Which Came First: The Chicken or the Egg?

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.

Related Links:

1. Bad science journalism the fault of chickens or eggs?  | Thoughtomics by Lucas Brouwers
2. Freeman C. L., Harding J. H., Quigley D., Rodger P. M. 2010. Structural Control of Crystal Nuclei by an Eggshell Protein. Angewandte Chemie International Ed. 49(30) doi: 10.1002/anie.201000679

Do ornithologists agree birds evolved from dinosaurs?

If you like birds, dinosaurs, anatomy, evolution or paleontology, you need to go read this post... twice.  Here's why...

Over at Tetrapod Zoology, Darren Naish has a great exposition on the question above (as well as a recommendation/review of a book that any bird-nerd should have on their shelf) which I encourage you to go read at least once.  The title of Darren's post (and his book recommendation) is Gary Kaiser's The Inner Bird: Anatomy and Evolution.

I find that most people who aren't biologists or bird-nerds are unaware of the idea that birds evolved from dinosaurs. While most of my ornithologist friends accept the idea, I'm not sure how many really understand the evidence behind the claim (in their defense - it's well outside of their areas of expertise, so this is hardly a criticism).  That said, this book (and even Darren's post) could help clear up some of that evidence.

Here's a little of what Darren writes on the origin of birds...

Kaiser is convinced by the evidence for the dinosaurian origin of birds, and long sections of the book are devoted to discussing the similarities and differences seen between birds and their non-avian relatives*. The notion that birds cannot be dinosaurs is heavily promoted in the ornithological literature - most notably in Alan Feduccia's The Origin and Evolution of Birds (Feduccia 1996). Because Feduccia's book is one of the most visible of volumes on bird evolution, audiences can be forgiven for thinking that ornithologists as a whole reject the hypothesis of a dinosaurian ancestry for birds. This is absolutely not true, and those interested should take every opportunity to note that all of Feduccia (et al.'s) criticisms are invalid or erroneous (e.g., that non-avian theropods are too big to be ancestral to birds, that they occur too late in the fossil record, that their anatomy bars them from avian ancestry, and that other Mesozoic reptiles make better potential bird ancestors). It is also worth noting that many of Feduccia's proposals about the phylogeny of neornithines are idiosyncratic and that his volume does not accurately represent current thinking on avian evolutionary history. The Inner Bird helps provide part of the antidote, bringing home the point that the dinosaurian origin of birds is well supported and robust, and adopted by many ornithologists interested in palaeontology.

You can read the rest of the article here.

Steve Martin, Atheism, and The Age Of The Universe

I was going to try and somehow weave together the video below and the results of this poll mentioned over at the NCSE. But then I decided not to, knowing that you'll check them both out anyway - 'cause you're just that awesome.

The Poll Results

QUESTION: Most astronomers believe the universe formed about 13.7 billion years ago in a massive event called the Big Bang. Do you think that's about right or do think the universe was created much more recently?

Women were more likely than men to accept the 13.7-billion-year figure (64% versus 60%), Democrats more likely than independents, and independents more likely than Republicans (71%, 66%, and 44%, respectively), blacks and Latinos more likely than whites (75%, 73%, and 58%, respectively)

... and for something completely different...

The Hilariously Awesome Video

New Website on Human Evolution

On March 17th, the National Museum of Natural History will open the David H. Koch Hall of Human Origins. Leading up to that opening, the Smithsonian Institute has launched a new website on human origins that's well worth checking out.

Figure 1: "Staring contest... ready, go!"

The website includes a look into the evidence of our ancestry, research news, information for teachers and students, upcoming events and exhibit information (if you're ever in the neighborhood, ), and a section on "Religious Perspectives":

The Hall of Human Origins offers a welcoming place to explore one of the most exciting areas of science, the study of human evolution. Despite strong public interest in the science, however, many people find this topic troubling when viewed from a religious perspective. Representatives of diverse religious communities encourage a larger, more respectful understanding of both the scientific evidence and religious belief.

No doubt some will find this sort of language a bit too friendly to any religious claims regarding human origins, but given the Smithsonian's role as an educational institution I can appreciate their pragmatism. Reading a bit further (emphasis added)...

