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Twine.com - bookmarking and social networking

I'm experimenting with Twine.com, which is a newish bookmarking and social networking site. That is, it's a combination of Del.icio.us (and the like) and (a rather simple) Facebook sort of thing.

The social networking isn't anywhere as nearly comprehensive as Facebook, but it's the same idea. The bookmarking, on the other hand, is as spiffy as Del.icio.us and others of that genre, with extras.

Bookmarks are organizied into groups called "twines", which can be public or private, and typically cover some recognizable topic area, or whatever people want to use them for. Each bookmark can also have a description and any number of tags, specified by the user creating the bookmark. Each bookmark also allows for comments, which anyone may add.

Underlying all this is "semantic web" technology. It's a cool computer-sciencey set of concepts and conventions for organizing heterogeneous collections of data in a way that (supposedly) is easier to search and navigate than the existing anarchy of Web pages, blog posts, etc. But I'm still waiting to see some compelling practical results...

In any case, I've set up some twines that I will use for bookmarking interesting scientific articles I come across. These items tend to be fairly non-technical, intended for an interested but not highly specialized audience, rather than articles from professional, refereed journals.

If you follow any of the links below, you will have to register with Twine, and should then get to see the various bookmark collections. You may choose to "join" any of the twines, which simply means that the system will keep track of the ones you have joined so you can visit them later. There is an option for receiving email notification of additions to individual twines. You can start your own twines too, if you like.

The social networking part is that you can set up a personal profile for youself, with whatever information you are willing to share. You can find out which other users have joined the same twines as you have, and "connect" with them if you have shared interests, as on Facebook or similar systems.

So, this is just an experiment to see if there is interest in something of this sort for groups of bookmarks to possibily interesting articles that deal with many of the topics written about here. If there doesn't seem to be much interest, or if I find it's too time consuming to be worth the effort, I'll stop.

On the other hand, if people give it a try, suggesting bookmarks of their own that are appropriate for one of the following twines, if desired, then maybe the experiment will yield something worthwhile.

You can leave comments to this post if you have questions or suggestions. Alternatively, you can send messages to other users on Twine itself.

Current twines I've started:

Scientific Readings: Neuroscience

Scientific Readings: Medical Biology and Biotechnology

Scientific Readings: Physics

Scientific Readings: Mathematics

Scientific Readings: Astronomy, Astrophysics, Cosmology
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Wordless Wednesday: Happy Thanksgiving

I took these photos at Litszinger Road Ecology Center (an Urban Nature Reserve) spring 2006.

Two Tom Turkeys (males) facing off.



Two Tom Turkeys trying to impress a Hen Turkey (female).
Can you see her? She's much smaller and to the right of the males.
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Broken Urban Landscape

This post is a submission to this week’s Thematic Photographic 25 - Broken. These pictures were taken July 2006 when a tremendous windstorm blew through the Midwest. It was devastating.

Several hundred, perhaps thousands of trees, were felled and split. Most of them were seemingly healthy large trees. But upon closer inspection they all had a hollow saw dust center or deep black strikes in the interior. These are signs of tree sickness and decay. The storm did a perfect job of culling these sickly trees.

































Less common were instances of younger healthier trees being split and taken down. The internal wood was light and healthy and moist.
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Update on my Contest and Media Adventures

Last week was a whirlwind week. Remember? I told you all about it with the post Having my own Adventures! Contests, Media and More.

Here is how the week ended.

1. The Blogging Scholarship Contest by College Scholarships.org - I did not win. But I am still very honored and excited to have made the finalist list. A hearty congratulations goes to the winner of the contest David Mauro (author of Burnt Orange Report); he gave the early favorite Dave Cameron (author of USS Mariner).
I am very satisfied with my showing, 547 votes total. Despite all of the feed reading services I subscribe to I am never certain of my reach. Thank you to everyone who voted, sent emails, solicited supported, and tried to vote but could not. But in a way I feel like I did win. My page gained a lot of exposure from this contest and I hope I have earned some new readers/fans.

2. AAAS Dance Your Ph.D. Contest. I did not win this one either. But, again I got a lot of exposure. Did you see me on ABC News? Seriously, check out the story on ABC News Webcast – Technology and Science. I make a quick cameo appearance. Tee hee hee.
Plus, my Microtus Shuffle Video has over 3000 views in a week. That’s the most popular video I have posted. I should also this and my other urban Science Adventures on ScienceTV. But just learning how to use Vimeo has me swamped.
3. Made new Friends. I made some new online friends.
a. Mario Armstrong. A BIG THANK YOU to him for letting me speak to his radio audience. Last Wednesday (19th) I was on his show - Digital Spin Radio Show on WEAA - 88.9 FM, Baltimore’s NPR and Jazz Radio Station.
b. Lisa of Lisa’s Chaos. I met her and her husband for breakfast this weekend. We discovered we share a love for the outdoors, nature photography, and Cracker Barrel.

Whew! I’m tired and must get back to work.
Thanks for your continued support and visits.
DNLee
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Politics as beauty contest

Perhaps interest in politics has dropped off a lot now that the U. S. elections are over (for this year). But there's still some interesting political science that came up before the big event.

