Yearly Archives: 2007

New and Exciting on PLoS ONE

There are 21 new papers on PLoS ONE published this week. Here are some titles that got my personal attention:
Climate Change, Genetics or Human Choice: Why Were the Shells of Mankind’s Earliest Ornament Larger in the Pleistocene Than in the Holocene? by Peter R. Teske, Isabelle Papadopoulos, Christopher D. McQuaid, Brent K. Newman and Nigel P. Barker:

The southern African tick shell, Nassarius kraussianus, is the earliest ornament known to be used by humans, dating back ~75,000 years. This study investigates why beads made from these shells in more recent times are smaller. It is likely due to increased temperatures produced by climate change at the beginning of the present interglacial period, making N. kraussianus fossil shells a possible biomonitor of climatic conditions.

Cortical Modulations Increase in Early Sessions with Brain-Machine Interface by Miriam Zacksenhouse, Mikhail A. Lebedev, Jose M. Carmena, Joseph E. O’Doherty, Craig Henriquez and Miguel A.L. Nicolelis:

Brain-machine interfaces (BMIs) use the activity of cortical motor neurons to control external actuators, such as robot limbs. This study investigates the effects of the BMI itself on neuronal activity. Monkeys showed characteristic changes when they first starting training on BMIs that decreased as they gained experience, alluding to the formation of an internal model of the external actuator.

Do You See What I Mean? Corticospinal Excitability During Observation of Culture-Specific Gestures by Istvan Molnar-Szakacs, Allan D. Wu, Francisco J. Robles and Marco Iacoboni:

People all over the world use their hands to communicate expressively. Autonomous gestures, also known as emblems, are highly social in nature, and convey conventionalized meaning without accompanying speech. To study the neural bases of cross-cultural social communication, we used single pulse transcranial magnetic stimulation (TMS) to measure corticospinal excitability (CSE) during observation of culture-specific emblems. Foreign Nicaraguan and familiar American emblems as well as meaningless control gestures were performed by both a Euro-American and a Nicaraguan actor. Euro-American participants demonstrated higher CSE during observation of the American compared to the Nicaraguan actor. This motor resonance phenomenon may reflect ethnic and cultural ingroup familiarity effects. However, participants also demonstrated a nearly significant (p = 0.053) actor by emblem interaction whereby both Nicaraguan and American emblems performed by the American actor elicited similar CSE, whereas Nicaraguan emblems performed by the Nicaraguan actor yielded higher CSE than American emblems. The latter result cannot be interpreted simply as an effect of ethnic ingroup familiarity. Thus, a likely explanation of these findings is that motor resonance is modulated by interacting biological and cultural factors.

The Population Dynamical Implications of Male-Biased Parasitism in Different Mating Systems:

Although there is growing evidence that males tend to suffer higher levels of parasitism than females, the implications of this for the population dynamics of the host population are not yet understood. Here we build on an established ‘two-sex’ model and investigate how increased susceptibility to infection in males affects the dynamics, under different mating systems. We investigate the effect of pathogenic disease at different case mortalities, under both monogamous and polygynous mating systems. If the case mortality is low, then male-biased parasitism appears similar to unbiased parasitism in terms of its effect on the population dynamics. At higher case mortalities, we identified significant differences between male-biased and unbiased parasitism. A host population may therefore be differentially affected by male-biased and unbiased parasitism. The dynamical outcome is likely to depend on a complex interaction between the host’s mating system and demography, and the parasite virulence.

‘Sexual’ Population Structure and Genetics of the Malaria Agent P. falciparum:

The population genetics and structure of P. falciparum determine the rate at which malaria evolves in response to interventions such as drugs and vaccines. This has been the source of considerable recent controversy, but here we demonstrate the organism to be essentially sexual, in an area of moderately high transmission in the Lower Shire Valley, Malawi. Seven thousand mosquitoes were collected and dissected, and genetic data were obtained on 190 oocysts from 56 infected midguts. The oocysts were genotyped at three microsatellite loci and the MSP1 locus. Selfing rate was estimated as 50% and there was significant genotypic linkage disequilibrium (LD) in the pooled oocysts. A more appropriate analysis searching for genotypic LD in outcrossed oocysts and/or haplotypic LD in the selfed oocysts found no evidence for LD, indicating that the population was effectively sexual. Inbreeding estimates at MSP1 were higher than at the microsatellites, possibly indicative of immune action against MSP1, but the effect was confounded by the probable presence of null mutations. Mating appeared to occur at random in mosquitoes and evidence regarding whether malaria clones in the same host were related (presumably through simultaneous inoculation in the same mosquito bite) was ambiguous. This is the most detailed genetic analysis yet of P. falciparum sexual stages, and shows P. falciparum to be a sexual organism whose genomes are in linkage equilibrium, which acts to slow the emergence of drug resistance and vaccine insensitivity, extending the likely useful therapeutic lifespan of drugs and vaccines.

