Springtime in New York (part I)

Saturday, April 25, 2009 at 9:25 PM Bookmark and Share
Here in western New York, winter can drag on well into April. Hope for spring comes early as the non-stop cold of winter subsides. For nearly two months afterward, rare spring-like days fuel hope for an early spring, but those hopes are quickly squashed by the next bitter cold storm.

This past weekend, however, it became abundantly clear - spring has finally arrived!

A spotted salamander (Ambystoma maculatum) crossing a road
near a breeding pond - 26 March 2007, Tompkins Co., New York.

Here, the first signs of spring begin with the reappearance of rain, around late March into early April. For many nature-loving biology students here at Cornell, this is the much anticipated cue for the local frogs and Ambystoma salamanders to migrate to nearby ponds and vernal pools for their annual orgies. To witness these mass migrations (and hear the sometimes deafening roar of so many calling frogs) is a pretty darn cool experience!

Other than the novelty of the whole experience, it's also great opportunity to learn about these cute little critters. For example, salamanders are somewhat unique among amphibians as nearly all other amphibians fertilize their eggs externally (sperm doesn't meet egg until after the female has deposited them). In most salamander species, males produce a "sperm packet" called a spermatophore which they release during amplexus with the females. This spermatophore is then taken up into the reproductive tract by the female to use for internal fertilization of the eggs.

More signs of spring begin to appear while the amphibian eggs are incubating, preparing to hatch another generation of tadpoles and larval salamanders. The remaining winter birds have mostly left and some locally breeding ("summer") bird species begin to return to the area. Trees are beginning to bud, plants begin sprouting, insects come crawling out of the woodwork and begin to fill the air again.

A female Rough-legged Hawk (Buteo lagopus) on the
wintering grounds - 28 Feb 2009, Tompkins Co., New York.

Here again, we can witness this spectacle of migration, though this time on a much, much larger scale!

The past few days of warm weather and winds out of the south make up great conditions for bird migration: basically these weather patterns are a sort of climatological express train for birds wintering south of the U.S. When the weather is right, these migrants can catch a ride north high up on some of those northbound winds, maximizing their energy use over the long journey and minimizing the time spent in unfamiliar territory exposed to predators.

This spring, however, things are a little different. This weekend (April 25), we had near perfect weather to hail the arrival of our returning migrants. Being the bird-o-holic that I am, the start of spring migration is usually more than enough to keep me entertained.

This year, instead of out running around with my new telephoto snapping bird pictures, I have a new toy... a new 100mm macro lens! How does this change things? Stay tuned for "part II" where I'll share a few photos of the small-scale side of spring.

A mass of amphibian eggs from a roadside wetland.
25 March 2007, Summerhill, Cayuga Co., NY

Gene regulation in mammalian cells: a complex democracy?

Monday, April 20, 2009 at 9:25 PM Bookmark and Share

[From Sandwalk]

A (perhaps oversold?) press release entitled "International team cracks mammalian gene control code" is making the rounds, and while maybe a bit overreaching it looks pretty interesting!

For more details, check out this a blurb from Nature Genetics: "FANTOM studies networks in cells: Systems biology boosted by RNA-sequencing consortium" by Heidi Ledford. You can also read the abstracts at the links below (abstracts only - the articles aren't freely available online).

Publication Links:

  1. The FANTOM Consortium and the Riken Omics Science Center, The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics (2009) doi:10.1038/ng.375
  2. Taft, R. J. et al. Tiny RNAs associated with transcription start sites in animals. Nature Genetics (2009) doi:10.1038/ng.312
  3. Faulkner, G. J. et al. The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics (2009) doi:10.1038/ng.368

Reptiles sans scales?

Sunday, April 19, 2009 at 9:16 PM Bookmark and Share
I absolutely love it when I learn something new about the world that makes me stop dead in my tracks in amazement that this new information before me is actually true. Today, I had exactly one of those experiences, and at the risk of looking like a dunce in front of my herpetologists friends (who presumably have heard all of this before?), I thought I'd share.

While I'm not a huge fan of intentional inbreeding of animals (a common way to propagate rare mutations in domestic populations), I have to admit that inbred animals can provide remarkable opportunities to tackle otherwise impossible questions regarding genetics, evolution and development. The immensely valuable understanding of mouse genetics is the first example of this fact that comes to mind, though I'm sure there are others.

