Data Visualization: 200 Years of Health and Wealth

Wednesday, December 15, 2010 at 10:48 PM Bookmark and Share
This video is super awesome!  It's part of BBC 4's program The Joy of Stats and you can learn a little more about the data here or play with it using this web app on http://www.gapminder.org/. Now don't you wish you could do that with data?


The reason I wanted to share this video (beyond the fact that it's so amazingly awesome) is to let you in on a little secret... are you ready? Here it comes...
Data visualization is easy, and anyone with a computer can do it!
Seriously, it is not that hard! YOU can make cool little wobbling bubble graphs just like in the video! Aren't you excited to learn how?! Yeah? Fantastic!

Now that you're all psyched to visualize some data, I should mention that I am being a bit misleading here... because it does require a bit of computer know-how, and sometimes (ok, almost always) takes a bit of tinkering with the data to find the best ways of boiling down to just the relevant information. But frankly, these things aren't all that hard to learn and aren't always necessary if we're just poking around to get a feel for the data, so none of these words of caution should give you much pause.  Add to that the fact you can always hit up the internet for examples to download and use study and learn from and many of these obstacles are reduced to mere speed bumps.  If you've got a computer, we can get it to plot some data.

Figure 1. Tourist hot spots based on Flickr data. #1 of flowingdata's Top Ten Data Visualization Projects of 2010.

So here's the deal... there are some really cool data available from http://www.gapminder.org/, and I'm going to have a little free time these next few weeks in between birding trips, visiting family and friends, and doing thesis work.  Assuming that free time stays free, I'm going to walk through an example or two of plotting some of this data in R.  If you'd like to follow along, you'll need to download and install R on your computer, and if you don't already have software that can open excel spreadsheets, you'll also want to install something (free) like OpenOffice.

Sound good? Excellent!  Feel free to share any questions or suggestions in the comments section below.  Now hurry along and go install R!

Support Wildlife Conservation in Ohio

Monday, December 13, 2010 at 2:55 PM Bookmark and Share
Buy an Ohio Wildlife Legacy stamp!

While hunters automatically contribute funds towards the conservation coffers each time they purchase a hunting licenses, wildlife watchers (like birders and herpers) and native plant aficionados aren't required to make such contributions when they go outside to enjoy their favorite organisms. The result? Less money for habitat and wildlife conservation.

The Ohio Wildlife Legacy stamps are an attempt to fix this problem, by inviting all those non-hunters to contribute. With the holidays coming up, and at only $15 each, they make great gifts for that outdoorsy guy or gal on your gift list.  Even for those who do hunt or fish, and already buy licenses (which I believe can't be purchased as a gift) the Wildlife Legacy stamp might still be a much appreciated gift.

To purchase one (or more!), you can buy them online from the ODNR website, the Columbus Audubon Society's website, or you can buy them in person at the nearest ODNR Wildlife District Office.

Knotty Doodles

Wednesday, December 8, 2010 at 9:12 AM Bookmark and Share

Fast and Sloppy Root Finding

Saturday, December 4, 2010 at 3:21 PM Bookmark and Share
Disclaimer: While the approach to root finding mentioned below is both slow and imprecise, it's also a cheap and incredibly handy approach when all you need to do is get "close enough". If you like R quick and dirty (hey now, get your mind out of the gutter...) this is totally the root finding method for you!

I just read a post on Root Finding (original here) by way of R-bloggers.com which was timely given that only yesterday I'd needed to do some root finding in R to make a figure for a manuscript -- something like the following image.
The blog post prompted me to mention here how I did my root finding for two reasons:
  1. Precision and computation time sometimes don't matter all that much; and
  2. The way I did my root finding was way easier to implement than convergence-based methods described in the post above.
So here's what I was aiming for, and how I implemented it in R.

The Task: Suppose you're plotting two curves (say, y=f(x) and y=g(x)) and would like to indicate their intersection with an empty circle (i.e. pch=21). In my case, the intersection of these two curves was equilibrium point for a dynamic model, and I wanted to indicate it as such.

If you can find their intersection mathematically (i.e. set f(x)=g(x) and solve for x) then awesome -- do that if you can.  But if for some reason you can't, and you know a single root exists in some interval a≤x≤b, you can find that root quickly using some straightforward vector tricks.

The Solution: Lets use the example of finding the intersection of f(x) = x/(1+x) and g(x) = (5-x)/5 over the interval (0,5).

Step 1:  Define an x vector full of values between a and b.  The smaller the step size (or, the longer the list) the better.
> x = seq(0, 5, length=5000);
Step 2: Compute the square of the difference of your two functions over that interval using x.  This is as simple as the line of code...
> fgdiff = ( x/(1+x) - (5-x)/5 )^2;
Step 3: Using the which() function, we can pick out the index for the smallest value in our list of squared differences... Once we know this index (call it j) we know the intersection occurs at, or very near, the x value x[j], and we're basically done! 
> j = which(fgdiff==min(fgdiff))[1]; 
> j; x[j];  ## show the value of j, x[j]
For a closer look at what's going on with that which() statement, check out the help for which() and following example.
## A Closer look at the which(fgdiff==min(fgdiff))
> ?which
> which(c(F,F,T,T,F))
[1] 3 4
> which(c(F,F,T,T,F))[1]
[1] 3
> xample = c(5:1,2:5); xample
[1] 5 4 3 2 1 2 3 4 5
> min(xample)
[1] 1
> xample==min(xample)
[1] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
> which(xample==min(xample))
[1] 5
> which(xample==min(xample))[1]
[1] 5
Step 4: Since both functions are (approximately) equal at this x value, it only remains to decide whether you want to indicate the point of intersection using (x, f(x)) or (x, g(x)).
> points(x[j], x[j]/(1+x[j]), pch=19, cex=2)
All done!

If you'd like to tinker with this example, here's the code to produce the image above.

New Rule for Science Journalism...

Saturday, November 27, 2010 at 1:17 PM Bookmark and Share
Agreed!



[Hat tip to PZ Myers]

Happy Turkey Day!

Thursday, November 25, 2010 at 9:46 AM Bookmark and Share
There's a Turkey in my fridge waiting to be cooked, but I couldn't resist writing a quick post full of links on today's official bird. Enjoy!

