, inlaid wood, and animal skins/prints used in creative and sweeping forms and patterns. Streamline Moderne, a style of Art Deco, is apparent in the pastel colored buildings of South Beach. It is characterized by long horizontal lines, curving forms, and automotive and/or nautical elements. So is architecture science? That might be a bit of a stretch, but here are some South Beach pictures anyway.

Yep, South Beach has an actual beach. How else would everyone show off
their surgical enhancements :-) It was a cloudy day so not much beach traffic.

This site gives lots of information on the arts, culture, dining, and shopping in South Beach:

Here is the website for the City of Miami Beach:

And at the risk of turning into a travel guide, here's another what-to-do-in-South-Beach site:

Sink or Swim?

For a follow-up post for the Keys I tried to find an an article that incorporated both the magrove habitat and the coral reefs that we visited on the trip. That's when I came across this article about the linkages of fish populations between the two habitats.

It is well known that subtropical mangrove areas around the globe are habitats for the juvenile stages of many coral reef fishes. The submerged prop-roots are ideal areas for these young fishes as they provide protection and food. Mangroves found adjacent to coral reefs may be important in maintaining the diversity of reef habitats. That is, of course, if these mangroves are actually acting as nurseries for the reefs (rather than ecological sinks) and if maturing fish migrate out to the reefs to live as adults. Much of the past research has focused on the individual habitats themselves and the individual fish life histories. But, as the threat to mangrove habitats has increased over the years much study has been done on this ecosystem as well as looking at the inter-habitat connectivity between mangroves and reefs. However, this connectivity is difficult to observe and long-term studies are very few. This study focuses on mangroves as nurseries for reef fishes in Biscayne National Park in southeastern Florida. The analysis was performed to evaluate the connectivity of these two habitats and to determine if there were contemporaneous fluxes between magroves and reefs for fish replentishment.

Data was collected and analyzed from two independent, fishery-independent fish survey projects which have been going for more than a decade. The mangrove data was collected by conducting visual surveys along transects running parallel to the shoreline. The coral reef data was collected by placing 15 meter circular quadrants and using a stationary visual method. Both projects recorded things such as abundance and size of each observed taxon. A total of 99 mangrove and 365 reef fish species were found with a total of 68 taxa occuring within both habitats. It was determined that 10 target species from 7 families had the potential to exhibit "ontogenetic shifts" (migration) between the two habitats (Haemulon flavolineatum, H. parra, H. sciurus, Lutjanus apodus, L. griseus, Sphyraena barracuda, Abudefduf saxatilis, Gerres cinereus, Lagodon rhomboides,and Scarus guacamaia). Additionally, three habitat strata were defined: mainland (ML), leeward key (LK), and all reef quadrats (RF). Age classes were determined for each target species by using length-frequencies (basically, the size of the fish), and plots of relative abundances made for each age class in each habitat. These age class abundances were then used to calculate mean annual abundances in each of the three strata. Further abundance indicies also allowed for age classes and habitats allowed for species-specific assessments. This study provides evidence of inter-habitat connectivity for 4 out of the 10 target species (Abudefduf saxatilis, Lutjanus apodus, L. griseus, and Sphyraena barracuda). The authors go into a long discussion about the other 6 of 10 species which came out as non-significant in the connectivity analysis, I'll not discuss them here. The results of the study support the hypothesis that mangrove shoreline habitats serve as nurseries for reef fishes. The authors conclude that (1 )there is a spatial segregation of life history stages in a number of reef fishes in this area with juveniles occupying mangroves in the bay and adults on the reef, (2) that mangrove and reef habitats are connected through ontogenetic migrations, (3) that for some species the linkage results in the propagation of year-class strength of bay populations to reef populations, and (4) that this strength is indicative of the nursery role of mangroves and their role in population replentishment.

Read more here:
Jones, David L. (2010) Connectivity through ontogeny: Fish population linkages among mangrove and coral reef habitats. Marine Ecology Progress Series: 401, 245-258.

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Tales from the Road: The Florida Keys

The Florida Keys are located in Monroe County, the southernmost county in Florida and the United States. It is composed of a string of islands connected by U.S. Highway 1 (US1) which ends at mile marker 0 in Key West, 150 miles south of Miami. There are 1700 islands in the Florida Keys and they have been broken up into the Upper, Middle, and Lower Keys. The Upper Keys are defined as Key Largo south to Lower Matecume Key. This area is characterized by tropical hardwood hammock habitat and well developed and protected Atlantic-side reefs. The Middle Keys are from Long Key southwestward to the end of the Seven Mile Bridge. They are characterized by grass beds and hard-bottom communities with a good diversity of fish. The islands are relatively far apart which allows for rapid water flows and big tides resulting in turbid, underdeveloped or absent Atlantic-side coral reefs. The Lower Keys include all of the rest of the islands south and west of the end of the Seven Mile Bridge. They are relatively separate from the other islands but have a good amount of land area and well developed, protected Atlantic-side coral reefs.

Key Largo, the first and largest island in the Florida Keys, is focus of these pictures. Because of its reefs and fish diversity it is a popular spot for snorkelers and sport fishermen. Due to storms to the north and south we had quite a bit of chop, and more than usual turbidity, out on the reef but still managed to see some great stuff. After snorkeling we took a look around the mangroves.

A view from the first bridge driving into the Keys.

The above are some underwater pics from reefs off of John Pennekamp State Park.