Even though political scientists, year in and year out, are as busy publishing as any other kind, quite a number of research announcements were noted recently outside of traditional professional venues. That has tapered off now, but there were a number of items that seem to call for some comment here. So I'll do some of that despite what is bound to be a declining interest in the subject.

A perennial favorite of election-oriented political research centers around questions of how the appearance of a candidate affects electoral success. That's no different this year. Here's a fairly typical example:

A Pretty Face Can Make A Difference In Whom You Vote For (10/30/08)
According to new Northwestern University research, it is not at all surprising that everyone also is talking about the great looks of vice presidential hopeful Palin.

Whether or not you believe the McCain campaign's $150,000 expenditure for Palin's wardrobe and the much-talked-about salary of her makeup artist are over the top, the decision to play up the looks of the former beauty queen is a winning strategy.

Even in 2008, a perception of competence -- a strong predictor of whether people will vote for political candidates -- is not enough to give women the winning edge in political contests, according to the new Northwestern psychology study.

For both men and women, female political candidates needed to be seen as attractive as well as competent to get their votes. ...

While gender bias related to a female candidate's attractiveness was consistent across both male and female voters, good looks was almost all that mattered in predicting men's votes for female candidates. And, true to prevailing stereotypes, competence was almost all that mattered in predicting men's votes for male candidates.

The idea that good looks positively affects electoral success has been researched many times – as well as being often suspected by a lot of people who aren't professional – in all kinds of elections from student councils on up. I discussed one study on this in a post here almost 2 years ago.

The new research I want to examine here was not entirely, or even primarily, about the importance of attractiveness in winning elections. Instead, experimental participants were first asked to rate candidates independently, based on their photos, on four different attributes: "competence", "dominance", and "approachability", as well as "attractiveness".

The politicians in question were actually candidates in 2006 U. S. Congressional elections. The politicians' photos were then presented in pairs actually competing with each other. Experiment participants were asked to chose which of each pair they would vote for if the office were actually the U. S. presidency.

The resulting data were analyzed in various ways. First, in comparison of participants' voting choice to how they had rated the candidates on each of the four attributes. Second, in comparison of candidates' gender and facial appearance to actual Congressional election outcomes. And third, in comparison between how the candidates won or lost in the simulated presidential election and in the actual Congressional election.

Since I want to focus just on the attractiveness issue, I won't attempt to summarize all the results here. You can find the summary in the research paper itself (citation below). I'll mention only two specific observations: (1) "Female candidates were more likely to win votes if they were more attractive." (2) "Male voters were significantly more likely to vote for candidates that appeared attractive." (I presume these statements represent correlations between opinions of attractiveness and voting behavior of each experimental participant.)

Now, it may be true as the research asserts, that attractiveness matters more for female candidates, while a perceptions of "competence" is relatively more important for male candidates. However, the attractiveness of male candidates (especially in contests exclusively between two males) is a still a net positive.

There's another possibility that should be considered even when voters seem to make their voting choices based on judgment of "competence" of male (or female, for that matter) candidates. Namely, that "attractiveness" (perhaps in a form not consciously associated with the term) might bias this judgment. One has to wonder exactly what visual characteristics might signify "competence" to voters, and whether certain factors – such as a "strong jawbone" (for a male) – don't contribute simultaneously to judgments of both attractiveness and competence.

Humans are fairly sophisticated in making judgments about traits like "competence", since evaluations of other people's character and ability are important in deciding whom to trust. The ability to do this reliably has a lot of evolutionary importance. This doesn't mean people are infallible about such judgments – clearly they aren't. But people probably can do better than chance in making such judgments, at least when not faced with situations where the person being judged is skilled at faking appearances. Perhaps it's more a case of detecting lack of competence, as might be signaled by poorly managed facial expressions (e. g. simply looking perplexed or "stupid").

But judgments about good looks and attractiveness are even more natural. We make them all the time, hardly giving any thought to the matter. Research has shown that people tend to make judgments about facial attractiveness very quickly. (See here.) This suggests people tend to use simple heuristics that may well be hard-wired.

Research apparently shows that even babies prefer to stare at beautiful faces. Note, too, how illustrated children's literature (and now movies) usually portrays virtuous or heroic characters as beautiful or handsome, while evil or villainous characters are ugly, often very ugly, and much to be feared. So there may be an element of social conditioning here, at least for children beyond infancy.

An interesting observation in the report of the research just mentioned, about the quickness of making judgments, is that "It seems that pretty faces 'prime' our minds to make us more likely to associate the pretty face with a positive emotion." ("Priming" is a hot topic in current psychological research.) So, comparatively speaking, a face that isn't "pretty" would be associated with less positive emotions. That alone would be enough to influence voting choices, if "everything else" is assumed to be equal.

There are different possible factors that may enter into such a judgment. So let's consider further what factors and heuristics might be used in judging facial attractiveness. It would be quite interesting to know how the various factors about to be mentioned perhaps have different effects on political choice.

A small number of factors are often suggested. One of the oldest is that the property of "youthfulness" is associated with attractiveness. That makes plenty of evolutionary sense, as fertility, reproductive capacity, and ability to nurture children all decline with age after the beginning of adulthood. It should be noted that youthfulness should be especially salient in the judgment of young people – such as the experimental subjects (college students, average age 19.5) in the research under discussion

A more recent suggestion is that "symmetry" is important, as that would tend to indicate general healthiness. (Recent research here.) That makes sense, too, but does it have any reasonably apparent relevance to voting decisions?

