The Obligate Scientist

The end of the world... and I feel fine!

2011-05-20T13:00:00.000-04:00

The end is very nigh. May 21^st is upon us and as you've probably already heard in the news or elsewhere that means it's time for ~~the rapture~~ The Rapture!

Predictions like these have a long track record of being correct, so best of luck to you come judgement and until then be vigilant for unmanned cars whizzing down the road, anyone flying up into the air, or any six-winged creatures covered in eyeballs. If you happen to see any of these things, do leave a comment below!

PS: if you're still here on the 22^nd consider opening your home to your ex-neighbors' earth-bound pets!

Happy Mother's Day!!

2011-05-08T13:57:00.000-04:00

If you were planning on sending your mom a nerdy video, make sure you don't go overboard on the nerdiness -- unless you're mom's a super nerd, then go for it! For example, this is an excellent choice

while this one -- although both nerdy and relevant to motherhood -- might not quite be the best choice...

Happy π Day!!! No, wait, scratch that...

2011-03-14T23:15:00.000-04:00

Lets face it -- π sucks. Not pie, pie is genuinely awesome and so is the fact that "pie" sounds like "π", so we can have fun with things like this. But seriously... π? It's totally off by a factor of 2!

For more on τ day, check out the Tau Manifest at http://tauday.com/ and of course http://halftauday.com/ if you're still a fan of π.

A request: I need your comments!

2011-03-11T16:54:00.002-05:00

I need your help! A reader recently tried to leave a comment on this blog, and despite the fact that I received an email notifying me of the new comment, it never appeared on the blog post...

Figure 1: I'm about this confused, if not more.

So, if you can spare a few moments, please head over to this post (and/or leave a comment below) and let me know the following:

Operating System:
Browser:
Comment type (Anonymous, Google, etc.):
Link to your favorite recipe^**:

** Totally unrelated, optional, but potentially delicious and therefore worth requesting. ;)

If the comment submission process seemed to work but your comment doesn't show up on the post, please drop me an email letting me know what happened.

Thanks! ~ Paul

Evolution is a pain in the ass, especially for herpetologists and ornithologists

2011-03-03T01:26:00.000-05:00

The reason? Imagine you have a kid, and your neighbor has 2 kids, then you both find out that really, one of their kids is sort of... yours. (-- awkward pause --) That's basically the problem here:

Herpetology is the study of reptiles and amphibians, however unraveling the evolutionary history of these two groups (along with birds) has shown us that birds are actually nested in among reptiles.

Now, to be fair, I think the comic has it wrong: I mean, shouldn't this justify lumping ornithology in a sub-discipline of herpetology?

Thesis writing...

2011-03-02T14:28:00.000-05:00

... has pulled me away from blogging the past couple of months. BUT, I'll hopefully be done and back to a regular posting schedule later this spring!

Figure 1: Mascot for my recent rate of new blog posts.

In the meantime, you should check out R-bloggers.com and "like" their facebook page to get regular updates on your news feed.

Shame on you, R... again! (But not really...)

2011-01-17T14:25:00.003-05:00

Remember how a few months ago I lamented the fact that the round() function in R uses a non-standard rule for rounding to the nearest integer? Instead of rounding k+0.5 to k+1 (k being an integer) R rounds to whichever integer k or k+1 is even. Well here's another example of R offending our mathematical sensibilities... R seems to think that even though

1 * Inf = Inf

somehow it can get away with telling us that

1 * (Inf + 0i) = Inf + NaNi?

"Gasp!" I know, insane, right? What's going on here? Whatever happened to "anything times one is equal to that same number"? Granted, infinity isn't really a number so sometimes we can't assign a value to an expression like Inf*0, but deep down inside I can't shake the feeling that 1 * Inf really should be Inf!

It turns out that R and I are both right - we're just making different assumptions about how we interpret all these 1s, 0s and Infs in these two statements. Let me explain...

Despite using sound, puppy-approved logic in this case, R gives the offending result because of how it implements everyone's favorite section in Calculus class: computing limits. To understand why, take a closer look at how the multiplication is happening in each case above. The first case is hopefully straightforward. In the second case 1 is treated as a complex number instead of a scalar which gives

1*(Inf+0i) = (1+0i)*(Inf+0i) =

= Inf + (0*Inf+0)i = Inf + NaNi

We could also throw in a third case and multiply these two complex numbers in the more natural context of polar coordinates. Writing each in terms of their modulus r (distance from the origin) and argument θ (angle off of the positive real axis) instead of in terms of their real and imaginary parts, we have

1*(Inf+0i) = (1+0i)*(Inf+0i)

= 1exp(i0)* Inf exp(i0)

= (1*Inf) exp (i0)

= Inf exp(i0)

= Inf + 0i

Whew! So what's "wrong" with multiplying things in x+yi form??

R recognizes that any computations involving infinity really require the algebra of limits, and acts appropriately (albeit conservatively) to evaluate such expressions. This discord then comes from what R assumes is the result of taking some limit and what is to be treated as a constant. Unless you've taught a calculus class recently some explanation might be in order.

In general, expressions involving infinity are treated as limits where some unspecified variable is going to infinity: For example, statements like Inf*0 can't be assigned a value because in it's most general interpretation we're asking "What is the limit of the product of x*y as x→Inf and y→0?" Here, whether y goes to 0 from above (e.g. y=1/x) or below (y=-1/x) or neither will determine where the limit of the product goes to zero, some non-zero number, plus or minus infinity, or will have no limit at all. (Open any calculus text to the sections on limits for examples leading to these different outcomes). Note this example does have an answer if y is always assumed to be 0, since it's always the case that x*0=0.

That means that, depending on how we interepret the zero, our example might equal either

Inf*0=NaN

Inf*0=0

This is exactly what's going on above.

Returning to the two statements at the top of this post, we can now understand why R gives these two different answers. By making the zero implicit vs. explicit R treats these expressions differently. R interprets Inf as "the limit of x + 0i as x→Inf," allowing for the result that

1 * Inf = Inf

whereas in the second case R treats Inf + 0i as "the limit of x + yi as x → Inf and y → 0" which has no general answer and therefore gets assigned a value of NaN.

The take-home message: as soon as there's an Inf in an expression, R proceeds assuming everything is a limit, even though it might be clear to the user that some of those key 1s and 0s should be treated as constants.

Data Visualization in R: Part... 0

2011-01-14T15:26:00.000-05:00

I haven't forgotten that I promised to do a series of posts on data visualization using R - just a bit busy catching up after some excellent holiday R&R. Hopefully I'll get a post out soon!

In the mean time, check out these two posts from the R-bloggers network.

Data Visualization: 200 Years of Health and Wealth

2010-12-15T22:48:00.004-05:00

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

2010-12-13T14:55:00.000-05:00

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

2010-12-08T09:12:00.000-05:00

Fast and Sloppy Root Finding

2010-12-04T15:21:00.001-05:00

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:

Precision and computation time sometimes don't matter all that much; and
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.

win.graph(5,4)   ## Open a new window, 5in x 4in.

## Plot the two functions
curve(x/(1+x), from=0, to=5, lwd=3, ylab="f(x), g(x)", 
                             ylim=c(0,1), cex.lab=1.5)
curve((5-x)/5, from=0, to=5, lwd=3, lty=2, add=T)

## Find their intersection the quick n' dirty way
x=seq(0,5,length=1000)
fgdiff = (x/(1+x) - (5-x)/5)^2;
j = which(fgdiff==min(fgdiff))[1]; # Only 1st, in case of 2 mins
j; x[j]

## Plot an empty circle at the intersection, and label curves.
points(x[j], x[j]/(1+x[j]), pch=21, col="black", bg="white", lwd=3, cex=1.7)
text(4.5, 0.65,  expression(f(x)==frac(x,1+x)), cex=1)
text(3,   0.15, expression(g(x)==frac(5-x,5)), cex=1)

New Rule for Science Journalism...

2010-11-27T13:17:00.001-05:00

Agreed!

[Hat tip to PZ Myers]

Happy Turkey Day!

2010-11-25T09:46:00.008-05:00

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

From Dinosaur to Turkey | NatGeo (Jump to Video, Facts)
Your Holiday Dinosaur | Berkeley's UC Museum of Paleontology
Turkey Day Science: What Do Gobblers Gobble? | USGS Western Ecological Research Center Blog
This Thanksgiving, Make a Wish on a Dinosaur | Smithosonian Blog

Sex, Life, Death and the Scientific Method

2010-11-22T12:57:00.000-05:00

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

Austad, Steven N. 2006 "Why women live longer than men: Sex differences in longevity." Gender Medicine 3(2). doi:10.1016/S1550-8579(06)80198-1

U.S. Math & Science Students Need Our Help

2010-11-17T20:37:00.001-05:00

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?

2010-11-11T23:33:00.002-05:00

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:
The term brumation is (mostly) unnecessary jargon.
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.

If you happen to call that thing that snakes do each winter "hibernating" in front of an avid snake enthusiast, what usually follows is debate over whether the proper term is hibernate or brumate. Often, the rational for using the latter is that reptiles spend the winter in a different physiological state than mammals (i.e. somewhat awake instead of unconscious) which therefore necessitates a new term to make the distinction. So where does all this come from?

Searching online journal articles for the word "brumation" leads to an article by Wilber W. Mayhew (1965) on hibernation in horned lizards (see below for references). The final point of the abstract reads...

The term brumation is proposed to indicate winter dormancy in ectothermic vertebrates that demonstrate physiological changes which are independent of body temperature.

Searching for journal articles including the word "brumation" from 1965-1975 validates Mayhew (1965) as the origin of the term, as these later references usually cite Mayhew (1968) as the source. In the final paragraph of that article, Mayhew gives is a more clear version of his intended meaning of the word (emphasis mine):

Results to date show that relatively complex physiological changes occur during or immediately preceding winter dormancy in some ectothermic vertebrates. To this extent, these animals are similar to hibernating birds and mammals. However, they differ from these heterotherms (see Cowles, 1962) in their inability to control their body temperatures. Consequently, it seems advisable to have one term to designate winter dormancy in heterotherms and another for such ectotherms. Hibernation has been used to denote this condition in heterotherms particularly, so it seems best to retain this term for that group of vertebrates. Therefore, I propose the term brumation (from bruma, L. winter) to indicate winter dormancy in ectothermic vertebrates that demonstrate physiological changes which are independent of body temperature.

Clearly the term gained footing, but from the beginning some considered Mayhew's distinctions to be unnecessary. They simply saw no real need for the new terminology, leaving those looking to keep abreast of the latest jargon wondering what they should be calling... you know... that thing reptiles do during winter.

As relevant today as they were a few decades ago, some authors were kind enough to share their concerns about this new terminology in their publications. So lets have a look at a few of these objections.

The early references I dug up simply equate the two terms. For example in Gatten (1978)...

In this paper, hibernation will be used in a broad sense to refer to the general reduction in activity in snapping turtles following cold-acclimation or cold-acclimatization. As such, it is equivalent to the term "brumation" as originated by Mayhew (1965).

The two terms were equated elsewhere (e.g. Dunham 1980, Bauwens 1981) although some took it a step further and took issue with Mayhew's original definition of the term.

One early example comes from Ultsch (1989), who basically gives the term brumation a pretty solid beatdown (emphasis mine):

There has been some concern, particularly among physiologists, about using the term ‘hibernation ’ to denote the state of ectotherms during the winter. The argument is that the term should be reserved for the state of controlled torpor typical of ‘true’ mammalian hibernators, with body temperature regulated at a low level at which the animal is torpid, and with arousal characterized by an energetically expensive and relatively rapid increase in body temperature to its normal operative range. Any other pattern, it is argued, is something other than hibernation and should be given another name. In particular, cold ectotherms, although their activity and responsiveness are often greatly reduced, are usually not torpid, their body temperature is close to or at that of their microenvironment, and they do not warm themselves endogenously during arousal. Hence a variety of other terms have been used to describe the condition of wintering ectotherms ; dormancy, cold torpidity, overwintering, and brumation (Mayhew, 1965) are among them.

Hibernation is derived from the Latin for wintering quarters, and to hibernate therefore simply means to spend the winter in sequestration ; there is no implication in the etymology about the physiological state of the animal. As such, hibernation is a general term applicable to all animals that seek a local refuge (a hibernaculum) in which to overwinter. Attempts to restrict its use to mammals may be mostly a reflection of the fact that most of the early and extensive physiological studies were done with that taxon. I see no pressing reason to develop an array of jargon concerning the physiology of overwintering. Therefore ‘hibernation’ will be used throughout this review, with the understanding that hibernation strategies vary among and within taxa. ‘Overwintering’ is viewed as a more general term that means only what animals do in passing the winter; possible strategies include remaining active, migration and hibernation.

There are two fantastic points here that deserve reiteration:

The term hibernation asserts no specifics about the physiological details of the hibernating organism.
One can use the term hibernation while recognizing that the underlying details vary among and within taxa.

Why is this important? Because in reality, there really is a lot of variation in how different organisms deal with shutting down during winter. You can read more about them here, here, here, here, here, here and here. Using the term "brumation" implies that reptiles have some special way of doing this, and that interpretation of the term runs the risk of whitewashing over a lot of that variation. That is, to some it gives the false notion that we have all the details worked out and summarized nicely by these two categories.