On this blog

External Links

 

Sex, Life, Death and the Scientific Method

Monday, November 22, 2010 at 12:57 PM Bookmark and Share
Why do women live longer than men? That question caught my eye when it popped up in my twitter feed, so I followed the link over to a podcast on the Scientific American website.  Before I could even listen to the podcast I noticed that someone posted the following in the comments section:
"I have a possible explanation of why women live longer than men. Men have an XY sex chromosome while women have an XX sex chromosome. This results in both the greater potential for genetic (chromosomal) variation in men that successfully adapts to the environment (and passes the same to succeeding generations) and genetic mutation which results in both chromosomal deleterious deterioration and maladaptation that results in early cell and male human death (and which, therefore, is less likely to pass the deleterious chromosomal variation to succeeding generations). Thus, men, in general, live shorter lives than women because their environmental success has a significantly more profound influence on how appropriate their genetic make up is to adapting to the same. At the same time, men's genetic make up (XY vs XY) is much more susceptible to deleterious genetic aberrations and maladaptations. Of course, the aforementioned is simply theory."

Viewed through the lens of science, this suggestion makes a great hypothesis, so I thought I'd mention it here (total avoidance behavior, by the way - I've got a thesis to write!!). So why is it a good hypothesis? Because a good hypothesis is (among other things) one that suggests practical ways to challenge it's own validity. Using claims that logically follow from the original hypothesis, we can test those claims with experimental or observational data. In this case, our hypothesis is:
XY individuals lead shorter lives (on average) than do XX individuals because (on average) mutations in either the X or Y chromosome have the potential to result in greater phenotypic change.
So what statements or predictions follow from this claim that we can test empirically? How can we try and falsify this idea? In this case, we need to look beyond humans for the answer to that questions...

Now, before we get all myopic and try and pretend all gender differences in all species boil down to this single hypothesis, we should be mindful of the myriad other differences between males and females that contribute to longevity.  For example, in humans...


But hey, nothing in science would ever get done if we didn't take things one step at a time, so lets take a closer look at the hypothesis at hand.

I just so happens that here are other mechanisms of sex determination than the XX/XY system found in humans and other mammals. Many reptiles and birds, for example, have a ZW/ZZ system where unlike the mammalian system, ZZ=male and ZW=female. So putting this fact together with our summary statement above, we've come up with a quick prediction: that in birds and reptiles with ZW/ZZ sex determination, the females should be the shorter-lived sex.

So what's the story in birds?  A quick web search (sorry - I need to get back to work!) revealed that people have actually considered this hypothesis before and done some of the leg work for us already.  For example, in Austad 2006 (reference below) the author writes:
Another way to investigate the hypothesis that the sex possessing the heterogametic chromosomes is going to be longer-lived is to consider birds, because the sex-chromosome situation is reversed compared with mammals. In birds, it is the female that has 1 short and I long sex chromosome, and therefore does not have the backup of the 2 long sex chromosomes (the Z chromosomes) that the male has. The prediction is that if heterogametic sex is a key factor, then male birds should be longer-lived. In fact, in 3 species of birds,  including budgerigars, zebra finches, and Japanese quail, males outlive females, at least in captivity. For every bird species that I have been able to find in which there is good captive data, males outlive the females. Certainly, this is provocative evidence that would seem to favor the heterogametic sex hypothesis. It is of concern, however, that in some avian species, the female has been reported to outlive the male, but all of these reports were from field studies and are thus difficult to interpret for the reasons discussed previously.

I like the heterogametic sex hypothesis because it is biologically interesting. Unfortunately, that does not mean it is true.  There are some problems with this hypothesis that can be illustrated with Brandt's bat, a small bat that weighs about 7 grams and is a third to a quarter the size of a mouse... [author cites a study that found males appeared to be longer lived.]  We just don't know the answers to these questions because we do not know what the underlying physiology is and whether behavioral differences or physiological differences are responsible for this remarkable observation in a Siberian cave.

We are also aware of some mammals in which the males are significantly longer-lived than the females; we have very good captive data for 2 of these species, the guinea pig and the golden hamster. In both species, the males live substantially longer than the females, thereby contradicting the heterogametic sex and estrogenic hypotheses. Again, this is a problem in a general biological sense; it may very well be that one of these hypotheses is absolutely valid for humans but is just not generalizable to the rest of mammals. I would like a general explanation, and that is something we currently do not have.

So strictly speaking, this hypothesis is toast. Plenty of evidence to the contrary is floating around out there, so we can rule it out as an accurate summary of reality. But does that mean we just throw it out? Heck no!  Instead of viewing hypotheses as a black and white question of "true vs. false," we instead seek to refine the statement (if possible) and make a new hypothesis consistent with this new information.

For example, we may include the caveat that other processes might matter more in some species than accumulated deleterious effects, thus restricting the kinds of organisms we can apply our hypothesis to.  Also, better experimental investigations could better challenge the core idea behind our hypothesis: genetic changes in the sex chromosomes and their resulting phenotypic changes.  As you can see, all this hypothesizing and testing can snowball into an entire career of work fairly quickly.

As much as I'd love to continue probing the world of longevity and gender genetics, I'm afraid I've got work to do (thesis work!). If I've piqued your interest and you turn up any other interesting studies on the subject, feel free to share in the comments below.

References

U.S. Math & Science Students Need Our Help

Wednesday, November 17, 2010 at 8:37 PM Bookmark and Share
The U.S. ranks very low in math and science compared to other nations -- 35th in Math and 29th in Science. That's embarrassingly low, a threat to the future of our nation's economy, and most importantly it's a problem we can solve. So why are we so far behind?

While digging through TIMMS results can be thought provoking, you must, must, must watch this video which provides a sobering comparison between US student attitudes towards math and science with those of their counterparts from some of the top ranked countries. So click here if you can spare 3 minutes -- it's worth it! The video was produced as part of the Connect A Million Minds (CAMM) campaign, "Time Warner Cable’s philanthropic commitment to connect youth to ideas, people and opportunities that will inspire them to become the problem solvers of tomorrow."


You can see more CAMM videos here.  For more information, look here, here, here and here.

[Hat tip to DNLee]

Do Reptiles Hibernate or Brumate?