Magroves in Key Largo, Florida
The Florida Keys is in (or makes up) Monroe County. Visit their website for great information, news and history:

When it comes to the history of the Florida Keys this is one of the best websites I've found. It has some really great info and some amazing photographs:

Visit NOAA's Florida Keys National Marine Sanctuary website:

If you are looking for some more info but especially if you are looking to visit the Keys then check out this site:
Florida's Department of Enviromnmental Protection has a page on the watershed of this area:

Learn about the history of the Conch Republic:

Frommer's Travel Guide takes you to the Florida Keys:

John Pennekamp State Park has some of the best snorkeling and diving in the Keys:

Turtle Trauma

In keeping with the beach theme from the last post, as loose as it may be, here's an article published in the journal Ecological Applications all about sea turtle nesting.

The loggerhead sea turtle (Caretta caretta) migrates internationally, forages in subtropical and temprate oceans, and comes up onto sandy beaches in order to build nests and lay eggs. The populations of these turtles are have been depleted, especially in the Pacific, and the species has been listed as Endangered on the IUCN Red List and as Threatened on the U.S. Endangered Species Act. Nesting beaches are typically located between 19 and 36 degrees latitude in each hemisphere with large assemblages (up to 80-90% of the world population) in southern Florida and Masirah, Oman. Based on mitochondrial DNA, it is known that the turtles nesting in different geographic regions are genetically distinct from each other. Even looking on a finer scale you can see genetic differences within even a local region; for example, Florida has four distinct subpopulations. Why the divide? Most likely it is due to females returning to their natal beaches to nest and males providing the gene flow between beaches.

When it comes to counting nesting females, the job is relatively easy. After all, a giant turtle pulls herself up the beach, digs a big hole for her eggs, covers the nest, and then pulls herself back to the water. So if you don't see the turtle herself then you will most likely see the marks of her passage in the sand. You can even tell which species has passed just by looking at the tracks. As for clutch (nest) frequency, a female can lay approximately four clutches per season. By using these nests/marks organizations such as the Fish and Wildlife Research Institute of the Florida Fish and Wildlife Conservation Commission (FWC) are able to estimate the populations sizes of loggerheads, green turtles (Chelonia mydas), and leatherbacks (Dermochelys coriacea). Coordinated nest counting programs began in Florida in 1979, and as of 1989 a consortium of conservation groups has established a subset of Florida beaches to survey to take into accound the inherent variablility in nest counting over a broad geographic scale. The FWC leads what is called the Florida Index Nesting Beach Survey program which generates nesting indices. This program is especially useful in resolving spatial and temporal nest counts and generating trend assessments. This particular paper uses these data in this way with loggerhead turtle nesting on Florida beaches, particularly in characterizing a decline in nest counts and assessing the efficacy of recovery efforts.

When talking about nest-count surveys, the paper defines two complementary programs: "Statewide" beaches (n = 190) that aim to be complete in their seasonal and geographic coverage but are not highly consistent, and "Index" beaches (n = 32) that aim to be consistent and have a higher resolution but are not as complete in their coverage. With these data, the researchers conducted a trend analysis on both annual survey-region (SR) nest count totals (n = 18) and annual zone-level (ZL) nest counts (n = 18 x 368 = 6624). For more info on these zones and the stats used then take a look at the paper - there's also a ton of figures.

Whew. Ok, so what did they find? Over an 18 year period, loggerhead nest counts on Index beaches increased and then decreased, with a net decrease; Statewide beaches also showed a declining trend. Lots and lots and lots of stats and models simplified....everything declined and more steeply more recently, although there are some "peaks" and "valleys" going on, possibly due to loggerhead nesting distribution resulting from beach attributes. Locally, declining beach conditions, due in large part to chronic erosion, coastal armoring, artifical lighting, human beach activity, and cold water coastal upwelling are likely causing some of the effects within the spatiotemporal scale. These adverse conditions are probably not influencing the subregional differences in nesting trends as you would see similar effects on other sea turtle species in the same area and you don't (green turtle nesting is actually increasing), although subregionally loggerheads are still declining.

Are you confused yet? The authors conclude that the observed decline in loggerhead nests is best explained by a decline in the number of adult female loggerheads in the population. So why the decline in females? Well, that's a little harder to get at, especially considering that they travel all over the oceans and have a wide array of threats throughout their various life stages. After all, they don't even reach sexual maturation until they are 25-30 years old. Increased moratality at any life stage (hatchling, juvenile, and adult) could affect the overall population and nesting frequency. Let's add another complication: nest temperature determines hatchling sex ratios. It has been observed that female hatchling production on nesting beaches has also declined. These authors postulate that it is due to low incubation temperatures a generation ago that brought about a male-biased primary sex ratio. However, global warming might actually have positive effect in skewing the ratio towards more females.

How do we fix it? More attention from resource managers is one way. Turtles are charismatic megafauna and when people find out that the projected decline for loggerhead nest counts is 80% by 2017 I think they might care. That means that the individual person can do quite a bit too. Contact your local resource managers and state representatives and/or join your local conservation group. Have a voice.

Here's the paper:
Witherington, Blair, et al. (2009) Decreasing annual nest counts in a globally important loggerhead sea turtle population. Ecological Applications: 19(1), 30-54.

Since this is paired with my Ft. Lauderdale visit, I'll give you two great links for turtle nesting in that area:
Greater Ft. Lauderdale's article on Nesting Sea Turtles
Nova Southeastern's page on Broward County's Sea Turtle Conservation

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