Here's my advice: upwards of 99% of the time you should use the term hibernate/hibernation, although if someone else uses brumate/brumation (appropriatly) you probably shouldn't bother trying to correct them. Both terms suffice to get the point across, although hibernate/hibernation makes sense to a much wider audience making it the more appropriate choice in a public forum.

References

Mayhew, Wilber W. 1965. Hibernation in the Horned Lizard, Phrynosoma m'calli. Comparative Biochemical Physiology. Vol 16, pp. 103-119. doi: 10.1016/0010-406X(65)90167-2
Gatten Jr., Robert E. 1978. Aerobic metabolism in snapping turtles, Chelydra serpentina, after thermal acclimation. Comparative Biochemistry and Physiology Part A: Physiology. 61(2), pp. 325-337. doi: 10.1016/0300-9629(78)90116-0
Dunham, Arthur E. 1980. An Experimental Study of Interspecific Competition Between the Iguanid Lizards Sceloporus Merriami and Urosaurus Ornatus. Ecological Monographs 50(3), pp. 309-330. (JSTOR)
Bauwens, Dirk. 1981. Survivorship during Hibernation in the European Common Lizard, Lacerta vivipara. Copeia 3 (Aug), pp714-744. (JSTOR)
Ultsch, Gordon R. 1989. Ecology and Physiology of Hibernation and Overwintering Among Freshwater Fishes, Turtles, and Snakes. Biological Reviews 64(4), pp. 435-515. doi:10.1111/j.1469-185X.1989.tb00683.x

Fascism, Communism and Socialism and Other Awesome Signs

2010-11-09T23:15:00.001-05:00

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

2010-11-09T20:31:00.001-05:00

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.

[Hat tip to Hemant Mehta]

Using Reptiles For Public Education, Outreach

2010-11-08T20:20:00.000-05:00

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

2010-11-02T20:22:00.001-04:00

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?

2010-11-01T23:16:00.000-04:00

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?

2010-10-31T23:34:00.001-04:00

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

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

2010-10-30T17:46:00.001-04:00

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 preserved? Let 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:

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.
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?

2010-10-30T13:14:00.000-04:00

[Hat tip to ALT and TIFR]

Talk on The Math, Physics of Drag Racing

2010-10-29T17:00:00.001-04:00

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

2010-10-24T15:08:00.008-04:00

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.

To get a feel for how this works, we first need to recognize what an image really is: just grid of pixels, each assigned a color value. The location of each pixel in the image can be described by what row and column it's in, giving the images a ready-made coordinate system for doing math. You can imagine it looking something like this, but with a smaller grid size...

[Source]

How might we move around pixels for the desired effect? First, the image is carved up into regions that will each have different rules for being twisted and stretched, with the added constraint that all the pieces fit nicely together as the image morphs. For faces, this includes finding the location and shapes of the eyes, mouth, nose, etc. in the image.

Having identified the facial features in the image, we need a define some rules for how these regions move and thereby form our transitional images. Thinking about pixels, we'd like to somehow define the curve tracing the path followed by an individual pixel (say the left eye of image 1) so that it ends up in a location that matches the correct position in the left eye in image 2. A naive way to do this is simply having pixels follow straight lines, or maybe a series of straight lines so the image preserves the integrity of certain facial features during the transitions.

The challenge then is to find a way to do this for each pixel, all at once and to do so as efficiently as possible on the computer. Having boiled down the problem to the world of straight lines, it's no big surprise which field of mathematics is going to be running the show...

Why Linear Algebra??

Once we have in mind this notion of straight lines between pixels, we can bust out the mathematical big guns: linear algebra. Why? Linear algebra is often described as the study of matrices and vectors but it's important to remember that it's all motivated by the goal of solving systems of linear equations. Often times, questions about linear equations can be answered by doing some straightforward mathematical operations, but only after reformulating those equations in the context of matrix and vector equations.

So here's how it works. Many problems can be boiled down to a system of linear equations with known outputs, known equations, but unknown inputs. Take for example, the n equations below, assuming we know the coefficients C_ij and a set of output values Y₁, Y₂, ... Y_n. Our question is often How can we solve for the corresponding input values X₁, X₂, ..., X_m that gave us these outputs?

Y1 = C11 X1 + C12 X2 + ... + C1m Xm

Y2 = C21 X1 + C22 X2 + ... + C2m Xm

...

Yn = Cn1 X1 + Cn2 X2 + ... + Cnm Xm

(Here the C_ij subscripts just indicate which equation (row) and input variable (column) they belong to.)

Solving for each X_i by hand could be quite an undertaking (especially if the number of equations n and inputs m are large), but using linear algebra, it's actually pretty easy once you know the basics.

First, we need to bring our equations into the world of matrices and vectors. Defining the output column vector Y = (Y₁, Y₂, ..., Y_n) and the input vector X = (X₁, X₂, ..., X_n) we can rewrite the above system of equations in terms of multiplication using matrix C, defined as the grid of coefficients

C11  C12  ...  C1m

C21  C22  ...  C2m

...

Cn1  Cn2  ...  Cnm

Mathematicians have of course defined what it means to multiply matrices (and vectors) so that mathematically our n equations from above are equivalent to saying that vector Y is the product of matrix C times vector X, i.e.

Y = C X

Why go through the extra work to use matrix notation? Because it makes thinking about the problem so much easier. Honest!

How easy? Suppose for a moment Y, C, and X were just single numbers, and I asked you to find X where

6 = 2 X

No doubt you'd simply divide both sides by 2 (or multiply both sides by 1/2) and get that X = 3. That's about how easy it is to solve our n equations up above using basic linear algebra.

Defining the matrix inverse appropriately, we can solve for X (assuming C has inverse C^-1) by simply finding the inverse of C and multiplying it by Y.

C^-1 Y = X

While doing so by hand isn't trivial, finding the inverse of a matrix and multiplying is easy to do on a computer. For example, in R we can find the inverse of a matrix with a single line of code...

> C=matrix(c(0.25, -0.55, -0.12, 0.16), 2, 2); C
      [,1]  [,2]
[1,]  0.25 -0.12
[2,] -0.55  0.16
> Cinv = solve(C); Cinv
           [,1]      [,2]
[1,]  -6.153846 -4.615385
[2,] -21.153846 -9.615385

Multiply by vector Y and you're done! Problem solved!

Practically, if we're doing all this on a computer with lots of equations (i.e. one for each pixel in an image) we want it to be fast and automated. Computers work very well with matrices, and as we saw above, can do everything all at once so we don't have to worry about dealing with one pixel at a time.

Conceptually, knowing some of linear algebra basics makes it's much easier to think about solving these problems using vectors and matrices rather than individual numbers and equations. Thinking about things in more abstract terms can therefore help guide our intuition for better ways to approach these kinds of problems, and guide the development of techniques that can be applied more broadly.

Moreover, we can generalize this way of looking at things to more complicated representations of linear transformations using things like tensors which likewise come in handy for challenging computational problems such as facial recognition and image manipulation.

For more on the math, you can play with interactive demonstrations of some simple rotations, contractions and expansions using matrices here, here, here, and here. Math resources include most linear algebra texts and various websites (e.g. here).

You can read more details on face morphing algorithm here and here. If you'd like to play with some images on your own, check out the Face of the Future site for some interactive demos.

[Hat tip to Hemant and the J-walk blog]

Why did NPR fire Juan Williams?

2010-10-21T21:41:00.002-04:00

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?

Here's what Williams said on the O'Reilly Factor this past Monday.

This isn't the first time Williams has had problems with comments made while appearing on Fox, as NPR President and CEO Vivian Schiller mentioned when confronted over the firing. It's this pattern of behavior that NPR claims resulted in his termination - not the single instance captured in the video above. As evidence of this history, NPR claims these problems were behind an earlier decision to change his title from `staff correspondent to `news analyst' specifically because of his record taking public positions on controversial issues.

You can read the latest details straight from NPR from their blog The Two-Way in posts here and here, and from links off of the NPR main page.

How many species concepts are there?

2010-10-21T11:00:00.000-04:00

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?"

2010-10-20T17:50:00.002-04:00

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

2010-10-20T11:39:00.004-04:00

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.

First, the bible story from Exodus 14:21-22 KJV (emphasis mine):

And Moses stretched out his hand over the sea; and the LORD caused the sea to go back by a strong east wind all that night, and made the sea dry land, and the waters were divided.
And the children of Israel went into the midst of the sea upon the dry ground: and the waters were a wall unto them on their right hand, and on their left.

The results of the paper strike me as having little to do with Moses parting the Red Sea. Science aside, why do we need to even bother with a natural explanation for all this? Are we to think Moses just got lucky? Wasn't there some kind of divine intervention, not just a wind storm?

Moving onto the the PLoS paper...

Conclusions/Significance
Under a uniform 28 m/s easterly wind forcing in the reconstructed model basin, the ocean model produces an area of exposed mud flats where the river mouth opens into the lake. This land bridge is 3–4 km long and 5 km wide, and it remains open for 4 hours. Model results indicate that navigation in shallow-water harbors can be significantly curtailed by wind setdown when strong winds blow offshore.

A land bridge 5km wide for only 4 hours seems inconsistent with the bible story for a few reasons, but lets first take a look at the simulation and hear what author Carl Drews has to say about it (via the NCAR youtube channel).

Drews asserts that "What this study shows is that the description of the waters parting indeed has a basis in physical laws" and from the video above it seems he's quite eager to do so. I disagree with his statement, and here's why. First, just because a story is consistent with physics doesn't make it true. This is where Drews starts to seem like he doesn't quite get how science works. While we can disprove the story if we demonstrate it is inconsistent with physical laws, weakly demonstrating congruence with physics doesn't in any way make a story true. Plausible? Maybe. But confirmed? Not quite.

As I see it, Drews has actually cast doubt on the story by ruling out a wind set-down as a plausible mechanism for parting the waters as described in the story. His results seem inconsistent with the story in two ways: (1) they give no expectation of dry land, just mudflats; and (2) they give no walls of water. Without completely rewriting the story, these strike me as significant problems. First, it seems impossible for those winds to dry out the thick layer of muck at the bottom of that shallow lagoon. The bible mentions crossing dry land, not wading through a few feet of muck. Second, the simulations suggest the shoreline was pushed quite far away, multiple kilometers away actually, so no walls of water would be seen by Moses or the others.

That said, I think it's irresponsible of NPR (and Keim) to omit the author's rather significant conflict of interest, which was clearly stated in the PLoS paper...

Competing interests: The lead author has a web site, theistic-evolution.com, that addresses Christian faith and biological evolution.

Following that URL, we discover that his website does quite a bit more than just address the "Christian faith and biological evolution." As stated the first page (emphasis mine)…

Goals
The most important goal of this web site is that you will come to know Jesus Christ if you do not know Him already, and that believing in Him you will have salvation and eternal life.
The second most important goal is that you will Test Everything! I hope that you will be instructed and inspired to check and verify everything that you hear or read. There is not enough checking going on in the study of creationism and evolution. If you are a Christian, you should test everything because the Bible tells you to in 1 Thessalonians 5:21. If you are not a Christian, you should do it because you don’t want to be deceived by false teaching.

The lead author seems to have less personal interest in upholding good science than he does spreading Christianity. That is relevant and worth mentioning, which is why the PLoS article mentioned it. Might this be driving or coloring his interpretation of his own work? Perhaps someone has a pet hypothesis they'd like to see hold true?

So it seems Drews is really is just rationalizing his religious beliefs here, and not doing proper science. From the NPR piece:

While many researchers use science to disprove literal accounts the Bible, Drews looks at scientific evidence that supports biblical events. “I think my account matches the biblical account pretty closely,” he says.

Hmmm... That first sentence is quite telling. You see, intentions should be irrelevant - Drews is either following the evidence (aka, doing good science) or he isn't (aka bad science). More evidence that he's looking to confirm a story then follows...

Although, Drews admits, he cannot be 100 percent sure until someone actually finds pieces of a chariot in the area.

Science doesn't work that way. Drews really seems like he's rationalizing now... Chariot pieces only say there was once a chariot there. Not precisely when it was there, not what it was doing there (e.g. was it chasing Moses?), not how it got there (might it have fallen off of a boat). Finding pieces of a chariot in the area would likely have little to no impact on confirming or refuting the Moses story, and certainly shouldn't result in anyone's "100 percent" certainty, one way or the other.

Using this work, we can at best disprove that Moses and his followers crossed at this location during a wind setdown as detailed in the Bible. Whether it's at all possible hinges upon a number of other details Drews has yet to address: How long does it take to walk through deep mud for 3-4km in a "63 mph wind — a medium-strength tropical storm"? Could that mud have dried out in 4 hours? How quickly would the returning waters have reached any Egyptians following them? How deep would they be?

It's quite plausible that Drews is using bad science to rationalize religious dogma. It's unfortunate that little fact was hardly mentioned by the mainstream media.

References:

Drews C, Han W (2010) Dynamics of Wind Setdown at Suez and the Eastern Nile Delta. PLoS ONE 5(8): e12481. doi:10.1371/journal.pone.0012481

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

2010-10-17T17:56:00.002-04:00

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

2010-10-16T12:25:00.002-04:00

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?