Thursday, November 11, 2010 at 11:33 PM Bookmark and Share
Nearly everyone knows what hibernation means, but when speaking of reptiles the term brumation seems to reign supreme.  Why? Is one term more correct than the other?  To try make sense of these competing terms, I recently did some digging into the history of the word brumation which brought me to the following conclusions:
  1. The term brumation is (mostly) unnecessary jargon.
  2. Both hibernation and brumation should be acceptable terms to use in most (if not all) situations, however hibernation is the better term to use in a public forum.

As for why I've arrived at these conclusions, we need to look back a few decades to see where this word "brumation" came from, what we knew about hibernation way back then, and what we've learned about since.

Fascism, Communism and Socialism and Other Awesome Signs

Tuesday, November 9, 2010 at 11:15 PM Bookmark and Share
There are some great signs from the Rally to Restore Sanity up on HuffPo. Here are a few of the 800+ of them available for your browsing pleasure.

If you aren't already in that club...

Fascism a political philosophy or movement "that exalts nation and often race above the individual and that stands for a centralized autocratic government headed by a dictatorial leader, severe economic and social regimentation, and forcible suppression of opposition."

Communism is a social structure advocating elimination of private property.

Socialism includes any of "various economic and political theories advocating collective or governmental ownership and administration of the means of production and distribution of goods."

Moving on...






and the oh-so-appropriate...

Consider Humanism

 at 8:31 PM Bookmark and Share
The American Humanist Association has launched a huge ad campaign today, which "will include a spot on NBC Dateline on Friday, November 12, as well as other television ads." Fund raising for the campaign is ongoing, and is up to $200K as of today.
The Stiefel Freethought Foundation was the primary sponsor of the Consider Humanism campaign with a $150,000 donation. Another $50,000 was raised from supporters of the American Humanist Association for the launch of this campaign, bringing the total ad buy to $200,000 so far.
You can read more in the press release, watch the AHA's videos on vimeo, by visiting http://www.considerhumanism.org and by clicking the images below for higher resolution PDFs.

Using Reptiles For Public Education, Outreach

Monday, November 8, 2010 at 8:20 PM Bookmark and Share
Melissa Kaplan has a great website regarding reptiles in captivity, and included among her writing is some great advice for using animals in public outreach and education. Though geared towards reptiles, the comments I think apply broadly -- check it out!

The Power of Data Visualization & Comparison

Tuesday, November 2, 2010 at 8:22 PM Bookmark and Share

David McCandless: The beauty of data visualization (TED Talk)

Computational statistics and computer programming abilities are -- and will continue to be -- valuable skills in the job market (and in the sciences).  If I could offer any career advice to students, it is to work hard to learn these two things well!

Why Not Vote Republican?

Monday, November 1, 2010 at 11:16 PM Bookmark and Share

While some of those claims need fact checking, there are excellent lines in there! Feel free to quote any favorites in the comments below.

Do Night Shifts Cause Breast Cancer?

Sunday, October 31, 2010 at 11:34 PM Bookmark and Share
According to this review article, the answer appears to lie somewhere between maybe and probably.  While there seems to be a correlation between the two, more research is needed to determine whether or not there is a causal link as other plausible reasons for the correlation haven't yet been ruled out.
...Shift work. Excess incidence of breast cancer has been observed consistently in studies of women with prolonged exposure to shift work involving exposure to light at night (Kolstad 2008; Stevens 2009). Research needs in this area include a) a better definition of what is meant by shift work and related exposure metrics; b) studies of markers of circadian disruption in non–day workers; c) better descriptions of controls and their exposure to light at night; and d) investigation of the effect of variations in expression of circadian genes on cancer in shift workers. An emerging area of interest is the relative toxicity of occupational chemical exposure depending on time of day of that exposure. The marked circadian variations in cell division and DNA repair during the daily cycle are controlled by the circadian genes (Haus and Smolensky 2006; Stevens et al. 2007). Therefore, non–day workers may have very different susceptibility to occupational exposures compared with day workers. Studies are also needed to determine if shift work is associated with other cancers, especially hormonally related cancers, and prostate cancer in particular. If further experimental and epidemiologic evidence confirms a causal association between exposure to light at night and breast cancer, it will be important to develop interventions to reduce the risk.

You can read more here. For details, see the article and relevant references.

Reference

  1. Ward EM, Schulte PA, Straif K, Hopf NB, Caldwell JC, et al. 2010 Research Recommendations for Selected IARC-Classified Agents. Environ Health Perspect 118(10): doi:10.1289/ehp.0901828

    Fluffy the Python Dies

    Saturday, October 30, 2010 at 5:46 PM Bookmark and Share
    The Columbus Zoo's famed Reticulated Python (Python reticulatus) died this week at the ripe old age of 18.

    According to the Columbus Dispatch:
    ...Fluffy died Tuesday night, apparently of a tumor.

    The 18-year-old reticulated python was 24 feet long and held the Guinness World Records title of longest snake in captivity. She weighed 300 pounds, according to a news release from the zoo.
    Sad news, but this made me even more sad ...
    The snake will be cremated, zoo spokeswoman Patty Peters said.
    Cremated?!  Why not preservedLet Fluffy break another record and become the world's longest snake skeleton!  Surely there are people in the area that could prepare the specimen, it it really would make for an awesome display at the zoo. Beyond the immediate future, Fluffy's passing no doubt brings up another big question...

    Will Fluffy Be Replaced?

    I certainly hope so, and I'll go one step further and encourage the Columbus Zoo to not only replace Fluffy but to do so by doing one (or both!) of the following:
    1. Get a "normal" Reticulated Python.  If I'm not mistaken, Fluffy was a "tiger" morph - a pattern mutant commonly bred in captivity that looks like this instead of this or this.
    2. Exhibit this species' natural variation by acquiring (and breeding) some of the diminutive individuals that can be found in the pet trade, or at least individuals from (and representative of) a known locality. These island "dwarfs" (see here, here and here[PDF]) seem to only reach about 6'-10' long (tiny!) instead of 20'+ like individuals from other populations.
    Why a normal looking reticulated python and these tiny island dwarfs?  To quote Melissa Kaplan's article The Use of Reptiles in Public Education (emphasis mine):
    ...The education animal should be representative of a normal form of the species (Gibson, 1994a; San Francisco Zoological Society, 1983). One of the goals of reptile education is to teach not only about the reptile itself but how that species lives in its environment, including how it is camouflaged from predator and prey. In the case of indigenous species, normal forms will help the audience identify the species when they see it in their yards, parks or in wild areas. Captive-bred color and pattern morphs are best saved for use in teaching the basics of genetics and heredity or in lectures addressing reptiles as pets rather than where the focus is on creating an awareness of wildlife and conservation.