Why are they so useful? Scientists are pretty much limited to working with testable hypotheses (e.g. candidates for the correct answer to a given question) - so if it isn't something you can experimentally disprove (e.g. show its the wrong answer to the question), then science can't really help you out very much. For example, science can't answer questions like "Would a dog-horse hybrid run faster than a wolf-donkey hybrid?" without comparing actual hybrids of this sort (which to my knowledge don't and very likely can't exist). Unfortunately, these hard-to-impossible to answer questions aren't all this silly and useless. There are, less ridiculous questions that are similarly difficult if not impossible to test.

One such question, up until a few decades ago, was "Why do snakes have scales?" I mean, really, to test any hypotheses about this question we'd need to find some snakes that don't have scales, which we all know is impossible, right?

Wrong... that little fact is the fantastic little tidbit of information I stumbled upon today. As it just so happens, we DO know a little bit about why snakes have scales, because there ARE snakes who lack them! Even better, this isn't the case of some bizarre recently discovered species, but naturally occuring mutations in otherwise scaled species - giving us very comparable experimental controls (e.g. normal snakes of the same species, possibly siblings, etc.)!

Back before I was born, there was some work done to test existing hypotheses on the function of scales in reptiles. By chance, a scaleless Pacific(?) Gopher Snake (Pituophis catenifer) was collected near Oakland, California in 1971. The results of this work (and the image below) can be found in the article: A Scaleless Snake: Test of the Role of Reptilian Scales in Water Loss and Heat Transfer by Paul Licht and Albert F. Bennett (1972).

Now, science loves replicated experiments - they provide opportunities to test the generality of theories and a means to "double check" the work of others. Too bad there aren't any more of these scaleless critters around... Oh, right, nevermind - there are! In fact, there are a number of examples of scaleless squamates - and some are being bred in captivity (not necessarily for the good of science, mind you - think "hairless cats"...)

A quick scan through the world of reptile breeders turns up a number of other scaleless (or nearly scaleless) species including scaleless Bearded Dragons (details here), this photo of scaleless adder, a few scaleless rattlesnakes, this video of a reptile breeder and his hybrid scaleless rat snake which I assume are derived from scaleless Texas Rat Snakes (presumably different individual here), and of course among the more populer species (which are bred in large numbers) we have the scaleless Ball Pythons, and rumors of scaleless corn snakes. Whew!

More examples of research on these scaleless critters are out there if you're interested. For example, work done by these researchers interested in the diversity of kinds of skin out there in the animal world used some of these scaleless individuals and published this article about scaleless Western Diamondback Rattlesnakes, which don't seem to have any beta-karotin in their skin, giving them their very soft texture. Other references can be found in this (incomplete) list of references from Chad Arment via herper.com.

Experiments, Mathematics and Theory in Ecology (part II)

Wednesday, April 15, 2009 at 2:00 PM Bookmark and Share
I thought it was time that I made good on my promise to follow up my previous post regarding experiments, theory and science in ecology (and related disciplines). We left off asking the question "Why has it taken so long for some of the sciences [e.g. ecology] to progress to their current state?" For what it's worth, here are my two cents on the matter:

To avoid unnecessary suspense, here is the quick version of at least some of the major factors contributing to the (relatively) recent advancement of ecology (and other areas of science):
1. The proper application of the scientific method.
2. Technological advances and advances in other natural and physical sciences.
3. Various other factors (some helpful, some not) arising from our growing population. Foremost among this last category are some of the big questions regarding things like climate change, responsible (sustainable) use of natural resources, public health issues, and so on. On to the not-so-quick version!
So how have these factors shaped ecology? Lets have a look...

Ecology is a relatively new science - born of numerous biological disciplines, only arriving as its own field in the late 1800s to early 1900s. It is broad and overarching in scope, and is rooted in many of the other sciences - after all, that bit about the environment in the given definition of ecology frequently requires ecologists to dabble in other areas of the physical and natural sciences in order to answer ecological questions. Because of this, progress in other scientific fields affect progress in ecology (e.g. imagine doing ecological research without chemistry or genetics!).