There are a number of different approaches to the science-religion relationship. One approach is to see science and religion as separate domains that ask different questions focusing on separate interests in human life – for example, about the natural world in science and about God in religion. This approach depends on respecting and maintaining the distinctions but can sometimes overlook the ways in which scientific interpretations may have an effect on religious beliefs. Conflict is seen to arise when efforts are made to eliminate the separation that the first approach assumes. The strongest conflicts develop when either science or religion asserts a standard of truth to which the other must adhere or otherwise be dismissed.

This I like. I'm quite fond of using science and rational thought to understand the world, while keeping that knowledge distinct from any contrary claims based on religious beliefs.  The website continues ...

An alternative approach sees interaction or engagement as positive. Engagement takes many forms, including personal efforts by individuals to integrate scientific and religious understandings, statements by religious organizations that affirm and even celebrate the scientific findings, and constructive interactions between theologians and scientists seeking common ground, respect, and shared insight into how the science of human evolution contributes to an awareness of what it means to be human. 

So what do you think - too accommodating of religion, or did they do a good job of addressing religiously motivated objections to the claims of science? 

[Hat tip to Panda's Thumb]

4000 year old human genome from Greenland

There's a nice post over at John Hawk's Weblog on the recent news that a group of researchers sequenced nearly 80% of the genome from a human that lived in Greenland nearly 4000 year ago.  The paper can be read in full online via Nature (PDF). If you're going to read the paper, do check out John's post for his commentary on the open and collaborative nature of this work.

Evolution at the zoo

I just saw this post over at the Axis of Evo blog, and remembered a photo I took of a sign at the Denver Zoo on primate evolution... which included humans.  The photo was taken in early July, 2009 in front of the gorilla exhibit.

Figure 1. The sign.

First, I think it's fantastic that the Denver Zoo isn't being shy, and is trying to educate the public about where our species sits in the tree of life -- especially in relation to the (other) great apes.  I've seen lesser zoos completely devoid of such efforts.

That said, there were some problems with the sign:  It depicted an outdated relationship between humans and other apes, and it looked as though someone was trying to sugar coat those human-to-primate relationships further by including extinct groups that (conveniently?) introduce extra space between humans and the other primates.  In any case, I think the sign needs an update...  Here's a closer look at the bottom panel -- their presentation of the major modern primate lineages plus one extinct group...

Figure 2. The bottom panel from the sign in Figure 1.

I could be wrong here, but last I recall all the evidence suggests this picture (excluding the extinct "ape-men") should look something more like this:

Figure 3.  An edited (or maybe, corrected?) version of the sign above.

Only a few feet away, should any visitor get curious, were nice close looks at Gorillas and Orangutans.  I was able to snap this picture...

Figure 4. Hand of a female gorilla, napping a few feet away from the sign above.

Perhaps not as impressive as the big silver-back, but it does nicely illustrate how some of our human features maybe aren't as exclusively human as some like to think.

A Dinosaur on the Christmas Dinner Table

If you recall my post from back around Thanksgiving, the Wild Turkey -- like all birds -- is a modern day dinosaur.  What better opportunity to share this little fact with your friends and family than over the Christmas Turkey?

Below are some resources for turning the remains of your holiday feast into a biology lesson, but before we get into details I want to first answer a simple question: What exactly is a dinosaur anyway?

Dinosaur's are a group of (mostly extinct) reptiles that arose around the early Triassic period about 230 million years ago (mya).  They persisted until the mass extinction event that occurred 65mya at the end of the Cretaceous period, (also the end of the Mesozoic era and start of the Cenozoic era), when all of the dinosaur lineages save modern birds died out.

To put this talk of dinosaurs and birds into perspective, lets take a crash course in vertebrate taxonomy. Starting with the ancestor of all land vertebrates, we can follow evolution forward to the present, noting major points of divergence along the way.  We're of course skipping a lot, taking the fast track from the first vertebrate land animals to modern day birds.