    [Hat tip to Cindy Steinle via Kingsnake.com]

    Can Reptiles Fart?

     at 1:14 PM Bookmark and Share

    [Hat tip to ALT and TIFR]

    Talk on The Math, Physics of Drag Racing

    Friday, October 29, 2010 at 5:00 PM Bookmark and Share
    Thursday (4 Nov) there is a public lecture at COSI in Columbus you don't want to miss.  The talk will be given by Dr. Richard A. Tapia -- a big name in applied mathematics, an entertaining speaker, and long-time "champion of under-represented minorities in the sciences."

    Tapia has received numerous professional and community service honors and awards including the annual Blackwell-Tapia Conference being named in his honor (his reason for visiting Columbus) and being inducted into the Texas Science Hall of Fame (yes, such a thing really does exist!).

    Here are the details of his talk from the event flier (PDF):

    Math at Top Speed: Exploring and Breaking Myths in the Drag Racing Folklore

    November 4, 2010; 7:00pm @ COSI (doors open @ 6:00pm) Admission is free

    For most of his life, Richard Tapia has been involved in some aspect of drag racing. He has witnessed the birth and growth of many myths concerning dragster speed and acceleration. Some of these myths will be explained and validated in this talk, while others will be destroyed. For example, Dr. Tapia will explain why dragster acceleration can be greater than the acceleration due to gravity, an age-old inconsistency, and he will present his Fundamental Theorem of Drag Racing. Part of this talk will be a historical account of the development of drag racing and several lively videos will accompany this discussion.

    Speaker: Richard Tapia
    University Professor Maxfield-Oshman Professor in Engineering, Department of Computational and Applied Mathematics (CAAM), Rice University

    More about Dr. Tapia can be found here, here, and here.  More on the Blackwell-Tapia Conference can be found by clicking the "Blackwell-Tapia" link on this website.

    The Math Behind Morphing Faces: Linear Algebra

    Sunday, October 24, 2010 at 3:08 PM Bookmark and Share
    Animations of morphing faces or combinations of multiple images into one can be quite a thing of beauty.  But how exactly are those photos so carefully blended together? 

    While the answer to that question is beyond the scope of what I could put into a single blog post, understanding that answer requires some basic knowledge of one very important are of mathematics: linear algebra.  It's important not just for the number-crunching tools it provides, but because it helps us think about things differently and know how to ask the right questions and know whether or not those questions have answers.  Before I get too far ahead of myself lets first take a look at the video which motivated this post in the first place, which strings together 60 years of female actors from CBS (click the button in the lower right corner to watch it full-screen):


    CBS - 60 Years of Actresses from Philip Scott Johnson on Vimeo.
    More videos by Philip Scott Johnson (including CBS -
    60 Years of Actors) can be found on vimeo and on youtube.

    So how are these animations created?

    If you replay part of the video, you'll notice that there are two things going on: 1) facial features in each image are stretched and rotated to line up with the facial features of the next image, and 2) there's a fade from one image to the next. The fade seems simple enough, so lets just focus on the first process of stretching and rotating facial features.

    Why did NPR fire Juan Williams?

    Thursday, October 21, 2010 at 9:41 PM Bookmark and Share
    Fox News and other right-leaning media seem to be jumping out of their chairs over NPR's firing of Juan Williams, claiming it was unjustifiable and politically motivated.  But was he really fired over his recent comments on Fox (see the video below), or did he violate his contract with NPR?

    How many species concepts are there?

     at 11:00 AM Bookmark and Share
    Do you remember the definition of species from your high school or college biology class?  Me neither -- but worry not!  Even if you remembered it word for word, there's a good chance it's not the same definition your friends and co-workers learned and it's certainly not the only definition floating around out there.  So how many species concepts are there?

    According to John S. Wilkins in his recent guest post over at Punctuated Equilibrium (also here on John's blog) there are either 26-27, 7, 2, 1 or 0.  The article is well worth the read as John gives a nice, brief overview of the many different definitions of a biological species, their similarities and differences, and the key concepts behind those definitions. 


    If you don't mind my giving away the punchline, here's what it all boils down to:

    Final score: 26-27, 7, 2, 1 or 0.

    What to think? My solution is this:

    There is one species concept (and it refers to real species).

    There are two explanations of why real species are species (see my microbial paper, 2007): ecological adaptation and reproductive reach.

    There are seven distinct definitions of "species", and 27 variations and mixtures.

    And there are n+1 definitions of "species" in a room of n biologists.
    For a more detailed treatment of the idea of biological species, see John's book 'Species: A History of the Idea'.

    [Hat tip to John Hawks and GrrlScientist]

    Christine O'Donnell: "Where in the Consitution is the Separation of Church and State?"

    Wednesday, October 20, 2010 at 5:50 PM Bookmark and Share
    Christine O'Donnell is shockingly ignorant when it comes to science, creationism, and now apparently ( ... drum roll please ... ) the U.S. Constitution.

    Don't take my word for it, here it is straight from the witch's horse's mouth...

    (Her shockingly dumb question occurs just after the 2:30 mark in the video.)

    [Hat tip to Sandwalk]

    Wind May Have Helped Moses Part Red Sea? Probably Not

     at 11:39 AM Bookmark and Share
    This story got lots of coverage a few weeks ago (even NPR picked it up), but there were problems with the coverage and so I decided to write about it. Unfortunately, I just now realized that I completely forgot to post what I'd written!  So for better or worse, I decided to dredge up old news and clicked publish.