So what about that "using the scientific method" bit? Just to give things some context (and yes, this is a bit of a tangent), consider the question "How long have people been using critical thought and (even crude implementations of) the scientific method as a way to understand the physical and natural world?" If you need a refresher on the history of life and the geologic timescale, you might check out my previous post on the subject, or the geologic time scale page on Wikipedia.

The punchline here is that modern humans are thought to have appeared around 200,000+ years ago with the first known attempts to try and learn about the world through reason and careful observation of natural phenomena occurring a little over 3,000 years ago. So as far as human existence goes, we're pretty new to the game of doing science!

Why this little diversion back to the pleistocene and the formation of the earth? First, because a lot went on before we humans showed up to the party, and that immense history has shaped the world we live in. It took us a while to get even a crude understanding of the big picture (e.g. we recently thought the earth was flat!) and the more that history of life on earth is pieced together (thanks to the efforts of scientists in areas like physics, chemistry, geology, biology, and paleontology), the better we understand today's world and how it works.

Secondly, the human population size and ability to create and share knowledge has changed dramatically in recent centuries, and this has had a resounding impact on the world of science. As you may know, the human population has experienced near exponential population growth over the past few thousand years. It has more than doubled in the past 50 years, and has increased more than 20 fold in the last 1000 years. The increase has raised new problems and questions to address (although, human population growth isn't just a 20th century concern), and it has also lead to increased means of communication, transportation, the accumulation and availability of knowledge (e.g. the internet), and of course the simple increase in worker-hours available for doing scientific research. In short - demographic changes have had (and will likely continue to have) a bit impact on the progression and direction of scientific advancement.

With that, let's finish with a more focused look at ecology (and its ancestors like natural history, biogeography, botany, zoology, etc.), by comparing it to what are commonly considered "hard sciences" like physics and chemistry.

Reaching to my nearest chemistry text (Physical Chemistry, by P. Atkins) and opening it to page 1, the book begins with an introductory chapter laying out what physical chemistry is: "the branch of chemistry that establishes and develops the principles of the subject. Its concepts are used to explain and interpret observations on the physical and chemical properties of matter." The first section of this chapter isn't about chemistry, or physics for that matter - but instead something more basic and fundamental to the topic of physical chemistry: the section is titled "The structure of science," and gives an overview of terms like law, hypothesis, and theory as applied to the subject at hand. This is how (again, in my opinion) every science text book should begin: lay out the foundations of using the scientific method for the subject at hand, then build up from there.

This is in large part what makes a "hard science" - emphasizing how to do good science, and properly applying it to understand natural phenomena. Admittedly, it also helps that atoms and molecules are more predictable in their behavior when it comes to chemistry and physics (versus the behavior of organisms), and in many ways easier to measure for purposes of data collection.

Field ecology, for example has its roots in natural history - which I'll (perhaps unfairly) use here as an example of a field that was slow to move from making observations to making testable hypotheses and conducting experiments to see which ideas about how things work would hold up to empirical evidence. In addition to the significant practical difficulties of studying living organisms, this relatively slow acceptance to use the scientific method to understand ecological phenomena seems attributable to: (1) the fact that life is amazingly diverse, and broad generalizations about that diversity are hard to make. Plus, for some those generalizations can spoil the beauty and mystique of nature, leading to less focus on general and easy to understand phenomena, and more focus on things that are unique, complex and harder to understand; and (2) insightful observations of natural (undisturbed) phenomena were long deemed valuable enough - which can elevate the process of observation above the importance of doing experiments (that is, testing hypotheses) - distracting from the development of general theories by the scientific method, while perhaps over-focusing on describing observed phenomena.

As technology and our understanding from other areas in science have progressed, so to have our observational capabilities (and thus what sorts of things we can test experimentally). In ecology and other areas of biology, these advancements have opened up entire new worlds to observe and questions to be answered.