The first amphibian-like terrestrial tetrapods appeared over 350mya (Late Devonian into the Carboniferous period), with the Synapsids (whose descendants became the modern mammals) splitting off 25+ million years later.  Another 25 million years or so later, ancestral turtles and other Testudines appeared, then the sphenodonts (the tuatara) and the squamates (lizards and snakes), then crocodilians, then dinosaurs and birds.

These relationships can be summarized as follows (here I've included proper group names as well as extant representatives):

•  Amniotes - Descendants of the first egg-laying terrestrial vertebrates (~ 340mya) split around ~325mya
• Synapsids - Mammalian ancestors
• ...
• Mammals ~ 200 mya
• Primates ~ 55+ mya
• Human-Chimp Split ~ 5-10 mya
• Saurapsids - Modern Reptilians
• Anapsids - Turtles
• Diapsids - Other modern reptiles (including birds), split ~ 300mya
• Lepidosauria -Tuatara, Lizards and Snakes
• Sphenodonts - Tuatara
• Squamates - Lizards, Snakes
• Archosauria - Crocodilians, Dinosaurs (including birds)
• Crocodilia
• Dinosauria - Two dinosaur groups diverged ~250 mya
• Ornithischia - "bird-hipped", beaked - but not birds!
• Saurischia - "lizard-hipped", toothed ancestors of birds.
• Sauropodomorpha - big herbivores like Diplodicus.
• Theropoda - bipedal carnivores like T. rex, Velociraptor and...
• Aves - modern birds, originating ~ 150mya

Whew!  So to sum up, birds have been around since their divergence from the other dinosaurs during the Cretaceous period (145-65mya), and are the only surviving Dinosaurs of the big Cretaceous extinction 65mya. Their closest living relatives are the Crocodilians (together with dinosaurs and other relatives, these are the Archosaurs), then the lizards and snakes (which all together form the Diapsid reptilians), then turtles (all together, the Saurapsids). After all the reptilians, the next closest relatives are the mammals (all together, these are all of the living Amniotes), then amphibians, fishes, etc.

So how do you bring all this information to the dinner table?  Well the easiest way to see the relationship between dinosaurs and birds is from the differences and similarities in their skeletal structure.

Source: The Origin and Early Evolution of Birds | Geology Rocks

Other ideas can be found here, and for a nice reference you can bring with you to the Christmas dinner table...

Source: Image from here, modified by Tom Holtz here.

Resources:

---

1. Prothero, S. 2007. Evolution: What the Fossils Say and Why It Matters. Columbia Univ. Press.
2. The Dinosauria, from the University of California Museum of Paleontology website.
3. Wikipedia (links above).
4. Wedel, Matt. Your Holiday Dinosaur, University of California Museum of Paleontology website.
5. Holtz, Tom. Your Thanksgiving/Christmas Therapod from Dave Hone's Archosaur Musings.

NSF launches Evolution of Evolution website

The National Science Foundation has launched a new website called the Evolution of Evolution: 150 Years of Darwin's On the Origin of Species. A cursory look at the site revealed a nice (though a bit overpackaged) presentation at how the theory of Evolution has pulled together a broad array of scientific disciplines, and expounds upon a few cool, important or otherwise noteworthy examples of the recent scientific accomplishments as well as significant historical work.  Also a bit of history surrounding Darwin and his legacy - no doubt in celebration of his 200th birthday this year, and the 150th anniversary of On the Origin of Species this Tuesday, the 24th of November.

If you get a chance to work through any of the site in detail, feel free to leave your impression in the comments below.

Human Origins & The Aquatic Ape Hypothesis

I just saw this post by Greg Mayer (this Greg, not this one) over on Jerry Coyne's blog, Why Evolution is True, which knocks TED for spreading what Greg considers pseudoscience: the aquatic ape hypothesis. It does seem like a valid criticism, and not just a reaction to her calling evolutionary biologists "evolutionists" in the first few seconds of the talk.

Have a look at the video, and browse the above critique by Jim Moore, plus John Hawk's blog posts for more details.

How do you sequence a genome?

Have you ever wondered how genes or whole genomes are sequenced, or how DNA sequencing plays into our understanding of how life has evolved here on Earth??