2010-10-15T12:04:00.000-04:00

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.

What I took issue with was the interpretation of the data below (Figure 1) as evidence of a rise in perinatal mortality among home births. Early in the post, Tuteur's one-line take-home-message was that...

The death toll of homebirth in Colorado is enormous and RISING!

To be clear, that's two claims: 1) these numbers are enormous, and 2) these numbers are rising. Clearly the first point is the one we should all be concerned about, not the second which is my focus here. For more details, do read Tuteur's post over at the Skeptical OB and her other posts for links to more data.

So what does the data say?

Figure 1: Compiled by Tuteur from here and similar sources. Note these are women seeing midwives prior to birth. For example, according to Tuteur the 799 in 2009 comes from "the 639 women who received midwifery care exclusively + the 160 women transferred to the hospital either before or after labor began."

So are those numbers rising?

Figure 2: The perinatal mortality rates from above, produced by the script below.

Clearly it looks like they are, but how should we interpret them? The answer depends on the question, and here we're interested in primarily one thing: risk. So is this evidence of increasing risk? To answer that, lets compare whether or not this apparent increase is real or perhaps just due to "random chance." We can do this quite easily in R (see the script at the bottom of this post) to see if these numbers look statistically different from one another using the chi-squared test chisq.test()in R.

To do a two-group comparison, we can compare totals for the first two years with the totals for the last two years. Doing so gives...

Pearson's Chi-squared test with Yates' continuity correction

X-squared = 0.2729, df = 1, p-value = 0.6014

Comparing each of the four years separately gives

Pearson's Chi-squared test

X-squared = 0.8375, df = 3, p-value = 0.8405

So what does it all mean? We interpret the p-values as the probability that we would see these kinds of differences from chance alone. That is, in both cases it seems a little bit more likely than not that this apparent trend is really just "random chance." Typically we want p-values much closer to zero to rule out chance alone, therefore (statistically) there is no clear increase in perinatal mortality rates.

Importantly, this is all based upon (1) just these data and (2) just the chi-squared test. Furthermore "no evidence for an increase" is a different claim than "there is no increase" -- so more data or a better statistical analysis might give a different result. For example, this is a time series and not four independent groups so focusing on their increasing order would require a somewhat different approach. All that said, these large p-values make me doubt a more appropriate statistical test would give any meaningfully different results for these data.

The take home message here is that having data like these available allows the public to answer some of these very important questions. Data like these belong in the public arena and organizations like MANA (Midwives Alliance of North America) should be quick to share it instead of keeping it from the public and their critics (as seems to be the case).

R Code:

# Colorado Licensed Homebirth Midwives  
# Year, Patients at the start of labor (N), Perinatal Deaths (PD)  
Year=c(2006,2007,2008,2009);  
N = c(642, 696, 806, 799);  
PD = c(5,5,7,9);  
 
# Lump into two groups  
Yr = c(sum(Year[1:2]),sum(Year[3:4]))/2;  
n = c(sum(N[1:2]),sum(N[3:4]));  
pd = c(sum(PD[1:2]),sum(PD[3:4]));  
 
# Compute perinatal mortality rate.  
pd/n; # for each group, or  
mean(pmr); # lumped together.  
 
# Simple Chi-squared with continuity correction (by default in R) 
# p near 0 means statistically different, p near 1 means not.  
chisq.test(rbind(n-pd,pd)); #  <-- corrected version. 
chisq.test(rbind(N-PD,PD)); #  <-- corrected version. 

# For details of the chisq.test() function, see...
?chisq.test ## the help file or this link.
 
# Plot the data  
plot(Year, PD/N*1000, pch=19, cex=2, cex.lab=1.4,  
ylim=c(0,15), ylab="Perinatal Deaths per 1000 (CO)");

Templeton Foundation Talk Tomorrow in Columbus

2010-10-12T17:55:00.001-04:00

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.

I should first say a thing or two about my motivations for writing this post. I'm always wary that discussions like these (where both parties are funded by an organization like the JTF) might sacrifice an honest presentation of the science in order to not offend their largely religious audience. Such "less than honest" representations of the science aren't fair to the audience and shouldn't go unrecognized. Furthermore, religious claims about the natural world are not immune from scientific falsification. You can't do good science - or support good science - unless you are willing to call an idea false if that's where the evidence leads you.

Because the goal of the JTF's is to bring together science and religion, they deserve considerable scrutiny from the scientific community to ensure their efforts never undermine good science or good science education. So towards that goal of keeping them honest about the science, I decided to share a little about the JTF, the speakers' past involvement in the "science vs. religion" debate, and whether or not they've ever made (or repeatedly made) any big mistakes that might make one question their motives.

The John Templeton Foundation is an organization whose mission includes funding...

research on subjects ranging from complexity, evolution, and infinity to creativity, forgiveness, love, and free will.

Uh, "infinity"? Clearly this isn't a heavily science- or math-based organization. This becomes more clear when they go on to describe that their vision...

is derived from the late Sir John Templeton's optimism about the possibility of acquiring “new spiritual information” and from his commitment to rigorous scientific research and related scholarship.

While the Templeton Foundation seems far from the ranks of anti-science religious organizations like the Discovery Institute, they to me have every appearance of being more pro-religion than pro-science. They also seem keen to use science to somehow rationalize religious/supernatural beliefs while trying to avoid subjecting such beliefs to scientific falsification (where possible).

The emphasis on religion - and not science - is apparent elsewhere. For example, the Templeton Prize they award annually has the stated purpose of honoring individuals who have (emphasis mine)

made an exceptional contribution to affirming life's spiritual dimension, whether through insight, discovery, or practical works... outstanding individuals who have devoted their talents to expanding our vision of human purpose and ultimate reality. The Prize celebrates no particular faith tradition or notion of God, but rather the quest for progress in humanity's efforts to comprehend the many and diverse manifestations of the Divine.

Also note the implicit assumption of a monotheistic religion (I'm sure you can guess which one) behind that last statement.

For more on the JTF, you read a bit of criticism here, and here. On to the speakers...

Andrew Newberg is an MD who has received funding from the JTF to explore the neurophysiology of spirituality and religious experiences. By his own account, he - like many Americans - seems (1) to be a spiritual person unaffiliated with any particular religion, and (2) he seems quite hesitant to say anything bad about the religious beliefs of others (both in general, and in particular).

While his beliefs may be none of my business personally, as a scientist, doctor and public speaker his supernatural beliefs do have relevance if they inappropriately color his medical and scientific work. PZ Myers criticized Newberg back in 2006 (here) for overreaching in his interpretations of some brain imaging data, and others have leveled similar criticism at Newberg (e.g. here, and here) for letting his spiritual beliefs creep into his work.

You can get a better sense of Newberg by watching the interviews here (part I, part II), here and here.

Nicholas Wade is a science journalist who often writes about religion. He has also received funding from the Templeton Foundation. His popular book 'The Faith Instinct' received a fair bit of criticism for sloppy application of genetics and evolution, and for focusing on the alleged benefits of faith while largely ignoring the many problems attributed to faith (see the reviews below).

Wade seems to side with one of two main camps in the "evolution of religion" world. The first (Wade's) thinks that religious belief is a trait that we've evolved because it has been selected for. The second thinks it's more a by product of other evolved traits (e.g. those having to do us with being highly social, intelligent, advanced communicators) and not something with any real fitness value.

For some criticisms of Wade, Sam Harris takes him to task for botching his reasoning for holding the above view here. Wade seems to have gotten his philosophy wrong (also see here) while mincing words with Dawkins in his review of Dawkins' latest book , and has received broader criticism for being a bit too friendly to the anti-evolution crowd. Wade was interviewed by Stephen Colbert here (note his non-response to Colbert's cracks at young-earth creationism) and there's an interview with him in the American Scientist here.

Overall, it should be an interesting discussion. My impression of these two is that Wade is less likely to misinterpret (or otherwise botch) the science, whereas Newberg seems more inclined to package the science in a way that won't offend anyone's spiritual beliefs - even if it should, and even if it means twisting or omitting parts of the science. Neither strikes me as likely to champion a position that is critical of the assumption that spirits, god, etc. actually exist.

So what will I be looking for from the talks? First, I'm eager to learn something more about neurophysiology during religious experiences (though I'd prefer hearing it from a less biased source than Newberg). Second, I'll of course be looking for an honest representation of the relevant science with as few personal religious beliefs coloring the discussion as possible.

Science is all about using evidence and logic to rule out untrue ideas, leaving our best understanding of all the facts on the table for further scrutiny. Whether or not religion is in our genes - it's possible (even likely?) that it only exists in our heads. Hopefully that fact doesn't get brushed under the table.

Resources & Links:

Carolyn See. 2009 Book Review: 'The Faith Instinct' by Nicholas Wade. Washington Post.
Rhazib Khan. 2009. The Faith Instinct: How Religion Evolved and Why It Endures. Gene Expression (Discover Blog).
Khan and Wade on Bloggingheads.tv can be seen here.
A less critical review of Wade's book, The Faith Instinct., in the NY Times: The God Gene.
The John Templeton Foundation (official website, Wikipedia)
The Templeton Foundation - A Skeptic's Take by John Horgan.
Andrew Newberg's website.
Nicholas Wade's website.

Free Online Math Books?

2010-10-05T19:48:00.000-04:00

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?

2010-10-01T14:19:00.003-04:00

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)

2010-10-01T10:35:00.002-04:00

[via WEIT]

More music you¹ can do math to...

2010-09-29T18:50:00.007-04:00

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

2010-09-28T19:09:00.000-04:00

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...

2010-09-27T00:15:00.006-04:00

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"?

2010-09-23T18:11:00.001-04:00

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

2010-09-21T19:18:00.000-04:00

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

2010-09-20T16:51:00.001-04:00

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:

Dembski's juvenile attempt to anonymously thumb his nose at Judge Jones and others @ 1:20
Talk begins @ 4:14
Trojan Horse defined/discussed @ 5:30
Intelligent Design as a Trojan Horse @ 6:00
Dover Trial details begin around 7:50
Who's Who of the Discovery Institute: Center for the Renewal of Science & Culture @ 9:49
Their infamous Wedge Strategy (and Wedge Document) @ 11:45
Trial details begin around 13:30
More from Dembski starting @ 14:00 (followed by more shenanigans from the Disco'Tute)
Expert witnesses on the side of science (plaintiffs) @ 17:50
Summary of lessons learned from the trial are in a nice book (see resource links below) @ 18:28
Plaintiff's attorneys @ 18:43
Expert witnesses on the side of intelligent design creationism (defendants) including those who backed out @18:55
Dr. Forrest describes her role in the trial @ 20:50 (followed by a nice summary of "ID = christian creationism")
The evolution of the creationist-turned-ID text, Of Pandas and People @ 29:45
The origin of that accidental term, cdesign proponentsists @ 33:00
Cost of the Dover trial (including Dembski's $20K "for not showing up") @ 35:45
1982 source of "Complex specified information"; 1982 precursor to "Irreducible Complexity" @ 37:30
Behe continues on after the trial, his book, etc. @ 39:00
Key terms/phrases used by ID proponents - things to look out for @ 39:25
The new replacement creationist text? Explore Evolution @ 41:00
Nice book list of additional reading on the Creationism vs. Evolution conflict @ 42:34
Did you know Dembski helped A. Coulter write ID chapters in 'Godless'? @ 44:06
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

Scott, E. C., Branch, G. 2006. Not in our classroom: Why Intelligent Design is Wrong for Our Schools. http://ncse.com/nioc (purchase here).
Trial Documents from Kitzmiller vs. Dover available here on the NCSE website.
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

2010-09-17T12:39:00.007-04:00

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...

Native only to some of the cooler islands of New Zealand, the long lived tuatara are rather unique among reptiles as contrary to their looks, they are NOT lizards. Why? Lizards belong to the order Squamata, along with snakes, which is one of the four orders in the class Reptilia: Squamata, Testudines (turtles, tortoises), Crocodilia, and the order containing only 1 surviving genus, Sphenodontia - the Tuataras. That is, snakes and lizards are more closely related to one another than are any of them to the tuatara.

The evolutionary relationships between squamates and tuataras looks something like the cladogram to the right. The numbers and icons correspond to

Tuatara, order Sphenodontia.
Lizards along with...
Snakes form the order Squamata.
Order Crocodilia
Birds form the classical class Aves, though clearly that status is becoming dated.

In the wild, tuatara are considered threatened and some populations may have already been lost. The primary threat comes from introduced rats, which on some islands have been eradicated(!) specifically to protect local tuatara populations.

The short film Love in Cold Blood (official website), by Carla Braun-Elwert and Jane Adcroft, is part of the 2010 Reel Earth film festival and retells the story of how a tuatara named Henry (age 111-ish) came to hook up with a Ms. Mildred (age 80-ish) in a small zoo in New Zealand. To watch this low resolution version, use the password tuatara.

Love in Cold Blood from Love in Cold Blood on Vimeo.

Post Script: Ok, so this awesome little film got me thinking -- how do they know the age of these two tuataras? After all, Henry was wild caught only a few decades ago!