    This story is a classic case of "science journalism FAIL" - despite all the media coverage, it seems nobody gave the story a critical look to see whether or not the conclusions actually follow from the research, and nobody seemed to be calling the authors' motives into question. PZ ranted about it here, Brian Keim over at Wired Science wrote this rather uncritical piece (where I left a couple of comments), and it was covered here at the lead author's place of employment.  Like Brian Keim's article, the NPR piece seems to lack much criticism, so here's my take on what they missed.

    City Council Member to Gay Teens: "It Gets Better"

    Sunday, October 17, 2010 at 5:56 PM Bookmark and Share
    In the wake of multiple suicides among teens who are gay or perceived as gay, a single resounding message has emerged: "it gets better."

    Here's a particularly moving story from Ft. Worth city council member Joel Burns, told during a city council meeting earlier this month.


    More stories like Joel's need to be told, and the teens stuck in these seemingly hopeless situations need to hear them.  To help that happen, Dan Savage and his partner Terry started the It Gets Better Project which helps provide a platform for adults to share their own stories and tell their younger counterparts that they really can get through the bullying, they can get through school, and that it really does get better.

    You can see Dan and Terry's original video and the stories of others on the It Gets Better Project's YouTube channel. For additional resources, see the Trevor Project website, the Bullying Information Center, and resources for educators here and here.

    Alan Alda on communicating science to the public

    Saturday, October 16, 2010 at 12:25 PM Bookmark and Share
    The American Academy of Arts and Sciences has a new paper out on 'Science and the Media' (PDF). Alan Alda wrote chapter 3, and has some good advice for scientists (emphasis mine):
    The effort is not to oversimplify science. We need clarity and vividness, but not — please, not — dumbing down. Some of our great science communicators have shown that there are deeply engaging stories in science (science itself is the greatest detective story ever told) and that it’s possible to be personal and passionate about the study of nature without losing respect for the precision and accuracy at the heart of that study. Richard Feynman was both fun to listen to and precise. Even when he explained something in simple terms, he usually let you know that it was often more complicated than that. And when you were ready, he let you in on a little more of the complexity.

    Feynman was one of those extraordinary communicators that nature produces from time to time. But they occur by chance. Why should effective, inspiring communication of science be left to chance? Science is rigorous; can’t we be just as rigorous about teaching its communication?

    Is it too much to hope that there will be a time when the skills of communicating science will be taught as a regular part of the science curriculum, and not as something added on for a few hours at the end? Isn’t good communication fundamental to science? How else can it be successfully replicated, funded, and taught?

    But don’t let my high-flown arguments fool you. This is really a selfish plea. I’m too old to learn all the math and chemistry I need to understand the subtleties of the Higgs particle or the intricacies of reverse transcriptase. Even if I did, I’d only have access to one small part of the whole. I want to stand next to you scientists and gaze out at the entire horizon, while you point out what to look for.

    Every scientist reading this has a deep passion for science. I implore you: let your passion out. Share it with us. Warmly, with stories, imagination, even with humor. But most of all, in your own voice.

    Home birth death toll rising in Colorado?

    Friday, October 15, 2010 at 12:04 PM Bookmark and Share
    Dr. Amy Tuteur, the Skeptical OB, has a blog post up entitled 'Inexcusable homebirth death toll keeps rising in Colorado.'  Now I'm a big fan of science-based medicine (and of Tuteur's blog), however I have to call foul when it comes to that "rising" part of her post.  Yes, I think it's pretty minor point since the real comparison to consider is the home birth vs. hospital birth mortality rates - but this is a nice opportunity to do some basic stats. Having left a few comments to that effect on her blog, I figured I would summarize them here.

    Templeton Foundation Talk Tomorrow in Columbus

    Tuesday, October 12, 2010 at 5:55 PM Bookmark and Share
    Since 2006, the Ohio State University has hosted an annual discussion of religion, science and evolution entitled The Intersection of Science and Faith. It's funded by the John Templeton Foundation (JTF) and this year's discussion will be happening tomorrow (Wednesday) at 7pm at COSI in Columbus. Attendance is free, but registration is required to attend.

    If you're in town, you should check it out!

    Here's the announcement from the COSI calendar (PDF flier here):
    Beyond Belief: Is Religion in Our Genes?
    October 13, 2010 - October 13, 2010
    Wednesday, October 13, 2010 (7pm-9pm)

    Supported by a grant from the John Templeton Foundation

    Join COSI and moderator Neal Conan, senior host of the National Public Radio talk show, Talk of the Nation, for a lively panel discussion with Andrew Newberg, MD, Director of Clinical Nuclear Medicine, Director of NeuroPET Research, University of Pennsylvania, and author of "Why God Won't Go Away: Brain Science and the Biology of Belief," and Nicolas Wade, New York Times science writer and author of "Before the Dawn," and "The Faith Instinct." This program takes place inside the WOSU@COSI Studios on COSI's Level 1.

    Register: RSVP by calling 614.228.2674, registration is required.

    Cost: This event is free

    Admission: Free; registration is required - please call 614.228.2674 to RSVP.
    Sounds interesting, right?  But what might we expect from the discussion? What's the John Templeton Foundation?  Who are the speakers?  To answer these questions, lets take a closer look at the speakers and the funding source.

    Free Online Math Books?

    Tuesday, October 5, 2010 at 7:48 PM Bookmark and Share
    I was poking around the web for a copy of Euclid's Elements, and came across a nice list of over 75  freely available online math books. There's a good mix of material there, ranging from centuries old classics up to modern day course topics and modern application areas - something for everybody.  Check it out!

    How hard is it to forward a few emails?

    Friday, October 1, 2010 at 2:19 PM Bookmark and Share
    Apparently, kinda hard. I just learned that for at least the past 2+ weeks, certain emails haven't been making it to my academic email address. Not all of them, no, just the ones from (are you sitting down?) everyone at my own University.

    Figure 1. Author's rendition of how email works (black), and doesn't work (red).

    Our departmental email system recently throat-punched itself to death got an upgrade and it was decided that all emails should hence forth get forwarded to our main university email account. It makes sense, and doesn't sound all that hard to implement - right?

    For reasons I won't go into here, I like to keep the two separate so (as was the case prior to the throat-punching upgrade) I had my departmental email forwarded to a gmail account. Somehow, this resulted in all external emails and any emails sent from within the department getting through to that gmail account, but not any emails from others at my MRU - you know, like any administrative folks, professors, researchers, or other grad students I might need to be in contact with. To make matters worse, they don't bounce back or otherwise fail - they just disappear. That means anyone sending me an email doesn't get a warning that I won't ever see that email they just sent.