"Symmetry" is probably a looser criterion than in an older and fairly well-known theory of attractiveness, often called simply the "averageness" hypothesis. This holds that average phenotypes in a population are judged more attractive than phenotypes with notably atypical features. An average value on a particular facial metric (such as width of nose or chin) is considered to be what is "normal", yet for most features all to be close to average might be fairly unusual.

So "averageness" is used in a somewhat special sense here – literally, as having size and proportion of most important facial features being close to the overall average. Probably faces that have "averageness" in this sense are fairly rare, which might add to the quality of "attractiveness". So "averageness" as a descriptor of faces is not the same as "common" or "ordinary" or "typical".

Since averages of many faces will wipe out most asymmetry (e. g. some part being off center), an averaged face will be symmetrical. So facial symmetry is a more common characteristic than averageness. A symmetrical face could still have features that are far from average values in size or position.

Since facial symmetry will be more common in a population than faces that have the property of averageness (in the special sense used here), averageness is a more stringent criterion for attractivness. Consequently, a voter who perceives one candidate's face as more attractive than the candidate's opponent is making a more significant discrimination, which could have higher weight in the final choice. Indeed, two candidates might have equally symmetrical faces, or at least faces that are difficult to distinguish in terms of symmetry, yet differ considerably in averageness and hence (perhaps) in attractiveness.

And so, to the extent that people actually judge attractiveness based on averageness rather than symmetry, it will be more likely that judgment affects a voting decision. In other words, we would expect on these general considerations that attractiveness is more likely to affect voting decisions if the criterion is actually "averageness".

There is some amount of research supporting the idea that averageness is the important criterion for attractiveness, such as findings that images created by averaging photographs of many individuals tend to receive higher ratings for attractiveness. So at least for the sake of discussion, let's assume there's some validity to this notion.

Deviations from averageness do not imply deviations from symmetry, so they would not be expected to have the stronger negative implications for overall health and (hence) fertility that asymmetry does, so there would be a smaller indication of "riskiness". It would therefore be harder to understand the evolutionary importance of judging the riskiness of another person based on attractiveness if averageness is the underlying consideration. Is it possible that averageness is important in judging riskiness for other evolutionary reasons – reasons that apply to evaluating others in more general contexts than the context of mate selection?

Yes, I think so. As I wrote in my previous post, "people who are considered attractive within a population are those who are most 'typical' or 'average'. Or inversely, least atypical, least different from the largest number of people in the population. People who are considered less attractive have facial features that vary a lot from the norm, such as lips that are too thin or too thick (compared to the average), eyes too far apart or too close together, eyebrows that are too sparse or too bushy."

The evolutionary rationale at work here is that people who appear too "different" from the norm are more likely to belong to a different, more genetically distant tribe. Such people are probably less likely to deserve trust, and might even be "dangerous".

I think this matter of perceived trustworthiness vs. potential "danger" in the eyes of voters could be rather important, especially if it is unconsciously inferred from perceptions of a candidate's attractiveness. I've written more on that here, not too long ago, so I won't repeat it now.

More generally, I see conscious and unconscious issues of fear and perceived danger as especially important factors in a voter's attitudes towards, and relationship with, government. This is because, as a matter of both philosophy and sociology, one of the primary reasons for the existence of governments is to "protect" citizens from a variety of potential evils, whether they be dishonest businesspeople, common criminals, foreign and domestic terrorists, or whatever. I've written a lot more about that here.

The question, then, is whether the research now under discussion supports the idea of a connection between fear and voting behavior, or is even relevant to it. To be honest, the relevance is somewhat tentative, since it relies on the idea that there is a negative correlation between the attractiveness of a political candidate and whether a voter feels fear associated with the candidate at some level. It would be very interesting to see more research that addresses this issue more directly.

Regarding the present research itself, I have a few reservations as well. For example, the experimental participants were university students of average age 19.5 years. Quite possibly many of the participants had never even voted in a governmental election, and they certainly did not have a few decades of adult experience – with politicians, elections, and actual government performance – that could shape and inform their voting decisions. It's not surprising that individuals with little adult experience would base decisions on appearance factors.

Aside from that, there's also the question of whether the socioeconomic demographics of university students would skew the results from what would be found in the electorate as a whole. And then there's the whole other issue of possibly relevant cultural differences between the U. S. and other democratic countries.

So there's reason to suspect that typical, experienced voters, even in the U. S., might produce rather different results in a similar sort of experiment.

Here's the research paper, with some of the abstract:

The Political Gender Gap: Gender Bias in Facial Inferences that Predict Voting Behavior
Contrary to the notion that people use deliberate, rational strategies when deciding whom to vote for in major political elections, research indicates that people use shallow decision heuristics, such as impressions of competence solely from a candidate's facial appearance, when deciding whom to vote for. Because gender has previously been shown to affect a number of inferences made from the face, here we investigated the hypothesis that gender of both voter and candidate affects the kinds of facial impressions that predict voting behavior.