Today’s carnivals

Tangled Bank #84 is up on Voltage Gate.
The Ever-Present Past: Your Nearest Site – a one-time local-archaeology carnival (still accepting entries for a couple of more days) is up on Aardvarchaeology.
The Carnival Of Education #128 is up on The Education Wonks.
Carnival of the Liberals #43 is up on Stump Lane.

Online Science Discussion

Curtis, one of the founders of JeffsBench wrote a very interesting article comparing JeffsBench to PLoS ONE in their roles in fostering online scientific discussions. Register, look around and comment….

Blogathon

Well, I have the reputation about blogging around the clock, but every year more and more bloggers take that idea literally and they do it for one day for good cause, as a part of Blogathon.
Bill explains:

The mechanics are simple: bloggers sign up to blog for their chosen charity, and sponsors pledge either a lump sum or an amount per hour blogged. The goal is to blog for 24 hours straight, with one post every 30 minutes.

Over the past few years, more and more bloggers have been signing up and raising substantial amounts of money for good causes. Sign up here, then blog all day on the 28th of July and make a difference.

More science of Harry Potter

I can’t stay away (a charming spell?) from the series that Anne-Marie is churning out at a supernatural rate (what kind of magic?). Here are the latest three installments, totally enchanting:
Conservation Biology
The Botany of Wands
Kin selection

Welcome a new SciBling

Go say Hello to the Angry Toxicologist

Clock Tutorial #11: Phase-Shifting Effects Of Light

Clock Tutorial #11: Phase-Shifting Effects Of LightThe third post in the series on entrainment, first written on April 10, 2005, starts slowly to get into the meat of things…As always, clicking on the spider-clock icon will take you to the site of the original post.

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ClockQuotes

I have lived, tomorrow, I shall sleep in glory.
– Georges Jacques Danton (1759-94)

Nursing PLoS

Kim of Emergiblog explains nicely why you should support Open Access publishing:
The Public Library of Science:

You are writing a paper. You need to do some research, so you google your topic.
Ah ha! There it is! The perfect article for your paper. The abstract is right in front of you, but you must go to the actual journal for the full text.
Hmmm…you can access the full text of the article, but you must pay to do it! Anywhere from nine dollars to almost thirty dollars for twenty-four hour access.
“No way”, you say! “I have access to my university’s online library, I’ll just go there and look it up for free!”
Except the journal isn’t in the online database or it has to physically come from another library, and you happen to live two thousand miles away from your “campus”.
Reluctantly, you pay for access to the article. Or not….

An interesting case of plagiarism

The Purloined Bibliography:

My training in medieval history had acquainted me with the practice of identifying dependencies among manuscripts by tracing the repetition of errors. By analogy, I thought, if there were additional idiosyncratic errors on my Web site that also appeared in the book, each instance would be a discrete piece of evidence showing that the volume had lifted material from my work.
I found myself in the unusual position of hoping that I had made more mistakes. Could I find more evidence than just two bizarrely placed asterisks?

Congratulations to Rob!

My SciBling Rob Knop is leaving the academic circus for a cool job: designing Universes or some such astronomical stuff on Second Life. Just as he is about to leave his University, though, he got a nice parting gift from the academic world for his work on the expansion of the Universe – the Gruber Prize in Cosmology. Please go and say Hello and Congratulations to Rob!
Related:
Farewell and Hail
Science blogger (and soon to be former academic) shares Gruber Prize.
Is getting tenure Mission Impossible?
Kudos for Rob
I have shilled

Phylogeny vs. Aerodynamics in birds

A very interesting new paper was published today in PLoS Biology:
Flight Speeds among Bird Species: Allometric and Phylogenetic Effects by Thomas Alerstam, Mikael Rosen, Johan Backman, Per G. P. Ericson and Olof Hellgren:

Analysing the variation in flight speed among bird species is important in understanding flight. We tested if the cruising speed of different migrating bird species in flapping flight scales with body mass and wing loading according to predictions from aerodynamic theory and to what extent phylogeny provides an additional explanation for variation in speed. Flight speeds were measured by tracking radar for bird species ranging in size from 0.01 kg (small passerines) to 10 kg (swans). Equivalent airspeeds of 138 species ranged between 8 and 23 m/s and did not scale as steeply in relation to mass and wing loading as predicted. This suggests that there are evolutionary restrictions to the range of flight speeds that birds obtain, which counteract too slow and too fast speeds among bird species with low and high wing loading, respectively. In addition to the effects of body size and wing morphology on flight speed, we also show that phylogeny accounted for an important part of the remaining speed variation between species. Differences in flight apparatus and behaviour among species of different evolutionary origin, and with different ecology and flight styles, are likely to influence cruising flight performance in important ways.

Update: Grrrlscientist explains the study in plain English.

Update on Tripoli Six

The Tripoli 6 had their death sentence commuted to life in prison. Revere has the details.
Update: There is more.

Today’s carnivals

Oekologie #7 is up on The Evangelical Ecologist.
Four Stone Hearth #19 is up on Sherd Nerd.
Encephalon #27 is up on Neurocontrarian.
Gene Genie #11 is up on Med Journal Watch.
Grand Rounds, Volume 3, Number 43, are up on Vitum Medicinus.
The 12th Carnival of Mathematics is up on The Vedic Maths Forum India Blog.
Carnival of the Green #86 is up on AIDG Blog.
Pediatric Grand Rounds – A Blogging Anniversary – is up on Parenting Solved.
Carnival of Homeschooling #81 is up on Principled Discovery.

Open Science Session in October

ASIS&T 2008 meeting – Joining Research and Practice: Social Computing and Information Science will be held in Milwaukee on October 19-24, 2007. The Program is now available online and it is very exciting. Especially this session 😉

How to rate PLoS ONE papers

Jonathan Eisen demonstrates with a personal example.
First he did a keyword search for the topic of his interest and expertise. Then he read a paper that came up in the search. Then he rated the paper and left a brief comment with the rating.
Then he came back to his blog, wrote in more detail and linked back to the paper itself.
In other related news: Pedro takes a quick look at last week’s first two days of ratings.
Bjoern looks at competition in science and how Open Access can help alleviate it.
Bill Hooker discovers another Open Notebook Science example – a PhD thesis being written on a blog by Jeremiah Faith.
Finally, a very good and important discussion by Bill abot what does and what does not constitute Open Access.

What was the first blog?

Prompted by the WSJ article about blogs, Scoble, Scott Rosenberg, Duncan Riley, Dave Winer, CrunchNotes and Rex Hammock and others discuss the history of blogging.

Clock Tutorial #10: Entrainment

Clock Tutorial #10: EntrainmentThis is the second in a series of posts on the analysis of entrainment, originally written on April 10, 2005.

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ClockQuotes

Sleeping is no mean art: for its sake one has to stay awake all day.
– Friedrich Wilhelm Nietzsche

Things one learns at PLoS….

Tim Sullivan demonstrates the proper gear for blogging against Creationism – a banana and a helmet:
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Does tenure need to change?

There is a long and interesting comment thread on this article on The Scientist blog. What do you think?
(Hat-tip: Tanja)

Blogging Sex and Reproduction

Everyone seems to be blogging about sex (and reproduction) these days. Is it something in the air? Water? Anyway, here are some good recent examples:
Bush Administration Censored Talk On Birth Control And Sex Ed:

This administration got away with a trailblazer–using the FDA to decide a drug’s (Plan B) availability based strictly on party ideology. It set the precedent for a future administration to behave equally as irresponsible.
When a future administration institutes a one-child policy, or executes officials who don’t tow the party line, or makes stoning part of the treatment protocol for rape patients, we mustn’t forget to thank the Bush administration for its visionary conduct.

In Our Country, We Do Sex, Too:

When it comes to sex education, let’s hope India does a better job than we do

The Coolidge Effect:

It’s suggested that the renewed sexual motivation actually represents a dishabituation of the male’s sexual behavior. When the same female is repeatedly presented, the male’s sexual response toward the female gradually decreases and his copulatory efforts appear to become exhausted more quickly. That is, the male habituates to the presence of the female, failing to respond in the same way to her over time. But, presented with a novel female, the “context” of his copulatory experience changes and the male’s sexual response bounces back up to a high level. In other words, the male dishabituates in the presence of the novel female.