According to this article, a few Tuatara were individually marked in 1957 and their growth tracked over subsequent years. Since then, the current age guesstimates appear to be based on size and growth rates but (as above) come unaccompanied by any confidence intervals or other information indicating how certain we are of those age estimates.

I'm tempted to dig into the article for details, but for now I'm going to force myself to let it go and get back to thesis writing! ;)

Bed Bugs!

2010-09-17T11:35:00.000-04:00

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

2010-09-14T17:47:00.001-04:00

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...

2010-09-13T23:44:00.002-04:00

R Tip: Listing Loaded Packages

2010-09-13T14:22:00.000-04:00

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!!!

2010-09-12T22:40:00.005-04:00

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

2010-09-11T01:14:00.002-04:00

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!

2010-09-08T01:22:00.001-04:00

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 Richard Hoppe from Panda's Thumb.

Second, Tara's talk was awesome. I think everyone learned something new and valuable - myself included - and had a great time to boot.

Third, following the talk the organizer Dan Siegal-Gaskins moderated discussions between audience members and the speaker. Topics included the peer review process, how science gets communicated among scientists, the role of social networks and other digital media in communicating science, the dangers of being a science advocate (yes, they exist!), and challenges of confronting emotionally driven beliefs that run contrary to sound science.

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

2010-08-24T22:20:00.002-04:00

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)

2010-08-24T02:01:00.002-04:00

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)...

[An injunction] should be granted only when the party seeking the relief... carries the burden of persuasion... A party carries this burden of persuasion by establishing: (1) that there is a substantial likelihood of success on the merits; (2) that the plaintiff would suffer irreparable injury absent an injunction; (3) that an injunction would not substantially injure other interested parties; and (4) that an injunction would further public interest.

Criteria (2) and (3) seem like a hard sell in this case. Cutting off research funding is a HUGE deal, and it's hardly obvioius how these plaintiffs are suffering irreparable injury without the injunction. Regarding (4), it's also far from clear this injunction furthers "public interest." And what about prolonging the discovery of new medical treatments that may result from ESC research? How is this in the public interest? Lets see what the judge has to say about meeting these criteria.

(2) Irreparable injury to the plaintiffs?

The argument for this second criteria is almost hilarious it's so wrong. The judge bought into the idea that some of the plaintiffs would suffer irreparable injury without the injunction because ESC researchers outcompete them for funding...

Plaintiffs are researchers who work exclusively with ASCs. They seek funds for their research projects from defendants and allege “that obtaining NIH funding is necessary for their continued research.” ... The Guidelines, by allowing federal funding of ESC research, increases competition for NIH’s limited resources. This increased competition for limited funds is an actual, imminent injury.

Is this guy serious? Clearly he doesn't get how research funding works, and this argument smells of a false dichotomy. If the plaintiffs can't get grant money, it could also be because their applications are sub-par, because they have a lot of competition from other ASC researchers or because researchers in other biomedical fields are getting all the funding. Arguing that NIH funding is competitive and therefore injurious to the plaintiffs is simply absurd.

As you'll see below, the judge goes on to contradicts himself here by saying that ECS researchers won't be harmed by an injunction blocking them from NIH funding, because they still have access to private funding. So ESC researchers are more competitive for NIH funds, and that's injurious to the plaintiffs... but prohibiting ESC entirely from even joining the competition is somehow not injurious to them??

While we're at it - who are these ASC researchers among the plaintiffs? They appear to be James L. Sherley and Theresa Deisher.

James L. Sherley went on a hunger strike when he was denied tenure at MIT in 2006 citing racial discrimination as the cause of his tenure denial. He's currently a senior scientist at Boston Biomedical Research Institute.

Theresa Deisher doesn't appear to currently be doing research. She's the R&D Director for AVM Biotechology: a self-described "pro-life" organization that looks like it hasn't produced any real science... ever. Their "Research" page is laughable: a pretty unscientific list of three "websites" next to three links to journal articles -- none of which mention AVM Biotechnology and none of which appear to have anything to do with them. She's also President of the Sound Choice Pharmaceutical Institute which is also a pro-life organization that seems to do zero basic medical or biotech research... at least not yet.

Anyway, on to consideration of what an injunction would mean for the defendants...

(3) Not substantially injurious to the defendants?

Here's what the judge had to say in his ruling...

The balance of hardships weighs in favor of an injunction.

Um, why?

Defendants argue that two interested parties would be injured if the Court issues an injunction: ESC researchers and individuals who suffer from diseases that may be treatable in the future as a result of ESC research.

Yes, the "interested parties" are the researchers who would lose even the opportunity to compete for NIH funds, and the many sick individuals who wouldn't recieve whatever medial treatments are waiting to be discovered by continued ESC research. So what does the judge think about their situation?

The injunction, however, would not seriously harm ESC researchers because the injunction would simply preserve the status quo and would not interfere with their ability to obtain private funding for their research.

Um... WHAT!? Here the judge appears to be contradicting the argument given in criteria (2) above, saying that ECS researchers don't really need NIH funds, while ASC researchers do.

As for the suffering among us...

In addition, the harm to individuals who suffer from diseases that one day may be treatable as a result of ESC research is speculative.

In his own ruling the judge states that "Recent studies... suggest that ESCs will contribute to the development of medical knowledge in the future" and he clearly lays out the great potential embryonic stem cell research holds for future medical advancements. Where this dismissal comes from is beyond me.

Embryonic Stem Cell Research Halted... AGAIN

2010-08-24T01:03:00.005-04:00

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...

SEC. 509.
None of the funds made available in this Act may be used for—
the creation of a human embryo or embryos for research purposes; or
research in which a human embryo or embryos are destroyed, discarded, or knowingly subjected to risk of injury or death greater than that allowed for research on fetuses in utero under 45 CFR 46.204(b) and section 498(b) of the Public Health Service Act (42 U.S.C. 289g(b)).
For purposes of this section, the term ‘‘human embryo or embryos’’ includes any organism, not protected as a human subject under 45 CFR 46 as of the date of the enactment of this Act, that is derived by fertilization, parthenogenesis, cloning, or any other means from one or more human gametes or human diploid cells.

Note I've emphasized a single word here "research" which the judge has defined as "a systematic investigation, including research development, testing and evaluation, designed to develop or contribute to generalizable knowledge." To me this seems unbelievably vague, but without much justification the judge finds it "unambiguous." Again, I'm no legal expert so I might be missing something, but I suspect this will be a key issue in the appeal.

Crucial to the case (as recognized by the judge) is the established distinction between the acts of (1) deriving stem cells from embryos, and (2) doing research on cell lines previously derived from embryos. Mind you that both of these things are legal, it's just that federal funds can only be used to perform the latter under previous interpretations of the law above... until today.

Today, judge Lamberth decided that this separation is invalid. He asserts that...

...the language of the statute reflects the unambiguous intent of Congress to enact a broad prohibition of funding research in which a human embryo is destroyed.

He goes on to then argue that the Dicky-Wicker language actually prohibits the whole research process...

This prohibition encompasses all “research in which” an embryo is destroyed, not just the “pieceof research” in which the embryo is destroyed. Had Congress intended to limit the Dickey-Wicker to only those discrete acts that result in the destruction of an embryo, like the derivation of ESCs, or to research on the embryo itself, Congress could have written the statute that way. Congress, however, has not written the statute that way, and this Court is bound to apply the law as it is written.

He reiterates...

Having concluded that the Dickey-Wicker Amendment is unambiguous, the question before the Court is whether ESC research is research in which a human embryo is destroyed. The Court concludes that it is.

I think the judge is flat wrong, but hey - I'm not the judge, so we'll see what the legal analysts and the appeals court says about it.

The Internet = iDistraction™

2010-08-18T14:38:00.000-04:00

That's all. I should get back to work now.

Philosophy of Science

2010-08-17T23:01:00.000-04:00

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)

2010-08-16T12:44:00.002-04:00

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

2010-08-15T11:54:00.001-04:00

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

[via C0nc0rdence]

Warning!!!

2010-08-14T14:27:00.002-04:00

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"?

2010-08-13T13:26:00.001-04:00

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]

Perseid Meteor Shower Tonight! (Aug 12-13)

2010-08-12T11:10:00.000-04:00

Get outside with friends and family after dark, and check it out!

More details can be found here, here and here.

Creation Museum is Craptastic!

2010-08-11T20:11:00.000-04:00

Australian travel writer Ben Groundwater has included in his list of The world's most craptastic tourist attractions the Creation "Museum" just outside of Cincinnati, Ohio near Petersburg, Kentucky.

Here's why he thinks the place so craptastic...

The Creation Museum, Kentucky

Well, it was hardly going to be in Oregon, was it? Here, true believers can learn about how the Earth was formed by the big man upstairs, who manages to explain away such potential roadblocks as dinosaurs, billion-year-old fossils, and that whole science thing with room after room of ultra-religious tackiness. There’s actually been a lot of money poured into this, and it’s anything but half-arsed. Misguided, maybe – but not half-arsed.

My two cents on the Creation Museum (and a few more photos) are available here.

[Thanks to PZ Myers for sharing]

Monday (Tuesday?) Mammal #13: Sugar Glider

2010-08-10T12:28:00.001-04:00

It's Tuesday - I know, I know - but I had a bit of work to do, so this week's mammal is coming at you a day late. Fortunately, it's insanely cute and following last week's theme it's another marsupial. So I'm sure you won't mind the delay, right?

Meet, the sugar glider (Petaurus breviceps) - one of six species of marsupial "wrist-winged" gliders native to Australia and New Guinea.

And yes, like most mammals you'll no doubt find them extra cute when they're itty little balls of fluff...

Bishop Goes After Gay Marriage on CNN

2010-08-08T14:55:00.003-04:00

There's a somewhat bigoted opinion piece up on CNN.com, by Bishop Harry R. Jackson Jr. entitled Same-sex marriage will hurt families, society. In it, he tries to justify this claim but - not surprisingly - he fails miserably. While I have not doubts that the Bishop is operating under good intentions, I can't help but think he might be doing little more here than rationalizing his disapproval of same-sex couples under the false impression that he's looking out for the public good. Below is my take on his arguments.

Before I get into details, there are three things I need to make clear.

Gay marriage is a civil rights issue - just look up the definition of "civil rights". It's about whether or not the state can discriminate against two individuals seeking to get married, based on gender.
The Bishop is talking about legally recognized marriages (not marriages recognized by his Church) so his words need apply to all marriages in the U.S., not just those accepted by Christian religions.
In evaluating his arguments I want you to also imagine some racist community leader (ca. the mid-1900s) speaking out against inter-racial marriage. Why? Because a great way to check the validity of an argument is to see how it generalizes and applies to similar cases with different moral overtones. It highlights biases one might otherwise miss. I suggest this particular example because there are many parallels between bans on inter-racial marriage and bans on same-sex marriage (although there are some differences). Additionally, it's almost shocking how hard the bishop works to try and separate the issue of gay-rights from the issue of racial equality in the U.S. Frankly, I think that makes him look prejudiced, groping to justify his own personal feelings towards homosexuals. So there's my bias, for what it's worth.

Now, on to his arguments...

Failure #1: Speaking about the recent court ruling against the anti-gay-marriage legislation Proposition 8, he writes

The majority of Californians, including two-thirds of the state's black voters, have just had their core civil right -- the right to vote -- stripped from them by an openly gay federal judge who has misread history and the Constitution to impose his views on the state's people.

Nobody's right to vote was "stripped" - they voted - that vote was just deemed unconstitutional based on our core principles of equal treatment under the law. We live in a representative republic, not a pure democracy, and our Constitution provides a foundation to ensure individual liberties are not infringed upon, even by a majority vote. Making the race comparison, if most Americans voted to reinstate slavery our existing legal system would rightfully prevent that from going into effect.

Failure #2: Skipping over his attempt to pretend "opposition to same-sex marriage ... is not bigotry", he tries to then claim that

...it is biology that discriminates between same-sex couples and opposite-sex couples... A marriage requires a husband and a wife, because these unions are necessary to make new life and connect children to their mother and father.

Huh? No, their biology is such that they've decided to pair off and get hitched. Can they have children? No, not together. Does that matter? Hell no. If it did, then having children or being likely to have children in the near future would be a requirement for getting a marriage license. It isn't. This argument (like most of his arguments) is old, well-refuted, and implies a lot of repugnant things like the idea that married couples who can't or choose not to conceive a child are somehow unfit to be married.

Failure #3: This one is almost beautiful it's so horribly wrong - a grand wizard of the KKK couldn't have said it better (that is, having swapped "same-sex" with "inter-racial" and "man-woman" with "same-race"):

Advocates of making same-sex marriage a legally recognized right claim that this will have no impact on traditional marriage -- that it can peacefully coexist alongside traditional marriage. On the contrary, it will have profound impacts. It will create a conflict for people of faith (and nonreligious people as well) who fervently believe in traditional man-woman marriage and the law.

That's right - the Bishop is arguing that "it will bother people, so it should be illegal." Again, his reasoning is just plain wrong here, and it's starting to become clear why he works to try and separate same-sex and inter-racial marriages: His arguments for opposing the former unfortunately works equally well to oppose the latter. At any rate, this argument strikes me as simultaneously naive and repugnant.