ResearchBlogging.org
Joan Y. Chiao, Nicholas E. Bowman, Harleen Gill (2008). The Political Gender Gap: Gender Bias in Facial Inferences that Predict Voting Behavior PLoS ONE, 3 (10) DOI: 10.1371/journal.pone.0003666


Update on 11/24/08: I have extensively reworked the discussion about "attractiveness" and its relationship to "symmetry" and "averageness". One would like to see more experimental evidence to sort out these factors in general and specifically as to how they affect voting choice.

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Increasing Diversity in the Sciences

“The very large racial Ph.D. gap in the natural sciences is striking when we examine black Ph.D. awards in specific disciplines.” * I am all-too-familiar with this fact. I am the only African-American Ph.D. student in my academic department. That will make me the second African-American to earn a doctorate in Biology from my institution. People spout off statistics all of the time, in fact I heard that on average there are only 10 Black Ph.D.s in Biology a year. That seems low, but the fact is Blacks who obtain doctorate degrees in Science, Technology, Engineering, and Mathematics (STEM) is often a single digit percentage point.
* Quote from the article Doctoral Degree Awards to African Americans Reach Another All-Time High in Journal of Blacks in Higher Education.

Faced with these numbers I am relieved to discover programs that aim to attract and retain more Black students to study math and science. I recently learned about the Benjamin Banneker Institute for Science and Technology. The Institution spearheads a variety of programs with one goal in mind: increase the participation of young people in science and technology. One of their programs is the Decade of Blacks in Science 2007-2017.

(From the website)
The Decade of Blacks in Science is a campaign to mobilize, co-ordinate and coalesce the human and material resources needed to solve the problem of the low level of participation by African Americans in STEM fields.

However, this lack of representation isn’t just a concern of Black Academics. It is on the agenda of the entire scientific community. Universities and Professional Science Organizations alike have committees that are devoted to this very topic – increasing diversity – in the classroom, the laboratory, and the professoriate.

But it all starts with one question. What is going on with the pipeline?
How can we encourage students to major in science in college? How can we encourage them to go to graduate school? Where can we find qualified students to recruit into Ph.D. programs?

First, students of color, and of particular interest to me, Black students need to accept the idea that science is a viable, realistic, and pursuable career and line of study. More and more we realize we need to reach students at younger ages. High school may be too late to cultivate an interest in science – at least it seems so. Second, recruitment strategies may need change. Most doctorate degrees in STEM are obtained at majority institutions, however historically Black institutions produce more students with bachelor degrees who go on to complete Ph.D.s.** HBCUs are essentially preparatory programs for future Black Scientists and Engineers.
** From the article Who Produces Black PhDs? In Inside Higher Ed

I plan to spend some time discussing pipeline and retention of students of color in the sciences at the ScienceOnline09 Conference this January during the Race in science – online and offline Workshop. In the meantime, I encourage you to share with me your thoughts and proposed solutions to this diversity issue.




Article originally posted at YBPGuide.com
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Dr. Neil deGrasse Tyson Visits St. Louis


I was reading a local weekly paper – The St. Louis American – and there on the front page was *drum rolls* Dr. Neil deGrasse Tyson! He was in St. Louis last week to talk with students from the St. Louis Science Center "YES” (Youth Exploring Science) Program. It is a great outreach program that works with local teens and gives them hands on learning and career opportunities in science.

* long pause and confusing frown on face*

Dr. Neil deGrasse Tyson was in St. Louis and nobody told me? The awesome and grand NdGT was in my town and it was not heralded from every trumpet and posted on the news and internet. Wha..What?!!

If you’re like the average person you’re probably thinking - Who? But if you’re one of those nerd-groupies (like me) you’re already jumping in the air with fists and voices raised in outrage.
You see, Dr. Tyson is the MAN. He is an astrophysicist and director of the American Museum of Natural History's Hayden Planetarium. You may recognize his voice as the NOVA's "Origins" miniseries. He is a big deal. Moreover he is perhaps the most recognizable and popular Black Scientist of modern times. And as an aspiring Black Scientist and Educator, he is my role model for Science Outreach. I am still miffed; but be sure to read the article about Dr. Neil deGrasse Tyson’s visit to St. Louis.

Also check out his official webpage and listen to his podcasts, including "Communicating Science to the Public" Point of Inquiry Podcast - November 16, 2007.

Cheers
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Wordless Wednesdays: Leaf Litter


Various Maples Leaf Litter










Ash Leaf Litter









Sycamore Leaf Litter









Pine Needles
all pictures taken in St. Louis, MO-Benton Park, Tower Grove Park.
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Having my own Adventures! Contests, Media and More

This has been an exciting time! Very exciting. I have several updates.

1. My ranking in the Nature Blog Network has peaked. I'm in the top 100, my best ranking so far - #87 out of 500+ Fabulous nature blogs. Thanks for visiting and leaving comments.

2. Wordless Wednesday seems to be my most successful series of posts. I;ll continue to share my photographs of nature and environmental science.