Make sure you tune in to the Midwest Teen Sex Show:

If you’re a teenager feel free to enjoy the podcasts and pass the links on to your friends. If you’re a parent, sex educator or therapist share the site with your kids, clients and colleagues.
This is how sex education should be – something that we actually want to see.

The sex education issues parents worry about:

Here are some common concerns or issues parents have about sex education – and some of the evidence about giving sex information to young people which perhaps politicians should consult before recommending parent-only sex education.

The scam that never enZe: the wacky world of weenie-woo:

In fact, one well-known vendor of inert phallotropics has found itself in trouble. (The headline of the linked article is priceless.) Surely you’ve seen the insanely upbeat mascot known as “Enzyte Bob” who wears a giant permagrin to match his presumably equine manhood. Well, his Berkeley Premium Nutraceuticals employers might be feeling a little more droopy than he, what with the feds angling to jerk $100 million from the company’s once-cocksure executives.

Zoos see record attendance

Russ Williams (Director of NC Zoo Society) reports on his blog that the North Carolina Zoo is experiencing record attendance.
He also notes that San Francisco Zoo is enjoying record numbers as well.
Why do you think zoos are so popular lately?
Finally, he mentions that in the Oakland Zoo, one can bring in the appropriate food and go into the exhibit to feed the elephants.
Sounds like fun! I did not even know there was a zoo in Oakland. I’ll have to add it to my growing list of things to see while I am in the area.

Half a Mil!

This crept up on me – I was unaware it was so close yet. I just saw it and had to capture this historical moment:
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The 500,000th visitor came from Reading, UK.
After all this time, I still wonder why so many people come here so often: is watching compulsive blogging akin to watching a wreck? You just can’t stop yourself?

Clock Tutorial #6: To Entrain Or Not To Entrain, That Is The Question

 Clock Tutorial #6: To Entrain Or Not To Entrain, That Is The QuestionThis post from February 03, 2005 covers the basic concepts and terms on entrainment. This is also the only blog post to date that I am aware of that was cited in a scientific paper.

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ClockQuotes

Work ’em hard, play ’em hard, feed ’em up to the nines and send ’em to bed so tired that they are asleep before their heads are on the pillow.
– Frank L. Boyden

Ten years of blogging

The Wall Street Journal has an article about blogs, written by 10 or so people. Some of it is good, some of it is bland and out-of-date, and you can just skip Tom Wolfe’s piece (via Ed Cone).
Also, check out 55 Essential Articles Every Serious Blogger Should Read (which makes it the 56th such article?).
As always, take caution. A blog is no more and no less than a piece of technology – it is up to you to figure out how you are going to use it. So, go ahead and read those 55, but keep in mind that at least half of the ‘advice’ is not relevant or appropriate to you and your own blogging practices and goals. Sure, there are some experiences about things that (mostly) work and others that (mostly) don’t work, but don’t think of any of those as “rules” writ in stone. Use them, instead, as ideas that you can build on in your own way.

Science Envy

I missed this by weeks, but Dave asked a set of questions that I was pondering on, but found no time and energy to answer until now.
PZ, Janet, Martin, Chad and RPM responded (I am assuming some people outside SB did as well) and their responses (and their commenters’) are very interesting.

1. What’s your current scientific specialty?

Chronobiology, although I have not seen the inside of the lab for three years now. So, scientific publishing, education and communication – does that count?

2. Were you originally pursuing a different academic course? If so, what was it?

Yes, I went to vet school before I came to the States. Finished 3.5 out of 5 years of it, too.