Early on, physics and chemistry had had a few things going in their favor in this regard. First, they are by their very nature easier to think about and study in a quantitative and general sense (perhaps early physics more so than early chemistry). This imparts to them three important qualities as disciplines in science. First, theories apply broadly to natural phenomena (e.g. nearly all objects fall just the same when dropped from a moderate distance - contrast with understanding the basic aspects of respiration, which pose greater practical challenges to study and don't generalize as easily to broad categories of organisms). Second, the quantitative nature of important phenomena allows the use of powerful mathematical and statistical tools, leading to well defined predictions about measurable quantities and a greater ease in testing and ruling out bad hypotheses. Science is all about ruling out bad hypotheses, and doing this efficiently means efficient progress towards well supported theories. Finally, there are fewer ethical conflicts in studying things that aren't alive - people don't respond to seeing someone smash a rock, drop a marble, or melt down metals in the same way they respond to seeing someone dissect a live dog. All biologists know about animal rights but to a geologist, mineral rights are rarely a problem in the lab!

Finally, thanks to the suggestion by Nick Sly, I took a look at the 1964 Science article "Strong Inference: Certain systematic methods of scientific thinking may produce much more rapid progress than others". I highly recommend reading it over, as well as T.C. Chamberlin's 1890 paper "The Method of Multiple Working Hypotheses" which can be found here (from the Wikipedia entry on Chamberlin), plus the text here (ed. 1999) with typographical errors corrected, and subheadings added, and lastly this modern version re-written by L. Bruce Railsback in case you find "Chamberlin's paper is too long, too high-blown, and too sexist for modern students."

In Platt 1964, he describes how some areas of science fail to progress by leaving behind the method of testing multiple hypotheses and "strong inferences" - complete with a rather entertaining list of pseudoscientific approaches I'll leave you to consider:
I think, there are other areas of science today that are sick by comparison, because they have forgotten the necessity for alternative hypotheses and disproof. Each man has only one branch-or none-on the logical tree, and it twists at random without ever coming to the need for a crucial decision at any point. We can see from the external symptoms that there is something scientifically wrong. The Frozen Method. The Eternal Surveyor. The Never Finished. The Great Man With a Single Hypothesis. The Little Club of Dependents. The Vendetta. The All-Encompassing Theory Which Can Never Be Falsified.
If you've made it this far, I hope you enjoyed the read and found it at least somewhat thought provoking. Feel free to share any comments or questions by posting below :)

Dinosaurs, Birds and Interdisciplinary Science

Monday, April 13, 2009 at 6:44 PM Bookmark and Share
I just came across a 2008 NOVA program on bringing to life the biomechanics of an interesting type of dinosaur from over 110+ million years ago, known as microraptor. In short, this program documents the story of how a group of scientists used fossil information and a little bit of modern biology to construct a model of microraptor, and then teamed up with others to explore how it might have used its unique four-winged body.

You can watch the program from the NOVA page "The Four-Winged Dinosaur," and/or watch the preview for the program here.

Click to enlarge fossil image.

Why mention this little PBS show? Simply to point out a nice little glimpse of how science works in practice. The story line in this case is a pretty good example of how (what some would call "interdisciplinary") science works, and highlights the importance of having a working relationship between experts in different scientific disciplines.

For scientists, a recognition of this way of doing science can shape what we read, what conferences we go to, and the sorts of discussions we have with other scientists outside our area of expertise. More generally, this style of science typifies the notion that science is a community endeavor, which has implications for the way science is taught to future scientists and to the general public.

Another reason for sharing the program is to illustrate the pace at which science often progresses - it's an incremental process and often a lot slower than people think! Progress does occasionally happen larger steps, and these can sometimes be driven by (1) new empirical data or methods of data collection that result in new questions (how did this dinosaur use 4 wings!?) and (2) new ways of thinking about these questions and the tools those new ways of thinking bring to bear on trying to answer those questions.

Julia Clarke points out the role the microraptor work has played in this process towards the end of the program: "Microraptor has thrown our understanding into a new and productive chaos. It doesn't solve the problem, it doesn't give us an answer, but it gives us another way of thinking about the data, and I think eventually, we are going to get to some answers."

So where do those new tools and new ideas come from? Some sort of scientific genius or amazing luck? Well, sure, probably sometimes - but for your average scientist, the best place to start looking for those new insights can often come from "down the hall" - if done right, it can be very fruitful for some researchers to venture out of their own area of expertise, and to team up with experts in other fields on relevant problems. In the case of microraptor, questions about flight brought together expertise from paleontology, comparative vertebrate anatomy, ornithology, aerodynamics, and other disciplines and together these scientists have incrementally advanced our understanding of the origin of flight in birds and reptiles.