3. My Urban Wildlife Watch Watch Series has more entries. The one about Osage Orange Trees has been very popular, but the one about Winged Ants is still one of my most popular posts ever. I plan to do more of these and submit them to carnivals. I've previously submitted two posts to Oekologie Carnival this summer and I keep thinking about submitting something to the Carnival of the Green. Recently, I submitted something to the Festival of the Trees, oh and I'll be posting more about trees for the weeks to come. I haven't become a botanist or arborist, but trees are always there. I can always catch a great photo shot of a tree. Besides, trees are so dynamic, and now with many turning and losing leaves for autumn it's like a whole new thing to photograph and share.

4. The Blogging Scholarship Competition is heating up, but I'm still way behind. You can still help me. Email everyone about the competition and ask them to vote for me - Danielle Lee. Cross-post are very nice. Shouts to all of the support and cross-posts.
The Oyster's Garter
Women in Science
Black Web 2.0
Young Black Professional Guide (I wrote this one, just to be transparent)

I've also been invited to talk about the Blogging Scholarship and some of my other bogging ativities on Mario Armstrong's Digital Spin Radio Show on WEAA - 88.9 FM, Baltimore’s NPR and Jazz Radio Station. You can listen live on the internet Wednesday, November 19th, 7p-8p Eastern Standard Time. So please tune in...and vote!


5. My other Blogging Activities...
a. Co-moderating a workshop at the 3rd Annual ScienceOnline Conference, January 16-18, in Research Triangle, NC. I was also mentioned on AAAS Science Careers Blog. I'll be co-moderating the session on Race and Science: Online and Offline with Samia Ansari. Even if you can't attend the conference you can still participate in the discussion. Visit the Conference Program and wiki and share your concerns about diversity in the sciences and proposals to increase participation. These topics will be discussed and vetted at the conference and a final report will be posted online.

b. I submitted a video of a dance interpretation of my dissertation to the AAAS 2009 Dance Your Ph.D. Contest. I'm the first video on the official contest page, how crazy, but 1st place is attending the AAAS meeting in Chicago, guest of honor, 2 nights hotel accomodation, and seeing my dance performed by professional dancers. Aaah when arts and sciences come together. Results will be announced this Thursday (same day the Blogging Scholarship ends) Two questions: 1) can I list this video as a peer-reviewed publication on my CV? it is, kinda; and 2) can I just show this video for my public oral dissertation defense? I doubt anyone would fall asleep during this presentation.

Enjoy,
DNLee - Taking Science Outreach Waaay Out There.

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Dopamine and obesity

Dopamine is a neurotransmitter that's well-known for its involvement in several notable medical and behavioral problems, such as Parkinson's disease and drug addiction. But it is connected with many other issues of medical and psychological importance.

Perhaps the main reason that dopamine is so interesting is that it plays a big role in the brain's pleasure and reward systems. And therefore it is inevitably involved in reward-motivated behaviors of all kinds, from gambling, investing, substance abuse, and sex, to – eating. After all, isn't a high percentage of behavior motivated by rewards? There are other motivations for particular behaviors – fear and physiological needs, for example – but reward covers an awful lot of it.

Consequently, problems in the reward system can lead to excesses in some behaviors (e. g., gambling, eating), and perhaps also deficiencies in other behaviors (e. g. loss of interest in normal pleasures, as might accompany depression).

And because of the importance of dopamine in the reward system, problems with dopamine signaling can lead to problems in the reward system, with predictable consequences.

In the research we're going to look at, dopamine signaling is impaired in the presence of a particular allele associated with the D2 receptor for dopamine (known as DRD2). The conclusion is reached via the observation of decreased activity, as mesured by fMRI, in a brain region called the dorsal striatum. It is known that the variant allele causes a lower density of D2 receptors in this region.

The bottom line of the research is that individuals with this variant allele tend to have impaired ability to enjoy rewards from foods that most people like, such as chocolate. As a result, such individuals are disposed to consume more food in order to achieve an acceptable level of satiation of reward.

It might be thought, instead, that since the desirable foods produce less reward in individuals with the variant allele, they might consume less, due to reduced interest. However, that's not how the reward system seems to work. It seems to require achievement of a certain signal level in order to reach satiation and thus decrease the motivated behavior.

This is similar to the way signaling works with another hormone connected with eating, namely leptin. Normally, leptin levels rise when food is consumed. There are receptors for leptin in the ventromedial nucleus of the hypothalamus, a region that is responsible for appetite. There leptin inhibits the activity of neurons that contain neuropeptide Y (NPY).

A connection has been found between obesity and insensitivity to leptin, much as diabetes results from decreased sensitivity to the hormone insulin. Preseumably, individuals with reduced sensitivity to leptin don't know when to stop eating. Much the same state of affairs seems to exist in individuals with the allele (which is a DNA restriction enzyme called TaqIA) that affects DRD2 receptor density in the dorsal striatum.

Obesity, Abnormal 'Reward Circuitry' In Brain Linked: Gene Tied To Dopamine Signaling Also Implicated In Overeating (10/16/08)
Using brain imaging and chocolate milkshakes, scientists have found that women with weakened "reward circuitry" in their brains are at increased risk of weight gain over time and potential obesity. The risk increases even more for women who also have a gene associated with compromised dopamine signaling in the brain.