Failure #4: He then goes on to throw bible quotes at the issue... (sigh). Ok, again, plenty of bible versus have been used to justify opposition to inter-racial marriage. But importantly, why should bible versus matter? If he were talking about marriage in the Church, I'd have no problems here - he's a Bishop. But for religiously-neutral legal issues!? Should we not also then consult the Koran? The Torah? All of the other religion-based moral traditions practiced in the U.S., as well as the Humanist and other non-religious positions to see what they all have to say about gay marriage?

Here I'll defer to our Constitution - particularly the first amendment in our Bill of Rights - which says we should instead keep a healthy separation between religion and law. Bible passages have no special merit unless they stand on their own away from any claims of Divine authority. That said, the Bishop gives us nothing of substance here.

Failure #5: He next offers an appeal to emotion, voicing his concern about how civil recognition of same-sex marriages might harm children. Notice how there's no solid evidence backing up his concern? That's because nearly all studies (of which I'm admittedly not all that familiar) seem to show that growing up in a same sex household has no negative impact on children. This seems to be the consensus among folks with expertise in the relevant fields, and whose job it is to make such determinations. So the Bishop is either unaware of or ignoring the reality of this matter.

Failure #6: These next few points are particularly worthy of some ridicule. Basically, the Bishop seems to suggest that same-sex marriage is a bad thing, because it'll will prevent those who provide basic services from doing so, if they aren't allowed to discriminate against gay couples. Think again of applying this argument to inter-racial marriages. It's nonsense bordering on offensive, in my opinion.

Failures #7 and #8: He continues with the appeal to emotion mentioned above, by repeatedly questioning how same-sex marriage will impact children. This one actually made me laugh out loud and is worth a second look (emphasis mine):

...repeatedly, scholarly studies focused on adolescence show that early onset of puberty in girls is associated with negative psychological, social, and health problems including depression, alcohol consumption, and higher teenage pregnancy. An eight-year study of girls and their families showed that a father's presence in the home, with appropriate involvement in his children's lives, contributed to daughters' reaching puberty at a later age.

Here he's suggesting that we need households with involved father figures because (1) this will delay the onset of puberty for female children in the household, and therefore (2) this will reduce their chances of developing problems with depression, alcohol consumption and teenage pregnancies.

Now, I think this argument is crap because I suspect this may be a case where "correlation does not imply causation", but even if it were true, the Bishop is making an equally valid argument for married gay men to adopt daughters! This double-whammy earns the Bishop two Failures.

Despite the fact that he appears to be so demonstrably wrong, I'll reiterate that I have not doubts that the Bishop is operating under the best of intentions - I just think he's totally wrong an almost all of the points he lays out in the article, and these aren't just differences of opinion. I do however sort of agree with his closing points if we ignore their context and make a minor edit or two (emphasis and deletions are of course mine):

...our entire culture should advocate for family structures that promote the most positive environments for coming generations... leaders from all sectors of our culture, including our churches, must work hard at improving ~~heterosexual~~ [all] marriages.

In the end, if you'd like to support families, support kids and support couples looking to improve their relationships, go for it. But please, try and do so by working to implement proven solutions to specific problems -- problems we all can agree are actually real, and are having a significant impact on society. Otherwise, anyone looking to rationalize their biases by inventing new problems are strongly encouraged to keep their opinions to themselves, and find something more productive to do with their time.

Women in Mathematics

2010-08-08T09:24:00.001-04:00

[via S.C. Kavassalis, Bora on Twitter]

Benjamin Franklin on Wine, God, and Elbows

2010-08-08T00:15:00.002-04:00

Did you ever wonder if our founding fathers had a sense of humor? Well they did, and here's some evidence to prove that at least Benjamin Franklin knew how to get his drink on.

This story begins when a friend of mine posted this quote on facebook the other day:

"Wine is constant proof that God loves us and loves to see us happy." -- Benjamin Franklin

Curious as always, I decided to see (1) if this was really a quote by Franklin, and (2) if so, what the context was. Franklin was neither a devout Christian, agnostic or atheist so I suspected it would be interesting.

Before I get into Franklin's awesome drawings, the quote comes from a letter he wrote in 1787 to the Abbé André Morellet -- a friend of Franklin and member of the French Academy-- as a tongue-in-cheek response to Morellet. Previously, Morellet wrote a drinking song in honor of Franklin (awesome) and in it he joked that Franklin instigated the American Revolution just to replace English tea with the French wines he was so fond of (again, awesome).

You can read the letter in English here, or the original French version here with another English translation.

Here's where it gets entertaining: the original letter includes figures drawn by Franklin, illustrating how the elbow was further evidence that God wanted us to drink win... but nowhere could I find the figures! Most internet copies of the letter omit them, and in many cases they've even removed the references to the figures entirely (gasp!). So here's the post script, with figure references entact...

In French:

P.S. Pour vous confirmer encore plus dans votre piété et reconnaissance à la providence divine, réfléchissez sur la situation qu’elle a donnée au coude. Vous voyez, figures 1 et 2, que les animaux qui doivent boire l’eau qui coule sur la terre, s’ils ont des jambes longues, ont aussi un cou long, afin qu’ils puissent atteindre leur boisson sans la peine de se mettre à genoux. Mais l’homme, qui était destiné à boire du vin, doit être en état de porter le verre à sa bouche. Regardez les figures ci-dessous: si le coude avait été placé plus près de la main, comme en fig. 3, la partie A aurait été trop courte pour approcher le verre de la bouche; et s’il avait été placé plus près de l’épaule, comme en fig. 4, la partie B aurait été si longue, qu’il eût porté le verre bien au delà de la bouche: ainsi nous aurions été tantalisés. Mais par la présente situation, représentée fig. 5, nous voilà en état de boire à notre aise, le verre venant justement à la bouche. Adorons donc, le verre à la main, cette sagesse bienveillante; adorons et buvons.

In English (source) this reads something like:

P.S. To confirm still more your piety and gratitude to Divine Providence, reflect upon the situation which it has given to the _elbow._ You see (Figures 1 and 2) in animals, who are intended to drink the waters that flow upon the earth, that if they have long legs, they have also a long neck, so that they can get at their drink without kneeling down. But man, who was destined to drink wine, must be able to raise the glass to his mouth. If the elbow had been placed nearer the hand (as in Figure 3), the part in advance would have been too short to bring the glass up to the mouth; and if it had been placed nearer the shoulder, (as in Figure 4) that part would have been so long that it would have carried the wine far beyond the mouth. But by the actual situation, (represented in Figure 5), we are enabled to drink at our ease, the glass going exactly to the mouth. Let us, then, with glass in hand, adore this benevolent wisdom; -- let us adore and drink!

That's right - Ben Franklin took the time to draw 5 pictures illustrating how awesome elbows are, because they allow us to drink wine.

After a bit of searching found them here, in Morellet's biography Mémoires inédits de l'abbé Morellet sur le dix-huitième siècle et sur la Révolution (1967). The letter starts on pg 303, figures between pages 304-305. A few screen captures later, here they are for your viewing pleasure:

A question for monotheists

2010-08-07T18:49:00.001-04:00

Check out this video challenge to followers of Christianity, Judiasm, Islam, the Bahá'í faith and other monotheistic religions.

What do you think about non-believers asking religious individuals to justify their religious beliefs?

Wild Voices: Six Birds Species & Their Vocalizations

2010-08-07T13:52:00.000-04:00

Nicely done video showcasing six species, narrated by scientists from the Cornell Laboratory of Ornithology. In order of appearance: Common Loon, Barred Owl, Common Nighthawk, White-rumped Sandpiper (very cool vocalizations), Northern Cardinal, and Magnificent Frigatebird.

Like it? Let Cornell University know by clicking the video over to their YouTube page, and clicking on the "Like" button! IMO, videos like this beat the pants off of some of the other videos on their channel.

A Request From "Urban Science Adventures"

2010-08-03T20:18:00.000-04:00

Over at Urban Science Adventures, Danielle Lee has landed a spot among the top 5 finalists in the 2010 Black Weblog Awards for Best Science or Technology Blog (congrats!!). But why stop there? Wouldn't it be great if she won?

So help her out: by casting your vote :)

Danielle really does have a wonderful science and nature blog and it deserves more recognition. Plus, it would be fantastic to see her readership grow.

More details from Danielle...

Thanks to you all, this blog has once again made the short list and is a finalist for the 2010 Black Weblog Awards in the Science & Tech Category.

Thank you, thank you, thank you!

To vote, please visit this link and vote for all of your Black Weblog Favorite Finalists (there are some really great and new blogs) in the 35 categories. Check out all of the nominees. Voting ends August 31st. You will have to provide a valid email address to cast your ballot. And while you are there, consider makiing a pledge to the 2011 Black Weblog Awards Kickoff campaign. The award committee is actually trying to create a live award presentation program next year. So, maybe I could receive my blog award in person. Who knows.

Fire off a few emails, share her post on facebook, tell your friends, then go vote! :)

Ah, grad school...

2010-08-03T10:20:00.000-04:00

[Thanks to Judy for the link]

Monday Mammal #12: Virginia Opossum

2010-08-02T00:44:00.001-04:00

Mammals, you may recall, are often categorized into two groups: the Prototheria (monotremes like this one) and Theria (live bearing mammals). Within the Theria, there are the marsupials and placentals - the former being woefully neglected so far on this blog! So to give the marsupials a bit more coverage, I present you with everyone's favorite (and least favorite) North American marsupial, the largest (and the smallest) marsupial north of Mexico, the one, the only... Virginia Opossum (Didelphis virginiana).

[Source]

You can learn more about these cool critters here, via the Smithsonian National Museum of Natural History.

(photo)

2010-08-01T23:36:00.002-04:00

If you regularly read The Friendly Atheist, you could imagine what Hemant was really thinking when he put up a baby picture, and asked for a caption and some photoshopping...

"Look at this pot, now look at me. Now look at the shoe, now back to me…"

(Caption by Carolina)

"The most important step in preparing your infant is to brine it for 6-10 hours,

depending on size. Give it some toys to play with, and it’ll hardly make a noise."

(Caption by Richard)

More on what Fodor and Piattelli-Palmarini Got Wrong

2010-07-30T00:12:00.004-04:00

Jerry Fodor and Massimo Piattelli-Palmarini have received quite a bit of criticism since the publication of their book What Darwin Got Wrong, which attempts to argue that evolution by natural selection is basically nonsense. The consensus seems to be that Fodor and Piattelli-Palmarini don't understand modern evolutionary theory, and that they're plainly wrong. However, in case you think they might be onto something you should check out this July 2010 critique of their book, which also takes them to task for getting it wrong. The review is written by Harvard philosopher Peter Godfrey-Smith. You should of course click over to the review and give it a good read, but I thought I'd comment here on a few highlights.

Peter begins by recalling a young Noam Chomsky's scathing book review of B. F. Skinner's 1957 book Verbal Behavior, which seems to have rightfully blown those ideas right off the map. He suggests there is a parallel here, to what Fodor and Piattelli-Palmarini seem to have attempted with their book... except this time it's they who have it wrong.

... A young linguist, Noam Chomsky, published a review of Verbal Behaviour... It was perhaps the most devastating book review ever written.

Chomsky argued that Skinner’s theoretical vocabulary could be applied to human linguistic behaviour only in an empty, post hoc way. He also thought that Skinner’s behaviourism had a simple architectural flaw: it held that external factors – especially experiences of reinforcement – were of ‘overwhelming importance’ in the explanation of behaviour. Hardly any role was given to what Chomsky referred to simply as ‘the internal structure of the organism’. It is unusual to do serious damage to a scientific research programme with a set of general arguments – not by citing experimental or mathematical results, but by looking at the basic ideas and revealing a crack in the foundations. Though the impact of the review itself is sometimes exaggerated, this is the effect Chomsky had on the behaviourist study of humans.

Jerry Fodor now hopes to do something similar to Darwinism in biology. Fodor has been making sceptical remarks about Darwinian ideas for decades. Three years ago he wrote a direct attack on Darwinian evolutionary theory in the LRB, and he has now published What Darwin Got Wrong, along with Massimo Piattelli-Palmarini. Fodor and Piattelli-Palmarini believe that they can replicate Chomsky’s demolition job on Skinner because ‘Skinner’s account of learning and Darwin’s account of evolution are identical in all but name.’ As we shall see, ‘identical’ is quite a stretch, but there is a real analogy.

Peter then recounts the criticism others have made of Fodor and Piattelli-Palmarini, specifically the argument that natural selection needs to be an 'intensional process' that can distinguish between 'co-extensive' properties of organisms (translation: natural selection allows correlated traits to piggy back advantageous traits, and this somehow implies natural selection doesn't work...) Now, while there's a more to the book than that (again, see the review for details) this argument sounds so blatantly wrong that I wonder if I'm even understanding it correctly! I mean really? Correlated neutral traits are the big showstopper for natural selection? Sadly, I don't think I'm wrong. This really appears to be part of their argument! If that's true, then the book What Darwin Got Wrong should be given the more appropriate title, What Fodor and Piattelli-Palmarini Got Wrong.