    Fortunately, the tech team is on top of it as I type this and no doubt they'll have the problem resolved in short order. Just needed to rant about it a bit so I could get back to working on that thesis thing I'm trying to wrap up. ;)

    Update:

    So it turns out I was wrong (kind of...). My emails weren't being forwarded to the proper place, so no emails were lost - just misplaced. Thankfully, the technician in charge of our system finally has all my emails going to the right inbox. Problems solved :)

    The Sound of Science: Simon & Garfunkel (feat. Darwin)

     at 10:35 AM Bookmark and Share


    [via WEIT]

    More music you¹ can do math to...

    Wednesday, September 29, 2010 at 6:50 PM Bookmark and Share
    Apparently, Pandora insists I get at least one kick-ass song a day in which G. W. Bush is quote mined about war.  So far, so good.

    ¹ I should probably just say "music I can do math to" but that's hardly an interesting title for a blog post, right? Right.

    Math & The Oh-So-Musical Ministry

    Tuesday, September 28, 2010 at 7:09 PM Bookmark and Share
    While working on a proof just now, this little beauty came pouring through my headphones. Great beat for doing math to, hilarious quote mining... what's not to love!?

    In which a family cheers at the suffering and death of an animal...

    Monday, September 27, 2010 at 12:15 AM Bookmark and Share
    Science is cold, emotionless.  It takes no moral positions, it has no fears, it's just a method for rooting out incorrect ideas by challenging those ideas with logic and data.  This is a good thing: it's what makes science so successful at giving us relatively objective descriptions of reality and how it works.

    But scientists aren't science.  They do hold moral position, and sometimes they give a damn about something. That means the things they care about - be it puppies, women's rights, great music, historical buildings, or hot shoes - these things evoke emotion, and dictate action. Personally, I'm rather partial to snakes, which is why my blood boils when I watch this video of a family cheering as passing traffic repeatedly hits and eventually kills an Eastern Diamondback Rattlesnake...


    Interestingly, I don't hate these people - I don't even dislike them (which I'll admit feels a bit odd - I feel like I should). Certainly, if I were in their shoes, I would have jumped out of the car and tried to saved the snake. But that's me - I know a fair bit about rattlesnakes, and through that knowledge I've developed a great deal of appreciation for them.

    That's important, so I'll reiterate: my knowledge of snakes has brought me to appreciate them. Science may be cold and emotionless, but the factual details it provides can significantly shape our morality - our sense of good and bad, right and wrong - and I think this is generally true for nearly everyone.  I'll let Richard Dawkins and Sam Harris elaborate (although see Massimo Piggliucci's commentary for a critique of Harris's talk)...




    So when I see videos like the first one above, I don't see an evil family of ruthless sadists raising sociopathic  children.  In fact, I'd be surprised if they weren't actually a rather likable and otherwise decent family.

    What I do see is a family that doesn't live near a good nature center. That doesn't spend much time at high quality zoos. That lives where the schools have ineffective biology teachers. A family with no pet reptiles, maybe no pets at all. Mom and dad are almost certainly not biologists, probably don't get out into nature much, and the kids probably don't want to become doctors or social workers or biologists (yet!).

    What I see is the target audience of every science and nature educator ever to speak to the public.

    Ignorance is the problem, education the solution.  

    Should Scientists, Journalists "Take Sides"?

    Thursday, September 23, 2010 at 6:11 PM Bookmark and Share
    Ed Yong has a great post up on his (excellent) blog Not Exactly Rocket Science, which I hope you'll read. There, he writes (emphasis mine):
    It is clear to me that science journalists should not take the side of any particular scientist, of a specific idea, or even of science itself. But it is imperative that we take the side of truth. That may seem obvious but many of the strictures of traditional journalism are incompatible with even that simple goal.

    You can read more details on the topic of objectivity, science journalism, and "taking sides" in his post, here.

    Discover Magazine on Intelligent Design

    Tuesday, September 21, 2010 at 7:18 PM Bookmark and Share
    Discover Magazine has a 30 year anniversary issue out, and among it's pages is a short list of some big scientific blunders from recent decades. Included on the list: Intelligent Design/Creationism.
    Intelligent Design:
    Not satisfied with the biblical God who created the world in six days, creationists developed a "science" that aims to explain the supernatural force behind the whole shebang: intelligent design.  Because we cannot reverse-engineer things like the human eye, they say, it follows that all must be designed by a higher being. (The human knee presumably came together during a moment of distraction.)  This tactic had some success easing intelligent design/creationism into American public-school science lessons. But in 2005 a jury prohibited its teaching in the schools of Dover, Pennsylvania, delivering a stinging rebuke.
    If you saw my previous post, you've likely already noticed a mistake which the NCSE has rightly pointed out.
    Discover errs in attributing the verdict in Kitzmiller v. Dover to "a jury"; it was a bench trial, and the decision — which was indeed a stinging rebuke to the scientific pretensions of "intelligent design" — was due to Judge John E. Jones III.

    Intelligent Design: Creationism's Trojan Horse

    Monday, September 20, 2010 at 4:51 PM Bookmark and Share
    A nice look at the history of the ID movement in the talk below, by NCSE board member Dr. Barbara Forrest (see below to jump around the video by topic highlights). You can read more about her book "Creationism's Trojan Horse" in this review at Panda's Thumb, or in the links given below.