In wrapping up this post, I should mention the idea of "interdisciplinary science," the value of which is well illustrated by the very interdisciplinary team of researchers in this program. Scientists, technology experts and in this case artists coming together to try and answer a basic scientific question that demanded more than any one area of expertise to try and answer.

In practice, however, there are often significant challenges present in bringing together such a diverse group of "experts". These challenges include things like the problem of field-specific and/or conflicting terminology, and a great many other challenges that can hinder the development of a productive meeting of minds on a given project.

I'll keep myself from running off on this tangent, but if you're interested a little digging on the web should turn up some of those challenges to doing "interdisciplinary science" plus ways to avoid and deal with them (feel free to comment below if you find anything worth sharing!)

Is Science Agnostic??

Thursday, April 9, 2009 at 9:29 PM Bookmark and Share
Here's Eugenie Scott, director of the National Center for Science Education giving a pretty darn good answer to that question back in January of 2006.

I first came across this footage as the first clip below, but found it was really part 5 of 10 of a 2006 talk on Intelligent Design Creationism (also provided below, or go here for part 1 of 10). Originals available from the Research Channel.

Can you recognize a flawed argument when you hear one?

Monday, April 6, 2009 at 5:45 PM Bookmark and Share
Most of us have surprisingly bad "bull-crap" detectors when it comes recognizing flawed arguments supporting our favorite beliefs and ideas. Would you like an example? If you have some time, here's a (long) video of a debate between outspoken atheist and author Christopher Hitchens and christian authors Douglas Wilson, William Lane Craig, Lee Strobel, and Jim Denison at the 2009 Christian Book Expo. I promise you won't have to watch the whole thing to get your fill of logical fallacies, bad reasoning, and plenty of other nonsensical banter!

The topic? "Does the god of Christianity exist, and what difference does it make?"

Christian Book Expo 2009

[Picked up from Sandwalk]

First, give some thought about some of the assertions and "logical" arguments put forth. First to speak, Lee Strobel makes this common blunder - can you see other problems with what he calls evidence (which one can easily distinguish as beliefs)? He and others go on to make numerous similar "bad arguments." For example, can you find cases of folks making an appeal to authority, speaking loosely with equivocation (using a word with multiple meanings in a series of logical steps with more than one meaning used variously along the way), making the fallacy of an appeal to ignorance and so on?

Second consider some of the problems of terminology here. How often are the panelists discussing "apples and oranges" (so to speak) in their different understanding and use of words like moral, immoral, morality (which Hitchen's touches on around 1:13:00), know, knowledge, true, fact, evidence, and so on.

I'll leave you to dwell on the many claims and arguments in the video (yes, christian and atheist panelists alike!) and see how many logical misteps are taken during their little "debate."


I have always thought it unfortunate that "winning the debate" and "making a good point" weren't at all the same thing. In a later debate between W. L. Craig and C. Hitchens days after the panel discussion posted above, Hitchens seems to have lost the debate (according to his opponent's supporters, at least). So how could he have done better? Check out this advice for debating William Lane Craig (part I) from the blog Evaluating Christianity.

How old is the earth?

Friday, April 3, 2009 at 10:09 PM Bookmark and Share
I've recently been trying to get a better grasp on the geologic time scale, and thought others might like to share in pondering what some of those gigantic numbers really mean. To do this, we'll do a comparison with the one thing we have some experience with that spans this huge range of numbers: distance.

So what kind of numbers are we talking about here? Lets start way back to the beginning when this little rock called home (ok, or "Earth") came into existence. This happened roughly 4,500,000,000 years ago - or typing a few less zeros, 4.5 billion years ago.

Not quite sure how big 4.5 billion is? Consider the following: suppose a millimeter represents 1 year. That makes me "3cm old" since 1cm = 10yrs, and I'm almost 30 years old.

Continuing this line of reasoning (using the metric system, just to keep the math easy), we can get an idea of some larger numbers of years: 1 meter = 1000 yrs, 1 kilometer = 1 million yrs, and so on.