Now, I'm not just making this interpretation up... and neither is Peter Godfrey-Smith. Here's what F&P-P had to say in their response to an earlier criticism by Block and Kitcher (links below, emphasis mine):

For example, suppose random variation produces a trait that tends to make its bearers invisible to their predators. Then, all else equal, the predators gobble up the creatures that don’t have it, and the relative frequency of the trait in the population increases from generation to generation. To repeat, we haven’t the slightest doubt that this is the process that Darwin called natural selection and that Darwinists have always believed in some or other version. In fact, it sounds pretty good. It sounds like it ought to work.

But it doesn’t. A way to see that it doesn’t (not by any means the only way) is to consider confounded (linked) phenotypic traits, one but not the other of which is fitness-enhancing. Both traits are then correlated with fitness, so both should count as adaptations according to the formulation of natural selection given above. But only one of them is a cause of selection, so only one of them is an adaptation, and, though both are selected, only one is selected-for. Thus the free-rider problem. Prima facie, free riding is a counterexample to natural selection.

Massive sadness... They botched it. Prima facie, Fodor and Piattelli-Palmarini are simply confused about modern evolutionary biology (which is forgivable) and publicly wielding some philosophical sledge hammers at it, creating some confusion in their wake (this fact is way less forgivable, in my opinion).

Peter I think sums it up nicely when he writes...

Fodor and Piattelli-Palmarini criticise the tendency to talk of selection as if it were an agent. They are right that this is often misleading, but they seem to be making a similar mistake when they treat it as something over and above the ordinary facts of life, death and reproduction.

After all, recalling how natural selection works in a population, there really isn't much more to it that "life, death and reproduction." Just combine (1) some variation that is (2) heritable with (3) those variants achieving differential reproductive success. Let that process run for a few generations, and blammo - evolution happens. The distribution of variation in the population changes and the rest is (natural) history. Darwin nailed it, over a century worth of scientific progress has confirmed it, yet unfortunately it appears Fodor and Piattelli-Palmarini simply got it wrong.

But... perhaps one day they'll recognize their mistake, do the right thing, and admit they were wrong? After all, they themselves say in their reply to Block and Kitcher (again, emphasis mine)...

Everybody makes mistakes. Even biologists do; even lots of biologists assembled together do; even great biologists like Darwin do...

Yes, gentlemen, so do very respectable cognitive scientists and philosophers, even those not unlike yourselves.

How to disprove evolution

2010-07-29T00:30:00.002-04:00

... according to a Texan.

Oh, right, I should of course mention that this particular Texan is a wickedly sharp scientist and creator of some hugely popular YouTube videos on creationism, evolution and science education. Nothing wrong with knowing how to disprove a scientific theory - after all, that's how science works!

Now head on over and check out AronRa's youtube channel for more of his great videos.

Monday Mammmal #11: Mastodon or Mammoth?

2010-07-26T22:22:00.000-04:00

So which one's which, and what's the difference? Who lived where, and when did they live there?

You can learn more about mastodons and mammoths from the The Field Museum in Chicago, jump ahead to their page on how to tell the difference between the two (or here from the Smithsonian), read more about Mastodons here, more about Mammoths here and more about the group as a whole here and here.

Secular Student Alliance 2010 Annual Conference

2010-07-25T20:11:00.002-04:00

A few thoughts from the 2010 Secular Student Alliance (SSA) annual conference that took place this weekend in Columbus, OH. All in all, a great conference from a top notch organization - one you should definitely have on your radar!

I first found out about the SSA last summer, when my wife and I joined 300+ attendees of the 2009 annual conference (including PZ Myers) on a tour of the Creation "Museum" in Kentucky (photos and commentary from that trip are in this series of posts). Though I couldn't make the actual conference last year, I was impressed with the organization and the work they do to meet the needs of Freethought, Rational Inquiry, Atheist, and Humanist student groups nationwide. This year, I decided to give up a few hours of thesis work and head to the conference -- here's a quick overview.

First, they had a great line up of speakers including well known bloggers like keynote speaker Greta Christina and the Friendly Atheist, Hemant Mehta. Also on the program were various student leaders from across the U.S. sharing lessons learned from successfully starting and growing their organizations. You can learn more about the speakers from the conference website (plus a few minutes chasing down names on the web). You can read more about the SSA, what they do, and check out their resources for students and for educators through the SSA website. Also, check out the SSA's Facebook Page, and look for videos of the talks and other conference events on the SSA's YouTube channel.

What is the Secular Student Alliance (SSA)?

According to the "About" page on their website the purpose of the SSA is

...to educate high school and college students around the country about the value of scientific reason and the intellectual basis of secularism in its atheistic and humanistic manifestations.

The approach they take is to

...offer students and their organizations a variety of resources, including but not limited to leadership training and support, guest speakers, discounted literature and conference tickets, and thought-provoking online articles and opinions.

They also facilitate networking between these organizations by hosting meetings like their annual conference.

Now, it would be wrong to characterize the SSA as a group of firebrands fixated on getting a rise out of religious people. To the contrary, these folks seem to genuinely recognize the importance of mutual respect and to maintaining an open dialogue with religious individuals and organizations.

Why support humanist, freethought, & related student groups?

Organizations like the SSA bring together like minded students to promote the open discussion of (sometimes taboo) topics with significant social implications. They work to protect the freedoms of non-religious individuals, and to support students who speak out against religiously motivated efforts to subvert science literacy, to rewrite history, to silence free speech, or to attack groups with opposing religious (or non-religious) views. These groups not only provide a support system for these students during school - but they prepare them to continue their efforts off-campus after graduation and to continue having a positive impact on their communities.

Finally, you may also be interested in learning more about the Secular Coalition of America (SCA) and the American Humanist Association (AHA). The SCA is an "advocacy organization whose purpose is to amplify the diverse and growing voice of the nontheistic community in the United States. [They] are located in Washington, D.C. for ready access to government, activist partners and the media. [Their] staff lobbies U.S. Congress on issues of special concern to [their] constituency." The AHA, in addition to promoting Humanist values, also publishes The Humanist: A Magazine of Critical Inquiry and Social Concern. Check out their websites for more information, or other ways to get involved.

I Join Twitter

2010-07-24T14:30:00.000-04:00

I've been super busy lately finishing up grad school, which means less blogging about newsworthy items like this bit of craziness. But have no fear! To keep you in touch with the latest posts and other news, I've joined Twitter. So click that "Follow" button, tell your friends, then carry on enjoying your weekend.

Looks like Boyd Haley is pulling OSR#1 following FDA warnings

2010-07-23T02:11:00.000-04:00

Antonio Perez, Chicago Tribune

You may recall a post or two about on this blog about an industrial chelator turned dietary supplement called OSR#1. It has been used by some to treat autism in children, despite a lack of evidence that it would be safe or effective to do so. Well after the FDA stepped in recently, CTI Science Inc. appears to be pulling the product until further notice.

Here's an update from Orac at Respectful Insolence which includes part of what appears to be an email from CTI Science president Boyd Haley. According to that email:

...CTI Science has voluntarily agreed to remove OSR#1® from the market effective Thursday, 29 July 2010.

If you were wondering why they're going to wait until July 29, Orac offers up an answer:

My question is this: Why don't Haley and CTI Science simply shut down production and sales now? Why sell OSR#1 for another week? My guess is that the answer is that Haley wants to milk his cash cow for one more week. All the quacks who "prescribe" or recommend OSR#1 to their clients will rush out to buy a boatload of the stuff before Haley cuts off the supply. It's pure profit, because the stuff costs only $0.25 per gram to synthesize. I don't know what Haley sells OSR#1 for wholesale, but Kathleen Seidel points out that certain retailers sell it for $60 to $105 for 30-100 mg capsules of OSR#1. That's right: $20 to $35 a gram--seriously righteous bucks, a markup of up to 14,000%. Given that the Univesity of Kentucky bore the costs of development, and the packaging and filler can't cost all that much...

"Welcome to this world..."

2010-07-23T00:09:00.000-04:00

This should be an easy one, but can you guess the religious persuasion of the folks who made the video below? (answer at the end...)

Here's a hint...

Poe's Law states:
“ Without a winking smiley or other blatant display of humor, it is impossible to create a parody of Fundamentalism that SOMEONE won't mistake for the real thing. ”
Poe's Law points out that it is hard to tell parodies of fundamentalism (or, more generally, any crackpot theory) from the real thing, since they both seem equally insane. Conversely, real fundamentalism can easily be mistaken for a parody of fundamentalism.

Mid-week Reptilians #22: Why do snakes have scales?

2010-07-22T00:27:00.000-04:00

Here's a quick video on why snakes (and other reptilians) evolved scales, including footage of some pretty sweet looking scaleless snakes. At least watch the video up to around 3:23, then maybe consider some of the other videos on SnakeBytesTV.

Disclaimer: I almost didn't post this video because of some aversive racism that sneaks in at the end -- but those scaleless snakes are just too awesome to not share! While I love the SnakeBytesTV videos and Brian seems like a stand-up guy, I think he made a big mistake showcasing that comment. Was that really the best comment he could dig up? If "mexican" were replaced with "black" would he still have aired it? Replace "mexican" with "white" and you might see how pointless it is to even mention race there in the first place.

Anyway, if the race thing has piqued your interest, you might find more to read elsewhere in the blogosphere.

BP Climbs Higher On My Shit List

2010-07-20T11:22:00.001-04:00

BP seems to be up to some really sleazy stuff. I have zero respect for any organization that tries to pay away an entire community of scientists, just to cover it's ass when the shit hits the fan. Really, really bad form BP. So scientists, please keep your wits about you and help your colleagues in kind. As for BP, I decided to channel my disgust into something a bit less caustic than might actually be appropriate...

Monday Mammal #10: Yagán “dog”

2010-07-19T08:15:00.001-04:00

What's even cooler than those $5,950 domesticated Russian red foxes?

How about the (now extinct) Yagán dog - a domesticated South American fox (Pseudalopex culpaeus) that once lived among the Yagán people on the islands off the southern coast of South America.

I knew you'd agree.

47% of High School Teachers Believe in Intelligent Design Creationism?

2010-07-18T14:45:00.007-04:00

Recent posts by PZ Myers at Pharyngula and Jerry Coyne at Why Evolution is True have brought attention to the figure below, which suggests 47% of high school biology teachers believe in intelligent design creationism (ID). The figure comes from this PLoS Biology article which summarizes the results of a survey of 939 high school biology teachers. While these numbers are troubling, I think they and others are making two big mistakes in their commentary on these results.

Figure 1: A stripped-down and prettied-up version of Table S2 (see below).

First, we shouldn't give a dead rats ass what any teacher's personal beliefs are - only what say and do in the classroom. Period. When their personal beliefs become a problem in the classroom, then it's their actions that become fair game, not their personal beliefs.

Second, it's a mistake to say that 47% of high school biology teachers "believe in intelligent design" given these data. To be clear, I'm not saying that those 47% aren't a concern - just that many of them might be doing a good job of teaching evolution in the classroom and that (as a group) they're much less of a concern than are that whopping 16% who are young earth creationists (YECs). Again, these data don't quite clarify what's being taught in the classroom or how it's influenced by a teacher's personal beliefs, so I'm cautious to jump to any strong conclusions.

Both Myers and Coyne claim, as does the figure above, that 47% "believe in intelligent design" because those teachers believ there was some intervention in human origins and/or evolution from a supernatural entity. Sorry, but that isn't intelligent design and not all creationists are equally problematic.

Consider this definition from Wiktionary (emphasis added by me):

Etymology:
Coined in the 1987 draft of Of Pandas and People by Percival Davis and Dean H. Kenyon, as a repackaging of the term creationism after the U.S. Supreme Court ruled against the teaching of creationism in Edwards v. Aguillard (1987).

Proper noun:
intelligent design
A conjecture claiming that biological life on Earth, or more broadly, the universe as a whole, was created by an unspecified intelligent agent rather than being the result of undirected natural processes.

That "rather than" is important, and largely why I disagree with Coyne and Myers. ID rejects the idea that complex organisms and structures can result from natural processes alone, and I can't assume all 47% believe that. Without further evidence that those 939 high school biology teachers actually knew what ID was when they took the survey, I can't get too worried about them failing to teach evolution properly. Other information in the PLoS paper (I think) supports this interpretation.

That same study suggests some of that 47% of teachers don't subscribe to the more troubling aspects of ID. That is, they're a more science-minded group than the general population, and they do a better job teaching evolution than the YECs (though not as good as that 28% who don't believe a god intervened in human evolution).

First, table S4 provides a bit more information than the figure above and Figure 2 in the paper (also posted by Coyne). To add to what's been said already, the lack of young earth creationists relative to the general population really is good news.

Second, consider the data on the perceived importance of teaching evolution in the biology classroom.

Table S2 from that same paper shows 60% of those same 939 teachers agree that "Evolution serves as the unifying theme for the content of" their high school biology course. Furthermore, 82% think it's impossible "to offer an excellent general biology course for high school students that includes no mention of Darwin or evolutionary theory." While something more like 100% would be best, these numbers paint a much less troubling picture than focusing on the teachers personal beliefs alone.

Lastly, take another look at "how all these beliefs translate into education" by checking out table S5.

Now, 9.6 vs 13.4 vs 16.9 is something worth worrying about. I'd really like to see how other covariates like school curriculum requirements, etc. impact these numbers and just how much of that drop from 16.9 to 13.4 is due to personal religious beliefs relative to those other factors, but again this is what we'd expect to see from a group that contains a mix of good and bad high school biology teachers.