The results, drawn from two studies using functional magnetic resonance imaging (fMRI) at the University of Oregon's Lewis Center for Neuroimaging, appear in the Oct. 17 issue of the journal Science. The first-of-its-kind approach unveiled blunted activation in the brain's dorsal stratium when subjects were given milkshakes, which may reflect less-than-normal dopamine output.


Here's the research paper, with abstract:

Relation Between Obesity and Blunted Striatal Response to Food Is Moderated by TaqIA A1 Allele
The dorsal striatum plays a role in consummatory food reward, and striatal dopamine receptors are reduced in obese individuals, relative to lean individuals, which suggests that the striatum and dopaminergic signaling in the striatum may contribute to the development of obesity. Thus, we tested whether striatal activation in response to food intake is related to current and future increases in body mass and whether these relations are moderated by the presence of the A1 allele of the TaqIA restriction fragment length polymorphism, which is associated with dopamine D2 receptor (DRD2) gene binding in the striatum and compromised striatal dopamine signaling. Cross-sectional and prospective data from two functional magnetic resonance imaging studies support these hypotheses, which implies that individuals may overeat to compensate for a hypofunctioning dorsal striatum, particularly those with genetic polymorphisms thought to attenuate dopamine signaling in this region.

The idea that problems with dopamine signaling might be related to overeating and obesity isn't new. The following research announced in July involved rats rather than humans and considered other dopamine insufficiency mechanisms, but the basic conclusions are the same:

Obesity Predisposition Traced To The Brain's Reward System (7/29/08)
The tendency toward obesity is directly related to the brain system that is involved in food reward and addictive behaviors, according to a new study. Researchers at Tufts University School of Medicine (TUSM) and colleagues have demonstrated a link between a predisposition to obesity and defective dopamine signaling in the mesolimbic system in rats.

The mesolimbic system is a system of neurons in the brain that secretes dopamine, a neurotransmitter or chemical messenger, which mediates emotion and pleasure. The release of the neurotransmitter dopamine in the mesolimbic system is traditionally associated with euphoria and considered to be the major neurochemical signature of drug addiction. ...

Pothos says, "These findings have important implications in our understanding of the obesity epidemic. The notion that decreased dopamine signaling leads to increased feeding is compatible with the finding from human studies that obese individuals have reduced central dopamine receptors." He speculates that an attenuated dopamine signal may interfere with satiation, leading to overeating.

Paper abstract:

Evidence for defective mesolimbic dopamine exocytosis in obesity-prone rats
In electrophysiology studies, electrically evoked dopamine release in slice preparations was significantly attenuated in OP [obesity-prone] rats, not only in the nucleus accumbens but also in additional terminal sites of dopamine neurons such as the accumbens shell, dorsal striatum, and medial prefrontal cortex, suggesting that there may be a widespread dysfunction in mechanisms regulating dopamine release in this obesity model. Moreover, dopamine impairment in OP rats was apparent at birth and associated with changes in expression of several factors regulating dopamine synthesis and release: vesicular monoamine transporter-2, tyrosine hydroxylase, dopamine transporter, and dopamine receptor-2 short-form. Taken together, these results suggest that an attenuated central dopamine system would reduce the hedonic response associated with feeding and induce compensatory hyperphagia, leading to obesity.


News reports of the human dopamine results:




ResearchBlogging.org
E. Stice, S. Spoor, C. Bohon, D. M. Small (2008). Relation Between Obesity and Blunted Striatal Response to Food Is Moderated by TaqIA A1 Allele Science, 322 (5900), 449-452 DOI: 10.1126/science.1161550


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Fellowships to Study Urban Ecology

Urban Ecology is a very new discipline within the fields of ecology and environmental sciences; and it means slightly different things to different people. Very broadly it is the study of plant and animal interactions with in an urban or human-built environment. But it also includes the study of how humans affect the natural landscape, how plants and animals survive human encroachment, and how we (humans) can create an urban world that is balanced and respects nature.

If you are college student (or know one) who is interested in Urban Ecology then you (or he/she) should seriously consider attending Arizona State University in Tempe and apply for a National Science Foundation Integrative Graduate Education and Research Training (IGERT) Fellowship.


The main objective of the Integrative Graduate Education and Research Training (IGERT) in Urban Ecology is to educate a new kind of life, earth, or social scientist who is broader, more flexible, more collaborative, and more adept at linking science and social issues.

Arizona State University's IGERT in Urban Ecology will be accepting applications for Fellowships and Associateships for students who can begin their studies fall 2009. The Fellowship applications are for 2 years and one summer of support for approved summer activities (Fall 2009/ Spring 2010, Summer 2010, and Fall 2010/ Spring 2011). Applicants may apply for one additional summer (2009) of support before they being their first academic year as an Urban IGERT fellow. This is the perfect amount of time to obtain a Master’s degree.

To be considered for this support, include in your Fellow application form a brief plan including who the supervisor will be. Recipients must be at ASU during the summer 2009 or working closely with an Urban IGERT faculty person. Visit the department website, School of Sustainability, the Nation’s first School of Sustainability to learn more about the faculty.

Deadline: Application review process begins February 1, 2009.