    A few bookmarks for those of you who'd like to jump around or don't have time to watch the whole thing:
    1. Dembski's juvenile attempt to anonymously thumb his nose at Judge Jones and others @ 1:20
    2. Talk begins @ 4:14
    3. Trojan Horse defined/discussed @ 5:30
    4. Intelligent Design as a Trojan Horse @ 6:00
    5. Dover Trial details begin around 7:50 
    6. Who's Who of the Discovery Institute: Center for the Renewal of Science & Culture @ 9:49
    7. Their infamous Wedge Strategy (and Wedge Document) @ 11:45
    8. Trial details begin around 13:30
    9. More from Dembski starting @ 14:00 (followed by more shenanigans from the Disco'Tute)
    10. Expert witnesses on the side of science (plaintiffs) @ 17:50
    11. Summary of lessons learned from the trial are in a nice book (see resource links below) @ 18:28
    12. Plaintiff's attorneys @ 18:43
    13. Expert witnesses on the side of intelligent design creationism (defendants) including those  who backed out @18:55
    14. Dr. Forrest describes her role in the trial @ 20:50 (followed by a nice summary of "ID = christian creationism")
    15. The evolution of the creationist-turned-ID text, Of Pandas and People @ 29:45
    16. The origin of that accidental term, cdesign proponentsists @ 33:00
    17. Cost of the Dover trial (including Dembski's $20K "for not showing up") @ 35:45
    18. 1982 source of "Complex specified information"; 1982 precursor to "Irreducible Complexity" @ 37:30
    19. Behe continues on after the trial, his book, etc. @ 39:00
    20. Key terms/phrases used by ID proponents - things to look out for @ 39:25
    21. The new replacement creationist text? Explore Evolution @ 41:00
    22. Nice book list of additional reading on the Creationism vs. Evolution conflict @ 42:34
    23. Did you know Dembski helped A. Coulter write ID chapters in 'Godless'? @ 44:06
    24. Talk ends @ 44:40, Q&A begins.
    See anything else worth noting? Please take note of the time, and leave a comment below.  If it doesn't slip my mind, I'll try and include comments above on what's in the Q&A when I get a chance.

    Resources

    1. Scott, E. C., Branch, G. 2006. Not in our classroom: Why Intelligent Design is Wrong for Our Schools.  http://ncse.com/nioc (purchase here).
    2. Trial Documents from Kitzmiller vs. Dover available here on the NCSE website.
    3. Dr. Forrest's Creationism's Trojan Horse website: http://www.creationismstrojanhorse.com/ Both book info and info/resources from the Dover trial.

    Mid-week Reptilian #23: Tuatara

    Friday, September 17, 2010 at 12:39 PM Bookmark and Share
    I recently came across an excellent short film on a most fascinating reptile - the Tuatara (Sphenodon sp.) - so I've embedded the film below for your viewing pleasure.

    Figure 1: Tuatara (Sphenodon punctatus).
    Click image for source.

    But first, some background on the tuatara is in order...

    Bed Bugs!

     at 11:35 AM Bookmark and Share

    Don't forget to click the video and jump over to the youtube page to tell Cornell that you like their video by clicking the "Like" button. 

    More info on bed bugs can be found here, here and of course here.

    Texas Governor Perry Equates Creationism, Intelligent Design

    Tuesday, September 14, 2010 at 5:47 PM Bookmark and Share
    It's shameful that a sitting Governor would so blatantly advocate for religious pseudoscience to be taught as real science to public school students.  But I suppose there is silver lining to the story: at least Texas Gov. Rick Perry recognizes intelligent design as creationism:
    Explain where you stand on evolution-creationism being taught in school.

    I am a firm believer in intelligent design as a matter of faith and intellect, and I believe it should be presented in schools alongside the theories of evolution. The State Board of Education has been charged with the task of adopting curriculum requirements for Texas public schools and recently adopted guidelines that call for the examination of all sides of a scientific theory, which will encourage critical thinking in our students, an essential learning skill.
    He's right. While some of his fellow Texans have previously tried to pretend otherwise, intelligent design is a form of monotheistic creationism.

    As for that "teach the alternatives" nonsense - maybe he'd also be keen to start teaching about the Church of the Flying Spaghetti Monster alongside Christianity in Texas history and religion classes?

    [Hat tip to PZ]

    2010 Arctic Ice Update: It's Melting...

    Monday, September 13, 2010 at 11:44 PM Bookmark and Share

    R Tip: Listing Loaded Packages

     at 2:22 PM Bookmark and Share
    A friend recently asked how you list the packages currently loaded into R's workspace, as opposed to listing all available packages which is what library() does. The answer?
    > (.packages())

    Oh no! I (almost) missed IRFD, 2010!!!

    Sunday, September 12, 2010 at 10:40 PM Bookmark and Share
    Yikes! I somehow failed to recognize that today is International Rock Flipping Day, 2010!

    So what's a thesis-writing, easily distracted grad student to do? Why run outside and flip some rocks, of course. Pics will be posted below once I get them cropped and uploaded to the intertubes.

    [Brief pause while I run outside with a camera and flashlight...]

    Turns out, there aren't too many rocks worth living under in our yard - and the few that are are a bit on the huge end of the spectrum.  Still, I managed to snap some decent photos of a few of the invertebrates living around our house.  Pictures will be posted below tomorrow.

    50 Atheist/Agnostic Billboards Go Up In Atlanta, GA

    Saturday, September 11, 2010 at 1:14 AM Bookmark and Share
    The Freedom From Religion Foundation has really outdone themselves this time: 50 billboards!?



    That first one has some local significance...
    Atlantans can look out for a variety of small, colorful billboards around town, including one with particular meaning for FFRF and for Atlanta. It features actress Butterfly McQueen, who lived in Atlanta at the end of her life, and showcases her statement to the Atlanta Journal-Constitution made during the 50th anniversary year of the release of the movie, “Gone with the Wind,” in which she played the role of “Prissy.” McQueen, who rebelled her entire life against religion as she rebelled against stereotyped acting roles, said: “As my ancestors are free from slavery, I am free from the slavery of religion.”

    McQueen was a Lifetime Member of the Freedom From Religion Foundation, and made an appearance at FFRF’s 1989 national convention in Atlanta, where she was named FFRF’s premiere Freethought Heroine. She died in a tragic kitchen fire in 1995.
    You can find more details (and more billboards) here and here.

    Columbus Science Pub off to a GREAT start!

    Wednesday, September 8, 2010 at 1:22 AM Bookmark and Share
    Here's a few photos and thoughts after tonight's inaugural Columbus Science Pub (more on the event here), held at the Hampton's on King near the OSU campus. The first speaker in the monthly event series? Dr. Tara C. Smith, professor of epidemiology and author of the kick-ass ScienceBlog, Aetiology.  Not sure what the organizer(s) thought, but I thought the event was a great success.