All that said, I do agree with PZ and Jerry that these results do confirm what we already know and recognize as a problem: that there are a significant number of science teachers out there whose personal religious beliefs do negatively impacting their ability to teach science. I think the real take home message here is that these results highlight the need for schools and the communities they serve to keep working to ensure teachers keep their personal religious beliefs out of the science classroom.

Evangelist Kem Ham Embraces Bad Science Journalism

2010-07-17T15:02:00.002-04:00

In my previous post I mentioned a recent example of bad science journalism. Despite the fact that those news articles are a clear misinterpretation of the (freely available) original journal article at PLoS Pathogens, and that various bloggers have pointed out their mistakes, there are those who apparently really liked that incorrect interpretation and embraced it readily. So who might have such an interest in the chicken coming before the egg? None other than Creation "Museum" director and Answers in Genesis CEO, Ken Ham.

Remember, Answers in Genesis and it's Creation "Museum" exist to spread a particular, literalist version of Christianity - and they do so by denying basic science and working to cripple public science literacy.

So what did Ham say about the (erroneous) news that chickens came before eggs? It can be summed up in a single phrase: non sequitur.

Which came first: the chicken or the egg?

I smiled yesterday as I read this news story from MSNBC:
It is an age-old riddle that has perplexed generations: Which came first, the chicken or the egg? Now British scientists claim to have finally come up with the definitive answer: The chicken. The scientific and philosophical mystery was purportedly unraveled by researchers at Sheffield and Warwick universities, according to the Daily Mail newspaper. The scientists found that a protein found only in a chicken’s ovaries is necessary for the formation of the egg, according to the paper Wednesday. The egg can therefore only exist if it has been created inside a chicken. The protein speeds up the development of the hard shell, which is essential in protecting the delicate yolk and fluids while the chick grows inside the egg, the report said.
“It had long been suspected that the egg came first but now we have the scientific proof that shows that in fact the chicken came first,” said Dr. Colin Freeman, from Sheffield University’s Department of Engineering Materials, according to the Mail.
Well, the secular world is catching up to what the Bible has taught all along. At our student assemblies over the years, I have often taught children the answer to this chicken and egg problem this way:

“What came first: the chicken or the egg? Well the Bible teaches us that God made the flying creatures on day five of creation, and God told the animals to be fruitful and multiply. So obviously the chicken (a bird) came first, and then they laid eggs.” So the kids would learn it this way, “The chicken came first because God made the birds on day five of the creation week!”

Poor Ken Ham, if that blog post were a video, it would no doubt star in one of the "Why Do People Laugh At Creationists?" series on YouTube.

Ken goes on to ignore everything we know about eggs from fossils to the various kinds of living reptiles (the closest living relatives of birds), monotremes (egg laying mammals) and other egg-laying organisms. He rattles off this bit of unfounded nonsense...

Of course there is also the design issue, which is also alluded to in the article. All the parts/chemicals etc. have to be there for the egg-laying system to work in the first place—it certainly couldn’t evolve.

You can read the entire article at: http://www.msnbc.msn.com/id/38238685/ns/technology_and_science-science/?Gt1=43001

Oh, gee, right - the egg couldn't have evolved without a hard shell, because... wait, why? Hasn't Ken ever seen soft, leathery reptile eggs before, or gooey fish eggs? Is he intentionally ignoring all that evidence - which suggests how chicken eggs could have evolved - or is he just ignorant of those facts?

Listen, Ken, you shouldn't bullshit the people you're trying to convert - it makes you look dumb, and come off as an untrustworthy source of information. Also, you should direct your readers to the actual, primary sources of information (e.g. in this case, a link to the article at PLoS Pathogens). If it's available, quote the primary source - not a secondary source of information like a news article... well, unless you're more concerned with being persuasive than correct.

Anyway, this part of Ken's blog post made me smile...

By the way, even the evening TV news programs on Wednesday covered this story, including The NBC Nightly News with Brian Williams. The CBS Evening News program ended its segment on the chicken/egg study with the follow-up question, “And the chicken came from... ?” Well, the anchor did not offer an answer but maybe that’s good—he might have given an evolutionary answer.

Fortunately, everyone in central Ohio watching the news last night did hear the science-based answer: that birds almost certainly evolved from dinosaurs.

Ken then tries to poison the well to ward off any criticism:

I wouldn’t be surprised if atheist scientists will loudly complain that this study actually supports the creation account in Genesis and then try to attack the research.

Well I would be surprised, actually, and here's why: the study in no way supports the creation account in Genesis, so there's no need for even the most unscrupulous scientist to "attack the research" based on his or her religious beliefs. They need only point out the non sequitur, and they're done. Ken apparently didn't even read the abstract of original article, otherwise he'd know this.

Which Came First: The Chicken or the Egg?

2010-07-16T00:52:00.004-04:00

I was surprised to hear my local news anchor announce that scientists have "finally" answered the question of which came first: the chicken or the egg. The story is making rounds in the news - for example here, here, here, and here - but they're getting it wrong.

Three words: Bad. Science. Journalism.

Now, before you think I'm going off the deep end here - I'm not the only one who thinks this is crappy science journalism, and I try to keep things in perspective...

Back to our question. Ignoring the original causality dilemma, didn't we clear this up a century or two ago? The egg came first (yes, even the shelled egg) and it arrived on the scene a couple hundred million years earlier, so it isn't even close!

Despite the horrible news coverage, the real story behind the bad headline is interesting. In short, molecular modeling work suggests the role of a certain protein (ovocleidin-17) is to catalyze the deposition of calcium during the formation of the egg shell in chickens. This has been it's suspected role for a few years now, but it's great to have another line of evidence that also suggests this protein's function, plus it gives us a better understanding of how eggs are produced.

The news story does has a silver lining. After covering it, my local Fox news anchors went on to mention that the authors of the research did point out that birds evolved from dinosaurs, and that perhaps we should rephrase the question in terms of dinosaurs versus dinosaur eggs. If you missed that, let me reiterate: my local Fox News anchors pointed out that birds evolved from dinosaurs!

Given the results of a recent poll, that's a welcome statement on the evening news.

In the United States, almost half of respondents (47%) believe that God created human beings in their present form within the last 10,000 years, while one-third (35%) think human beings evolved from less advanced life forms over millions of years.

Half of people in the Midwest (49%) and the South (51%) agree with creationism, while those in the Northeast are more likely to side with evolution (43%).

These are similar to previous polling results from Gallup on Evolution, Creationism and Intelligent Design.

Photos of Wildlife Affected By The BP Oil Spill

2010-07-14T12:52:00.001-04:00

There is a growing collection of wildlife photos from the gulf oil spill up on the web (e.g. here, here and here), but like so many other wildlife photos in the media many organisms are woefully unlabeled, or even labeled incorrectly (gasp!). I mean come on folks, "bird" and "turtle"? We can do better than that!

Check out the photos below, for example, and if you're an ID-fiend feel free to take a stab at identifying these species (speculation and/or solid IDs are welcomed in the comments section).

On a side note, the media has basically been shut out of most of the affected areas. This basically cuts off public access to these kinds of images which portray the huge impact the oil spill is having on coastal and marine ecosystems. Images like those below or others like these from the Boston Globe, are less common in the press than they should be - so do take some time and check them out.

Photo #1:

A bird covered in oil flails in the surf at East Grand Terre Island along the Louisiana coast Thursday, June 3, 2010. (AP Photo/Charlie Riedel)

Photo #2:

A sea turtle is mired in oil from the Deepwater Horizon oil spill on Grand Terre Island, Louisiana June 8, 2010. (REUTERS/Lee Celano)

Photo #3:

An oil soaked bird struggles against the oil slicked side of the HOS Iron Horse supply vessel at the site of the Deepwater Horizon oil spill in the Gulf of Mexico off the coast of Louisiana Sunday, May 9, 2010. (AP Photo/Gerald Herbert)

Photo #4:

A dead turtle floats on a pool of oil from the Deepwater Horizon spill in Barataria Bay off the coast of Louisiana Monday, June, 7, 2010. (AP Photo/Charlie Riedel)

The (latest) Vaccine Song

2010-07-13T16:42:00.000-04:00

This one's making the rounds, so I thought I'd share. Enjoy!

Homeopathic Infertility Treatment

2010-07-13T15:58:00.000-04:00

[Thanks to Mike for the link to xkcd]

Live Video Saturday As Space Probe Passes 100-km Wide Asteroid

2010-07-09T19:50:00.003-04:00

Update: The first images of 21 Lutetia should be broadcast around 3pm EDT. See links or embedded video below.

This Saturday, 10 July at 11:45am (EDT), the European Space Agency will be steaming live video taken as one of their space probes flies within 2000 miles (3200km) of a sizable asteroid named 21 Lutetia. How awesome is that!? So be sure to gather up any family or friends that might be around, and make sure they get a chance to watch!

So how big is 21 Lutetia?

According to this site, it's about 2.57E^15 metric tons and between 80km and 100km wide. Translating that into something we can actually wrap our brains around, that means... it's really big. It's just a notch smaller than some of the largest asteroids in our solar systems's main asteroid belt, 2000 times larger than the Earth's estimated coal reserves, about half the mass of one of Saturn's moons (Hyperion), and we'd need too line up something like 15-25 Lutetias to span the diameter of our own moon.

Phil Plait over at Bad Astronomy has more details, and will be streaming video here. You can also watch directly from the ESA streaming video page here, or the embedded video below.

eurospaceagency on livestream.com. Broadcast Live Free

To learn more about why the Rosetta probe is out in space chasing around asteroids in the first place check out the ESA's Rosetta probe blog, this new article and of course it's wikipedia entry.

Paul Pick's Spain

2010-07-09T12:27:00.002-04:00

I don't follow professional sports much, so I was a little confused to read on Jerry Coyne's blog that apparently I had chosen Spain, and that Jerry agreed. Then I realized he was of course talking about Paul the cephalopod, not Paul the grad student who should be writing his thesis right now instead of blogging.

Despite the fact that I'll be content to see either country win, Jerry was right! I really did end up picking Spain! I didn't have an octopus handy, and no coins within reach of my computer, so I just used R to do the coin toss. See for yourself...

> date()
[1] "Fri Jul 09 12:09:24 2010"
> set.seed(09072010)
> ifelse(runif(1) <= 1/2, "Spain", "Netherlands")
[1] "Spain"
>

See, Spain wins! Wow - I mean really, what are the odds?

Animated Wall Art!

2010-07-08T15:02:00.000-04:00

Ten minutes of a jaw-dropping amazingness, starting in 3... 2... 1...

BIG BANG BIG BOOM - the new wall-painted animation by BLU

from blu on Vimeo.

[Hat tip to PZ]

ScienceBlogs Losing Bloggers Over Questionable Pepsi Deal

2010-07-08T10:43:00.002-04:00

Update: According to this post by PZ Myers, the Pepsi blog is gone. Science writer Carl Zimmer also chimes in.

If you don't follow the blog "Good Math, Bad Math" you should check it out - well, you should check it out once it finds a more permanent home. It looks like blogger Mark Chu-Carroll is done with ScienceBlogs, and headed elsewhere. He explains why here.

ScienceBlogs recently decided to host a blog on nutrition called "Food Frontiers," but it's run by the Pepsi company -- basically, opening up the potential for corporate pseudoscience or spin to appear along side blog posts from dedicated individuals without such conflicts of interest.

Basically, ScienceBlogs is selling their bloggers' science-cred to a corporation (i.e. a for-profit entity), with huge potential for some serious conflicts of interest. Not cool.

That said, some effort went to address these concerns before the blog went public (snippets from their first post, basically a welcome page):

PepsiCo’s R&D Leadership Team discusses the science behind the food industry’s role in addressing global public health challenges. This is an extension of PepsiCo’s own Food Frontiers blog.

This blog is sponsored by PepsiCo. All editorial content is written by PepsiCo's scientists or scientists invited by PepsiCo and/or ScienceBlogs. All posts carry a byline above the fold indicating the scientist's affiliation and conflicts of interest.

... As part of this partnership, we'll hear from a wide range of experts on how the company is developing products rooted in rigorous, science-based nutrition standards to offer consumers more wholesome and enjoyable foods and beverages. The focus will be on innovations in science, nutrition and health policy. In addition to learning more about the transformation of PepsiCo's product portfolio, we'll be seeing some of the innovative ways it is planning to reduce its use of energy, water and packaging.

You can read more about ScienceBlogs deciding to host a Pepsi blog alongside their other blog posts in the news here and here. To hear more from other sciencebloggers, you've got plenty of options including The Thoughtful Animal, Common Knowledge, Laelaps, GrrlScientist, Adventures in Ethics and Science, and some of those who have left ScienceBlogs over the Pepsi debacle: Neurotopia, Neuron Culture, and Science After Sunclipse.

You can glean more from the listing of the past 24 hours of ScienceBlogs posts, here.

Elements of Math, by Steven Strogatz

2010-07-08T00:19:00.000-04:00

Courtesy of the editors at the New York Times Opinionator blog:

Professor Strogatz’s 15-part series on mathematics, which ran from late January through early May, is available on the “Steven Strogatz on the Elements of Math” page.