Residual questions regarding ASU's IGERT program should be directed to:
Gail Ryser, Program Coordinator IGERT in Urban Ecology
Global Institute of Sustainability
Arizona State University
Box 875402 Tempe AZ 85287-5402
P 480.965.6073 F 480.965.8087
website
http://sustainability.asu.edu/igert/
e-mail IGERT.Ecology@asu.edu

Good luck!

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Non-coding RNA and gene expression

Human DNA consists of about 3.4 billion base pairs. A portion of that is actually genes that code for proteins required by human cells – roughly 20,500 genes. (See here.)

However, it's been recognized for a long time that only about 1.5% of human DNA (in terms of base pairs) actually codes for proteins. Little is known about the purpose (if any) of the remaining 98.5%, even though, by some estimates, 80% of human DNA is transcribed into RNA at some time.

This remainder is often called "junk DNA". But it's also known that a lot of it can't really be "junk", and must serve some useful purpose, because the sequences of large portions of it are highly conserved in evolution, being found almost unchanged in the genomes of human ancestors going back hundreds of millions of years.

Some of the 98.5% really does seem to be without useful function, consisting of stuff like transposons, which are DNA sequences that seem to be copied repeatedly and randomly into various parts of the genome (over evolutionary time spans)

The function of other portions of that 98.5% includes such things as introns found within genes, gene regulatory sequences, and "RNA genes" that code for various kinds of RNA that doesn't wind up being translated into proteins.

Such non-coding RNA can be further classified into things like ribosomal RNA, microRNA, small interfering RNA, and "long non-coding RNA".

This last, known as "long ncRNA" for short, is especially intriguing, because some studies have shown that there may be roughly four times as much of it (in base units) as there is of messenger RNA that is ultimately translated into proteins.

Even though a lot of these long ncRNAs are routinely found floating around inside cells, we're still in the dark about what, if anything, they actually do. But some recent research has revealed a little more about some long ncRNAs:

Early-stage Gene Transcription Creates Access To DNA (10/6/08)
Previously thought to be inert carriers of the genetic instructions from DNA, so-called non-coding RNAs turn out to reveal a novel mechanism for creating access to DNA required by transcriptional activation proteins for successful gene expression, according to Boston College Biology Professor Charles Hoffman, a co-author of the study with researchers from two Japanese universities. ...

Hoffman and his colleagues examined how the yeast cell senses its cellular environment and makes decisions about whether or not to express a gene, in this case fbp1, which encodes an enzyme. What they found was a preliminary transcription phase with a flurry of switches flicked "on" and then "off" as seen by the synthesis of non-coding RNA before the final "on" switch is tripped.

The non-coding RNAs initiate over one thousand base pairs of nucleotides along the DNA away from the known start site for this gene. The group discovered that the process of transcribing non-coding RNAs is required for the eventual production of the protein-encoding RNA. The transient synthesis of these non-coding RNAs serves to unfurl the tightly wound DNA, essentially loosening the structure to allow for gene expression. [Emphasis added.]

And here's the research article, with some of the abstract, providing a somewhat more precise description of what's going on:

Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs
Here we show that RNA polymerase II (RNAPII) transcription of ncRNAs is required for chromatin remodelling at the fission yeast Schizosaccharomyces pombe fbp1+ locus during transcriptional activation. The chromatin at fbp1+ is progressively converted to an open configuration, as several species of ncRNAs are transcribed through fbp1+. This is coupled with the translocation of RNAPII through the region upstream of the eventual fbp1+ transcriptional start site. Insertion of a transcription terminator into this upstream region abolishes both the cascade of transcription of ncRNAs and the progressive chromatin alteration. Our results demonstrate that transcription through the promoter region is required to make DNA sequences accessible to transcriptional activators and to RNAPII.

To expand on that just a bit, recall that chromatin is the form in which DNA is actually stored for safe keeping. It consists of the double-stranded DNA molecules wrapped around many protein complexes called nucleosomes. Before any stretch of DNA can actually be transcribed into messenger RNA, the DNA has to be unwound from the nucleosomes. The present research has determined that some long ncRNA takes part in this unwinding process.

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No more business as usual

A million thanks to SusanG at Daily Kos for mentioning this:

Obama's Victory: A Consumer-Citizen Revolt
As recently as this summer, while the economy unraveled (BusinessWeek, 7/14/08), I made two trips to Silicon Valley in the hopes of finding leaders who grasped the crisis—and the opportunity—inherent in the destruction of trust. I listened to Facebook executives but found them obsessed with how to monetize the site with advertising. Their users were not individuals, but "eyeballs." I asked Google (GOOG) CEO Eric Schmidt how he would develop and sustain the trust of his users. His response was to cite the provision of two classes of stock intended to insulate top management from investor pressures. I gave a talk on the crisis of trust. The response from self-described Internet court jester Esther Dyson was typical of what I had been hearing: "Personally, I'm not that concerned if people don't trust large institutions."

A few weeks later economic panic gripped the stock market. I flipped on ABC's Sunday morning news show with George Stephanopoulos only to hear economist Larry Summers explaining that the surprising depth of the economic meltdown was due to the loss of trust in institutions. What he didn't say was that this loss of trust is a vast sea whose level has been rising for decades. The subprime debacle and the ensuing credit freeze simply marked the moment when the sea wall was finally breached. ...