Next, pick your favorite reference points and see how big the distances get! How long ago was U.S. Declaration of Independence signed? About 20cm (or 8 inches). The Black Death that swept through 14th century Europe? 0.7 meters. The fall of the Roman Empire? 1.5 meters. Jesus? 2 meters. The age of the earth according to young earth creationists? About 10 meters. The last "ice age" in North America? About 13 meters. When did dinosaurs go extinct? About 65 kilometers (5 miles is about 8 km). And so on...

So with this time-distance comparison in hand, lets start back at the beginning.

That 4.5 billion years works out to 4,500 km (about 2,700 miles). The circumference of the earth is about 40,000 km (24,900 miles) you can think of this distance as about 1/10th the way around the world - say, from southern California to northern Maine, or roughly from New York to southern Florida and back.

U.S. map showing what 4.5 billion, 3.5 billion & 2 billion years

look if you equate 1 year = 1 millimeter. Click to enlarge.

Think about it - all adult humans are only a few centimeters old while the history of the earth spans comparatively enormous continental distances (see the figure above)!

With that, I'll leave you to ponder some other major milestones in the history of our little blue planet:
  • Life appeared about 1 billion years after earth formed, with the oldest known evidence of life dating back to around 3,500,000,000 years ago or earlier (that's 3,500 km - roughly New York to the Grand Canyon in southern Utah).
  • About 2,000,000,000 (yup, billion) years passed before multi-celled life appeared (This brings us to about the distance from Denver to Chicago - 1,500 km),
  • and things didn't really get "interesting" until the famed Cambrian explosion around 530,000,000 years ago, when life diversified into the major groups we recognize today (for example, this is when we see the first plants, animals, etc.)
  • During the next 50,000,000+ years (50 km or about 30 miles) organisms continue to diversify, though it takes around 300,000,000 more years for early mammals to arrive on the scene (yes, I skipped over a whole lot of invertebrates, fish, amphibians, and reptiles there), which brings us furry critters into existence a little over 200,000,000 years ago. The history of mammals' on earth (only 200 km /120 miles) is relatively quite recent!
  • So what about humans? The first hominids appeared around 7,000,000 years ago (that's right, it took approximately 4.493 billion years since earth was formed 4.5 billion years ago before anything vaguely human came into existence - about 3.493 billion years after the first known evidence of life!) - as far as mammals go, 7 km out of 200 km is also quite recent, at least in my opinion.
  • Finally, modern humans are thought to have appeared around 200,000+ years ago - a little over 200 meters ago!!!

Please, teach them Intelligent Design!

Wednesday, April 1, 2009 at 7:59 PM Bookmark and Share
Most scientists and science educators would prefer things like intelligent design (ID) be erased from halls of human thought, however some are advocating (with good reason!) that these ideas and beliefs should be taught in our public schools - all in the name of good science.

Before you tally this as a small win for the creationism/ID proponents out there, have a look at the following (roughly 9 minute) talk by American astrophysicist and educator Neil deGrasse Tyson:

Why teach ID and similar belief systems in our schools? Clearly, not for the reasons young earth creationists say we should - we can't teach religion in public schools! ID and related assertions should be taught, however, because they are part of the history of science and human thought - and more importantly, because of the threat they pose to scientific progress. To ignore them is tantamount to begging history to repeat itself, at some point down the line.

So yes, intelligent design should be taught in (at least some) public schools, but in classes about the philosophy of science, comparative religion or the history of science. Intelligent design does not, however, belong in the science classroom along side actual scientific theories. (This last point, I should mention, has repeatedly been the finding of numerous state and federal court decisions, and nearly the entire scientific and public education communities.)

Where does that leave us? Perhaps, with the following challenge:
1. To develop guidelines on teaching intelligent design (and why it isn't science) in public classes on the philosophy of science, the history of science and/or in comparative religions courses. With many suggesting ID belongs in these courses, and not in a science class, we need to ensure classes like this one don't pass muster as legitimate alternatives to sneak creationism into public schools.

2. To develop appropriate materials to put those guidelines into practice. This include changes to the K-12 curriculum, not just university level courses.

Will such educational guidelines and materials ever make it into mainstream classrooms? Who knows. Is this even a good idea? That is a discussion I have yet to have (so I especially welcome your comments on this one!).

Hopefully we'll all do our part to continue to ensure ID is taught where it should be taught (if at all), and not in the science classroom.