Without getting in to all the details, here's some great video footage that provides a glimpse into this world. Additionally, the video includes discussion (towards the end) of the role science plays in society and what that implies for the future of our species, and life on earth. At any rate - I think it's well worth watching despite the length of the video!

Here, Richard Dawkins is interviewing Craig Venter while getting a tour of his sequencing facilities - an impressive example of "industrial biology" driving the cutting edge of science. Even in the first 15 minutes or so, you get a feel for how much heavily these sequencing technologies rely on contributions from many scientific fields, including mathematics, statistics, computer science, chemistry and engineering.



If you pay attention, you can also glean some other interesting tidbits of information... For example, individual humans seem to differ not by the tenths of a percent we've been told, but probably more like 1% or 2%. Humans and chimps?? Well, we differ by more than the 1.2% so often quoted on such public forums as youtube -- apparently the difference is "more like 5-6%" (not to mention our differing number of chromosomes, etc.).

But, getting back to the original question: How do you sequence a genome?

To get a feel how this sort of sequencing works, let's first consider the 23 chromosome pairs in a single cell, all together holding a little over 6 billion DNA base pairs, which we could imagine lining up end-to-end as one single sequence - for example a book with 46 chapters each corresponding to an individual chromosome.

Next, imagine taking millions and millions of random snapshots of that DNA, each snapshot capturing only a very short sequence (e.g. a few hundred base pairs or maybe spanning a page or two if we stick to our "genome-as-a-book" analogy). Taken together, these tiny "snapshot" sequences (actually called "reads") cover the whole genome, with some of those reads overlapping one another. After taking enough snapshots, we know these reads contain all the information in the original genome sequence, but how can we put it all back together?

The answer hinges on the fact that these reads are in many places, overlapping. By using various mathematical and computational methods, all of the pieces can be matched up, eventually yielding the full genome sequence.

You can find more details here and here.

How old is the earth?

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!!!

Darwin Days @ Cornell: Dr. Massimo Pigliucci

This week, many people across the globe are celebrating Charles Darwin's 200th birthday (this Thursday the 12th), and the 150th anniversary of the publication of the Origin of Species. Cornell University and the Museum of the Earth have put together a fantastic lineup of lectures and events and a website with all the details which can be found here.

This evening, and yesterday afternoon during the Ecology and Evolutionary Biology weekly seminar, I had the great pleasure of listening to Dr. Massimo Pigliucci. I won't go into great detail, but the bulk of his second talk "What's science got to do with it? When scientists talk nonsense about religion" was a gem to listen to, and touched on a many interesting issues central to the conflict between religion and science.

I would strongly encourage you to check out his website and blog, where you can find some of his writing, publications, lecture slides, and mention of some of his books on science, evolution, and philosophy.

Here is a short list of points that caught my attention during his talk, here written in my words and not his. These mostly related to evolution and creationism/intelligent design, but touch on aspects of general science as well:

• When talking with someone (in his case, usually students) who is conflicted between their religious beliefs and learning about evolution, he gives these following words of advice: I won't ask you to believe it, I simply ask that you understand it.
  
• Quoting Richard Feynman (the physicist) from The Meaning Of It All: Thoughts Of A Citizen-scientist, he reiterated that the root of much conflict between religion and science comes from the notion that (to use another Feynman quote) "Religion is a culture of faith; science is a culture of doubt. "
  
• The conflict between evolutionary theory and creationism/intelligent design is not a scientific conflict, but a sociological and philosophical one. Science can only prove or disprove assertions about the natural world and is limited (if not unable) to prove or disprove assertions of a supernatural nature.
• That said, when religions make claims about the natural world (e.g. the earth 10,000 years old) a scientific approach can be used to evaluate them.
• Scientists would do well to learn about and apply the philosophy of science in their pursuits! Understanding the strengths and limitations of science can (of course) make for better science. I particularly enjoyed his commentary on statistics, which can be found on his website.
• Waiting until high school or college to teach basic science and critical reasoning is a no-no! This should be taught from early on, just like we teach reading, writing and mathematics.
  

My time is up for now, but I hope you get a chance to check out some of Massimo's work as well as any of the "Darwin Day" events that might be going on in your neck of the woods. That's all for now! :)