Go check it out! Strogatz is an excellent speaker and writer, and any minute spent reading his writing is a minute very well spent.

New Reptile Laws For Ohio?

2010-07-06T14:03:00.000-04:00

Last week Ohio Governor Ted Strickland made an agreement with the Humane Society of America and "agricultural interests" that may impact laws regarding the owership of large reptiles. You can read some press here, here and here. A copy of the agreement can be found here and here.

Of particular interest are these two points in the agreement (emphasis added by me):

2) The Ohio Department of Agriculture and the Ohio Department of Natural Resources will coordinate and take action on wild and dangerous animals including the prohibition of the sale and/or possession of big cats, bears, primates, large constricting and venomous snakes and alligators and crocodiles. Existing owners will be grandfathered in, but they could not breed or obtain new animals.
...

10) The HSUS will not submit a constitutional amendment on animal welfare in 2010 to the Ohio Secretary of State. Failure to implement the provisions related to wild and dangerous animals or the reforms recommended to the OLCSB by December 31, 2010 could void the agreement and allow the HSUS to pursue a ballot initiative whenever it chooses. However, if the terms of this agreement are met and implemented to the satisfaction of all parties, the agreement will extend to January 1, 2014. At that time the agreement shall be extended through January 1, 2017, and subsequently through January 1, 2020, if the terms continue to be met, and no party shall reasonably withhold its consent to the extensions. Any future pursuit of a ballot initiative by HSUS could nullify the limitation on gestation crate or battery cage facilities until and unless other lawful prohibitions come to exist.

It's sad the agreement uses such vague terminology. What about other large predators, like hyenas or wild canines? And what counts as "large" or "venomous"? Do they count venomous species like the harmless-to-humans Ringneck Snakes? Would a stringy, 13 foot carpet python be too big?

HSUS appears to only condone keeping pets if those pets are mammals, birds or fish. Reptiles and amphibians? Nah -- they all make bad pets.

Here's what HSUS has to say about snakes...

So many people seem to be afraid of snakes that some experts speculate this is a predisposition inherited from our distant primate ancestors. But snakes are not out to get us, and will avoid people as much as they possibly can. These incredible creatures fare best when left alone in their natural environment, not as pets.

As beautiful as some snakes are, they do not make good pets. A girl was killed by a python kept as a pet in 2009. People get snakes when they’re small and may let them loose as they grow. Burmese pythons have invaded the Everglades and could spread—and other species may follow. Help stop the trade in large constrictor snakes as pets.
...

Seems odd for them to include mention of a snake-related death here (e.g. no mention of deaths on their dog page) but I suppose it's an otherwise reasonable blurb. Well, except that they're wrong. Some snakes do make good pets! At least as good as fish and birds, if I do say so myself.

So why all the fuss? Maybe it's a safety concern? How big of a problem are large captive snakes?

According to REXANO (Responsible Exotic Animal Ownership) in this summary (PDF), the number of deaths from large constrictors in the U.S. between 1990 and 2008 was a whopping eight. Yup, eight deaths over almost two decades.

While each of those deaths is tragic, this statistic hardly warrants a campaign to completely ban "large" constrictors. Even correcting for the number of snakes in the U.S. over that time period, it still strikes me as a very low number. If 8 deaths in 18 years warrants a ban, then it's puzzling how we can still comfortably allow dogs, horses, and backyard swimming pools - each of which kill more people in a single year than large constrictors have killed in nearly two decades. Banning big snakes is not the solution.

My advice for HSUS is that it needs to reevaluate (or be more clear about) it's motives and rationale, particularly regarding why a ban is the best solution to whatever problem(s) they are concerned about. After all, "so many people seem to be afraid of snakes..."

ADDENDUM: All that said, there is plenty of room to improve the humane treatment of captive reptiles and to protect wild reptile populations. For more on the reptile trade, I highly recommend Bryan Christy's book and blog.

Monday Mammal #9: Marsh Rice Rat

2010-07-05T18:13:00.001-04:00

Many of this week's Monday Mammal, the Marsh Rice Rat (Oryzomys palustris), have likely perished recently as oil from the spill off of the Louisiana coastline has been recently been penetrating the coastal salt marshes. Fortunately, these little rodents aren't limited to these coastal marshes (unlike some species), and should (as a species, at least) persist beyond the recent disaster.

Figure 1: "Oryzomys palustris - lower image is silvery subspecies O. p. argentatus of Florida Keys

Credit: painting by Ron Klinger from Kays and Wilson's Mammals of North America,
© Princeton University Press (2002)" [Source]

This rather broad ranging American native was first described in 1837 from a specimen taken in the north of their range in Salem Co. New Jersey. They are semi-aquatic, mostly nocturnal omnivores and are found primarily in coastal (salt water) and interior (fresh water) marshes. Like many (most?) other species, their distribution hasn't always been restricted to their current range. Despite being endemic to the south eastern U.S. their ancestors likely trace back to central and South America.

These rats belong to the subfamily Sigmodontinae, the South American rats and mice. While there is one other species of Oryzomys that makes it up into North America -- the Coues's Rice Rat (O. couesi) which occurs in southern Texas -- the other species in the genus Oryzomys all appear to occur further south.

Oh, and here's one of those random facts you just don't find in species accounts any more -- just in case you were wondering how different these rats are from their domestic cousins. Unlike domestic rats, Marsh Rice Rats have 27 pairs of autosomal chromosomes plus two sex chromosomes for a grand total of 56 chromosomes...

[Source]

Hmm... this could make for a nice little pop quiz! Do you know how many chromosomes do we humans have?

Religious Fundamentalists vs. Religious Moderates: Tell Me Again Who's Got Their Religion Wrong?

2010-07-02T12:59:00.003-04:00

I'm not a religious or superstitious person, but for as long as I've thought about these things I've been in awe of how people acquire and adhere to these kinds of beliefs. It gets particularly interesting when someone is confronted with evidence contrary to a belief - or contrary to the justification for adopting that belief - or when one tries to apply some of those justifications across different religions with surprisingly mixed results.

But suppose supernatural entities like ghosts or gods do exist, and that some humans have knowledge of these things. Doing a quick survey of "who believes what," one thing quickly becomes clear:

Our beliefs are too varied and contradictory

for most people's beliefs to be correct.
Most people have it wrong.

But how can we tell who (if anyone) has the right religious/supernatural beliefs?

Today, while waiting for some computer simulations to finish, I read this post over at WEIT regarding this video and blog post over at the BioLogos website. Another example of the kind of verbal and psychological gymnastics that can happen when reality comes into conflict with religious dogma. (BioLogos, if you haven't heard of it, is a Christian organization founded by current NIH director Francis Collins to promote a happy coexistence between a loose-but-bible-based version of the Christian faith and our ever growing body of scientific knowledge. This, apparently is to be done by subscribing to a half-assed version of each of them.)

If we look beyond the core conflict presented in the BioLogos post -- the one between Genesis and science based claims about the origins of life -- there's a sizable religious conflict here: Biblical literalists vs. moderates who accommodate an empirically informed view of the world by adopting a trimmed down version of Christianity. I think it's fair to say most Christians (at least in North America) fall into this later category.

A quick read through blogs like WEIT or Pharyngula reveal that scientists who are die-hard philosophical naturalists don't like half-assed science. They value most a perspective on the external world that is checked against that same external world, and are wary of claims that may be rooted only in the human imagination. Before you fault these atheists for being stubborn or in denial, take note that religious people do this too... most fundamentalists I've encountered don't like half-assed Christians.

Unlike scientists who firmly adhere to methodological naturalism as the gold standard for adopting beliefs, religious fundamentalists who adhere to religious dogma get way more negative attention from their moderate counterparts. Science done according to the highest scientific standards almost always affords the scientists respect and support in their endeavour. How to religious moderates treat religious fundamentalists?

When religious extremists (of any faith) use religion to justify their actions to the rest of the world, moderate members of that religion frequently distance themselves by claiming those extremists aren't really being true followers of the faith, maybe that they're taking sacred texts out of context, or that they're somehow or another just not doing it right... even though they acted in accordance with some religious text or similar divine dictum.

In return, fundamentalists often waggle their fingers at (...or murder) those who aren't sticking to the rules, slacking off on their religious duties, those who reinvent "their religion" to suit seemingly arbitrary personal preferences. They somehow or another take them to task for not really being true followers of the faith. I can see the justification here actually - so to condemn such actions one really does need to either reject their religion and/or have good reason to say that they are the ones who have their religion wrong.

If you'd like another example: Ophelia Benson had a few posts recently going back and forth with Sholto Byrnes about Sharia law and Islam. See Sholto's series Rethinking Islamism, and Ophelia's posts here and here.

Or maybe this one: In Israel recently (emphasis added by me)...

More than 100,000 ultra-Orthodox Jews took to the streets across Israel [recently] for a showdown between religious and secular society over the way the Jewish state runs its education system...

Parents of European, or Ashkenazi, origin do not want their daughters to be educated in the same classroom as schoolgirls of Middle Eastern and North African descent, or Sephardim, claiming that they are not as religious.

See - they're just not ~~white~~ religious enough to be true Jewish schoolgirls! Uh, umm... Riiiiight.

So what's the outside observer to do?

It's all a bit confusing really... Should the rest of the world really avoid criticizing religious dogma when someone follows it and commits some heinous act as spelled out by that dogma? If not, why? Some sort of a "blame the readers for acting on what they read, and not the sacred texts that told them what to do" sort of thing?

Maybe we should join moderates and accuse fundamentalists of following their religion incorrectly? But on what grounds? No, but wait, aren't the fundamentalists the ones trying to follow the religion properly? So maybe we should support the fundamentalists in saying the moderates have it all wrong, while also criticizing both that religion and those fundamentalists for their respective teachings and actions?

But what if it's a good thing that moderates have their religion wrong? What if it really is wrong? We wouldn't want to make everyone into confused extremists all barking up the wrong tree, would we? And tell me again how we can determine which (if any) of the people on the planet have the right religious beliefs in the first place?

The First American Oil Spill?

2010-07-02T00:27:00.003-04:00

The Lucas Gusher at Spindletop Hill, Jan 10, 1901
[Source: The American Petroleum Institute & PRI]

I was watching the History Channel this evening, and caught part of a program that included some of the history of oil prospecting in the U.S.

One of the pivotal drilling attempts occurred at the turn of the century in - you guessed it - Texas. The particular location was on a hilltop called Spindle Top, located near Beaumont, Texas, and the find opened up the vast oil reserves below the Texas soil.

You can read more about those early days in the Hand book of Natural Gas by Henry Palmer Wescott (Yay, Google books!).

So why am I bringing all this up? Perhaps not ironically, this early find started with a bit of an oil spill - nothing like the current disaster in the Gulf of Mexico, but it still caught my attention as an example of the real challenges we still face tapping these deep, pressurized pockets of crude.

While I'm poking around in historical documents, here's part of a newspaper article published in the Houston Daily Post shortly after the find on January 11, 1901.

OIL STRUCK NEAR BEAUMONT.
A Stream of Petroleum Shot Into the Air for a Hundred Feet.
Prospector Who Has Been at Work for Two Years
Has His Faith Rewarded -- The Flow Is Esti-
mated at 5000 Barrels Per Day.

Beaumont, Texas. January 10.--Beaumont is excited tonight and it has good reason to be. About three mils south of the city there is spouting an oil well the equal of which can not be seen elsewhere in the United States and probably in the world.

Captaion A. F. Lucas, a geologist of Washington, D. C., made the lucky strike. The captain has been prospecting in the vicinity of Beaumount for more than two years. He has spent thousands of dollars with indifferent results until this morning, when the inside pipe in a hole in which he was operating blew high into the air, and it was followed by a six-inch stream of oil, which spouts nearly fifty feet higher than the sixtey-foot derrick.
...
The post correspondent visited Captain Lucas this afternoon, but that gentleman was so happy over his strike that he would not talk. He merely hugged the reporter and pointing to oil as it sailed high into the air, said: "Its equal can not be seen on this earth." Under existing conditions there is no way of estimating the flow of oil, but Captain Lucas says 5000 barrels per day would be exceedingly low...

By today's standards, it would indeed be exceedingly low, but at the time - that was quite a gusher! That well spewed oil for a few days before it was finally brought under control (if I can trust my recollection of what I heard on the History Channel...). While I doubt it got any bad press at the time - for better or worse - it went on to help fuel the last century of the modern industrial era.

Are Haeckle's embryos a fraud?

2010-07-01T08:09:00.006-04:00

Creationists often cite Ernst Haeckle's drawings of embryological development as a fraud in attempts to discredit evolution and pave the way for religious claims about how the world works. Like here, for example. But do they get it right? Not really.

Here's a clip from the movie Flock of Dodos on one case of these overblown claims by creationists...

Fortunately, it isn't too hard to find reasonable (i.e. science based) replies to clear up any misrepresentations about Haekle's drawings (e.g. here and here or just crack open a modern embryology textbook).

For an up-to-date response to some of these latest shenanigans, check out this post at Josh Rosenau's blog.

Hasn't somebody taken Haeckle's drawings and done a concise side-by-side comparison with more accurate modern images? Maybe something like this, but in the form of a spiffy web page??