3. Do you happen to wish you were involved in another scientific field? If so, what one?

It took me a while to respond to this, because it was really hard for me to answer this question. I love my field and would do it all over again. Yet, I also love evo-devo. And animal behavior. And comparative animal physiology. And palaeontology. And neuroscience. And evolutionary theory. And marine biology. And….well, pretty much everything in biology.
If I could go all the way back to early childhood and got to start all over again, no other science is completely out of the question, form math, physics and chemistry, to archaeology and psychology.
I also agree with some of my SciBlings on the Math/CS envy. I was REALLY good at math until I was about 18 or so. Decades of unuse, and now I can do little more than balance my checkbook.
In 1980 or so I had all the opportunities to turn myself into a computer programmer, but I decided that playing games was more fun, so, beyond basic HTML, I now know nothing about computers, code, and anything related and I really feel a big gap in my knowledge and ability to function bacause of this.
Another envy is philosophy – I never had an opportunity to take a single philosophy course, not even in high school, so I am completely self-taught and it shows.
But after all this thinking, I realized someting else – I am really envious of 19th century scientists! They felt no need to specialize. Why have to pick and choose, when you could do everything?
Just look at Darwin! He got to travel the world. He wrote papers, technical monographs, popular science books, a travelogue and memoirs. He did geology, palaeontology, taxonomy, comparative anatomy, natural history, plant physiology, animal behavior. Oh, yes, I heard he also dabbled in theory, so he could subsequently do evolutionary biology as well. And many consider him a philosopher.
Perhaps that is why I am so gung-ho about Science 2.0. I see a possibility that the new technology will give rise to new ways to do, publish and communicate science, forming connections between fields that were difficult or impossible to do in the 20th century, when a separate graduate degree may have been needed for such a thing.

Farm Bill

Michael Pollan will be on On Point on NPR, talking about the farm bill tomorrow (Monday) morning at 10am EST. This is in advance of some important votes in the House next week.

ScienceBlogs: The Movie?

Blake Stacey has some casting ideas…

How Period and Timeless Interact in Fruitflies

How Period and Timeless Interact in FruitfliesA very cool study that I could not help but comment on (January 18, 2006)…

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Science of Harry Potter

Both Eva and Anne-Marie have started a series of posts about the Science of Harry Potter, focusing on the genetics (i.e., patterns of inheritance) of wizardry vs. muggleness. Anne-Marie has already moved on to the second part of her series, on dragons. It will be interesting to watch what these two come up with over the next few posts in their series.
I have to say that I have been too busy and have yet to see the new movie (The Order of the Phoenix), but will try to see it soon. Also, my two copies of the book #7 will arrive in Chapel Hill on the 21st and I am wondering if I should buy a third one here so I could read it while in San Francisco (who can wait?!) and then give it to someone before leaving.

Building with flimsy materials….

…in an earthquake zone, is bad policy, I think, but Janet did it nonetheless:
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Tiger coprolites

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…are a great teaching tool for Janet.

Coprolites

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One can tell a lot about an animal from what comes out the other end…of a giraffe, in this case.

Thinking outside the box

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That’s what philosophers do.

Brain

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Observed

Sometimes Gravity Wins…

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Janet, here

Philosophy is a Balancing Act

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…and Janet is good at it:

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Reptiles above Berkeley

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In the biology room

Philosopher, above us mere mortals

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Janet, an adult primate observed in juvenile behavior.

Now I’m a Believer!

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After all, it was exhibited at a science museum

Climb on a short snippet of Alpha-Amylase

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Here

The Philosopher Does Not Like Getting Harnessed

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Janet, hoping to join the circus (outside of Academia).

Human Primate Juvenile Behavior

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The evolutionary relationship is apparent.

A Mastodon

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Greeting the visitors.

Axolotl

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One of my favourite animals, seen here.

Circus! Science Under the Big Top

Yesterday, I met Janet and her charming and brilliant sprogs at the Lawrence Hall of Science, where they have a cool exhibit called CIRCUS! Science Under the Big Top (which reminded me that I wanted to join the circus back when I was 18). One thing I did not know was that to get to the museum from Berkeley campus, it is a couple of miles of steep uphill, which I climbed on foot. Should have hitchiked!
Wifi is iffy right now, so I’ll post as many pictures per post as the system will let me. First, just to show how high up the place is, the entire Bay Area is clearly visible – though, of course, covered in fog:

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ClockQuotes – the Bastille Day edition

It was the best of times, it was the worst of times, it was the age of wisdom, it was the age of foolishness, it was the epoch of belief, it was the epoch of incredulity, it was the season of Light, it was the season of Darkness, it was the spring of hope, it was the winter of despair, we had everything before us, we had nothing before us, we were all going direct to heaven, we were all going direct the other way – in short, the period was so far like the present period, that some of its noisiest authorities insisted on its being received, for good or for evil, in the superlative degree of comparison only.
– Charles Dickens

Iron Science Teacher

Yesterday, a few of my friends from PLoS and I went to the Exploratiorium to see the Iron Science Teacher show. Lots of pictures (and a little bit of running commentary) under the fold:

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