    Figure 1.  Science education done right: on bed sheet, in a bar.

    Tara's talk was titled Science Denial and the Internet, and covered topics ranging from HIV denial, this history of the anti-vaccine movement, and advice for the audience (which included both scientists and non-scientists) on how to weed out misinformation and promote better communication of science to the public.  By my count, there were a little over 50 people in the audience at it's peak.

    Figure 2.  Some of the crowd.

    So why do I consider this first installment of the Columbus Science Pub a success?

    First, we had a good mix of folks in the audience: Non-science folks, science students, researchers and a few bloggers like myself and





    I'll try and get a copy of her talk to share some of the highlights, but in the mean time I'll share her closing slide which probably sums up the frustration my internet presence causes Dr. Wife™... ;)


    For more details on her talk, see this Newsvine article by Brent Jernigan.

    Hungover Owls

    Tuesday, August 24, 2010 at 10:20 PM Bookmark and Share
    It's been a while since there's been anything new posted on the hilariously vulgar blog "Fuck You, Penguin", so it totally made my day when a friend set me a link to "Hungover Owls" on tumblr.

    It's absolutely hilarious - go check it out!









    Eastern Screech Owl:  “Look, I’m sorry for blowing up earlier. It’s just…I can feel tequila…in my face.”

    Embryonic Stem Cell Injunction (Part II)

     at 2:01 AM Bookmark and Share
    More of my thoughts (part I is here) on the recent ruling by judge Royce Lamberth halting embryonic stem cell research in the U.S. Here are my thoughts on the judges decision to go forward with the injunction.  In his ruling he lays out the criteria for the decision and why he thinks the plaintiffs case was sufficient to pull federal research funding.   

    Part II: Did the judge meet the criteria for an injunction?

    In his ruling, the judge lays out criteria for issuing an injunction by quoting from another case which asserts that (emphasis mine)...

    Embryonic Stem Cell Research Halted... AGAIN

     at 1:03 AM Bookmark and Share
    If you haven't heard, there's plenty in the news here, here and here.  I recommend reading judge Royce C. Lamberth's 15 page ruling for yourself, as it clarifies much of what the media are glossing over at the moment.

    Below are my thoughts on the ruling.  I take issue with some of the judges arguments, and not because I have zero legal expertise - I think it's because he's gotten some things wrong.  I also think the judge didn't live up to his own standards, which I'll discuss in part two of this post which you can find here.

    Part I: Does "Embryonic Stem Cell Research = Killing Embryos"?

    The crucial legal language in this case is known as the Dickey-Wicker Amendment (also, see here). It's notable for (1) limiting how federal dollars are spent on embryonic stem cell (ESC) research, and (2) it includes an attempt at defining "human embryo." The definition seems overly broad in my opinion (e.g. if I culture some of my skin cells, they seem to fit this definition), but take a look and decide for yourself.

    The language can be seen in H.R. 3010 (see pg 48 in this PDF) section 509(a)(2) which reads...

    The Internet = iDistraction™

    Wednesday, August 18, 2010 at 2:38 PM Bookmark and Share
    That's all.  I should get back to work now.

    Philosophy of Science

    Tuesday, August 17, 2010 at 11:01 PM Bookmark and Share
    Massimo Pigliucci has a few videos up on his YouTube channel on the philosophy of science.  If you're unfamiliar with with the philosophy of science, you might enjoy them.

    Part I

    Monday Mammal #14: Collared Peccary (aka Javalina)

    Monday, August 16, 2010 at 12:44 PM Bookmark and Share
    The Collared Peccary (Pecari tajacu) is an inhabitant of the south western U.S. and Central and South America. Often confused for pigs (family Suidae), P. tajacu and the other 3-4 Pecari sp. are members of the related family Tayassuidae. Interestingly, this group illustrates that there's still a lot we don't know about wildlife diversity: only recently was the Giant Peccary (Pecari maximus) described and proposed as a fourth Pecari. For more on the Giant Peccary check out the Tetrapod Zoology posts here and here, and the technical paper on page 9 of this PDF.

    An Open Letter to Casey Luskin

    Sunday, August 15, 2010 at 11:54 AM Bookmark and Share

    Here are some links of interest:
    1. The article in question http://www.evolutionnews.org/2010/07/...
    2. The Nature brochure/pamphlet http://www.nature.com/nature/newspdf/...
    3. A funny story about Phil Skell http://whyevolutionistrue.wordpress.c...
    4. Gallup Poll (includes question about heliocentrism) http://www.gallup.com/poll/3742/new-p...

    [via C0nc0rdence]

    Warning!!!

    Saturday, August 14, 2010 at 2:27 PM Bookmark and Share
    Check out these awesome Journalism Warning Labels by Tom Scott.  Admittedly, I probably overuse (i.e. link to) Wikipedia here on the blog, but hey - at least I'm up front about!

    If you'd like to print some out yourself, there are two PDF templates at the bottom of the page you can download and print.

    [via PZ]

    The Difference Between "Intelligent Design" and "Creationism"?

    Friday, August 13, 2010 at 1:26 PM Bookmark and Share
    Here's a fantastic article you should check out: Still Trying to Get Creationism into Science Classes: Five Years After Kitzmiller v. Dover, Discovery Institute Hasn’t Changed its Playbook. The article covers the relationship between ID and creationism and gives a nice, brief history of the Discovery Institute (DI).

    If you're unfamiliar with their history...
    Let’s start with the so-called Wedge Document. In 1998, DI put out a fundraising document that plainly set forth its “governing goals,” which included these aims:
    To defeat scientific materialism and its destructive moral, cultural, and political legacies; and to replace materialistic explanations with the theistic understanding that nature and human beings are created by God.
    Sounds like a pretty clear mission statement to me. But there’s more...

    Also pointed out in the article is one big similarity between the Dover trial (covered in this documentary) and the recent ruling against Prop. 8 in California:
    An interesting comparison can be made to the recent decision of Judge Vaughn R. Walker about Proposition 8. In the Prop. 8 case as in Dover, the supposed scientific arguments of religiously motivated organizations often don’t hold up well in a courtroom where they are required to present the evidence of their assertions.

    [Hat tip to the NCSE]