So can we invent a business model in which advocacy, support, authenticity, trust, relationship, and profit are linked? Can I write that sentence without invoking fear, disbelief, cynicism, or peals of laughter? The ugly practices that killed trust seem intractable to most people, whether they are the ones trapped inside the money machine or on the receiving end of its operations. But after this election, the answer to these questions has irreversibly changed. The answer today would have to be not only "yes we can" but also "yes we must."

No, this is not about "science" per se, unless one considers the philosophical side of economics (rather than the quantitative side) to be a science. Rather, it is the simple observation that anyone reading the daily news with an open mind can understand: Basing a modern large-scale economy primarily on the evolutionarily ancient motivation of greed and personal self-interest is not working out very well...
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Power of Plants Contest for K-12 Students in Missouri and Illinois


The Missouri Botanical Garden is sponsoring a contest that helps students learn about the awesome power of plants and gives them a chance to win $1,000!

How can you participate?
The Missouri Botanical Garden would like students to learn more about plants! Some plants are just AMAZING —they grow in special ways, can survive in harsh climates, or provide humans with things that we use everyday. So, here’s the challenge:

Choose a plant that does great things for people and tell its story!
Create something to tell the world about your plant and send it to the Missouri Botanical Garden. You must include factual information about your plant’s super powers. Winners will be displayed at the Garden and on our website.

How does the contest work?
Participants can enter as an individual and/or part of a group. Entries will be divided into elementary, middle, and high school age groups. There will be a first, second, and third place winner, as well as Honorable Mentions for each of the three age groups in the individual and group categories. All participants must complete the Entry Form.

It's easy. 5 hours of class or after-school time can easily result in a big payoff.
1 hour: Brainstorm about all of the important things we get from plants
1 hour: Pick a plant and research its special characteristics in the library or on-line
1 hour: Draft a way to tell the world about why the plant is powerful
+
2 hours: Create a final project and submit for the contest by January 31st
=
5 hours: Learn about the power of plants in a fun and creative way!

You must create a unique and creative presentation like this image below. It tells us everything we need to know about the plant and how it helps us and it is creative and colorful. And I'm quite partial to pink to green...I think this image is both beautiful and aspiring.
Deadline submission is January 31 and is open only to Missouri and Illinois students (sorry, but it's still a great project idea...I say do it anyway and present in your school fair or for a school project or extra credit).

Get the full details about the project, objectives, submission guidelines, and deadlines here.

Please let me know if you decide to do this project. I would like to know how it goes. Plus, I am willing to offer any help and advice possible. Remember this website is a resource. Don't hesitate to use it.

Have fun with it!

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Deer found on Urban University's Campus

Photo credit – Washington University Students
Check out the Washington University Student Paper Story which includes more great shots of the deer on campus taken by students.

Earlier this week this yearling deer had been observed on campus - eating grass and just hanging around Washington University campus. The college is an urban campus in the heart of St. Louis, Missouri. It had been gently lead away from campus on Monday, but was back Tuesday morning. Since it wasn’t causing any trouble the grounds keepers let it be. It was an exciting day on campus but everyone pretty much admired the deer from a distance and did not startle it, which was the right thing to do.

When you encounter wildlife you may tempted to do one things.
A) Get excited and want to touch it, feed it, or help it – anything to get closer to it.
B) Get scared and want to shoo it away, throw something at or run – anything to get some distance from it.

I was that kid who did A, oh heck let me stop kidding, I’m that adult who wants to do A, that’s why I became a biologist. But the truth is both A and B are inappropriate.

Handling wild animals is risky and as a professional I have been trained to handle animals and more importantly, I assume the risk of handling an animal. That risk includes being injured. So I must insist you don’t do A, no matter how tempting….and I do understand how tempting it is. B is also wrong, too. Why? Startling can cause panic – in you and animal and panic results in unpredictable movements and actions. Panic leads to injury and we do not want that. If you remain calm, then very likely so will the animal. Remember, safety first, yours and the animals.


However, I’m convinced deer are very smart animals who can tell time. This time of year, autumn, is hunting season. I bet this guy was scouting out some ‘safe’ place to hang out for the season. And what’s safer than a college campus with students and faculty who are tolerant of cute woodland creatures? Almost nothing else. But seriously, this guy braved a few obstacles to get to the heart of campus. More than likely his primary home range is Forest Park which is across the street from the University. He had to cross a very busy five-lane street, so he is a lucky fellow. And I need to say this, I say he out of habit. I am not sure if the yearling is a male or female, but typically female young stay close to their mothers and males go off on their own.


Check out the news reel - Deer Turns Heads On Wash U Campus from KTVI - myFOXstl.com.
Now, this was an Urban Science Adventure!
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Wordless Wednesdays: Scenes of Autumn

I'm participating in the Thematic Photographic 23 - Autumn. Written Inc. asked for something more than pictures of leaves, but lately that’s all I’ve been snapping.

Autumn scenes in St. Louis - various trees - Sycamores, Crab Apples, Oaks and some unknown species.






































Scenes of Autumn in Tennesse - Cumberland Plateau, from Cookeville to Knoxville - various trees - Crap Apple, Gingko


























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I love Fall. Can’t you tell.

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