Do ornithologists agree birds evolved from dinosaurs?

Monday, June 28, 2010 at 1:15 PM Bookmark and Share
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.

FDA Warns Maker of Chelation/Antioxidant Pills OSR#1

Friday, June 25, 2010 at 11:56 AM Bookmark and Share
Update:  See this post by Orac on Haley's response to the FDA warning.

I previously wrote a post about a chelating agent marketed as an antioxidant supplement called OSR#1, an unproven product that's been given to children to "treat" autism.  So far it's unclear whether these little pills have any therapeutic effect (seems doubtful) and whether or not they're safe (seems like they're not).

Well the FDA has been paying attention, and recently issued a warning to the maker: CTI Science (previously Chelation Technologies Inc.) run by president and CEO, Boyd Haley.  You can read the full letter from the FDA website.

(No worries - I'll pause here while you read the FDA's letter...)

Journalist Trine Tsouderos of The Chicago Tribune writes...
The FDA's June 17 letter to Boyd Haley, a retired Kentucky chemist and hero to the autism recovery movement, details five violations of the Federal Food, Drug and Cosmetic Act related to his product, OSR#1. Failing to correct such violations can result in fines, seizure of products and even criminal prosecution.

The Tribune in January reported that the compound, sold as OSR#1, had been developed to treat mining wastewater, and that it had not undergone rigorous testing to ensure it is safe and effective. The report was part of an investigation into unproven autism therapies offered by health providers who say they can reverse the disorder.

Haley did not reply to repeated requests for an interview Wednesday. An FDA spokeswoman said the agency has not received any communication from Haley, who has 15 working days from the date of the letter to respond.
...

In the interview last year, Haley called the product "a food" that is "totally without toxicity." Haley said the compound had been tested on rats, and a food safety study was conducted on 10 people. Asked to provide documentation of the research, he stopped communicating with the Tribune.

The FDA letter lists side effects recorded during Haley's animal studies: "soiling of the anogenital area, alopecia (hair loss) on the lower trunk, back and legs, a dark substance on lower trunk and anogenital area, abnormalities of the pancreas" and a rapid increase in normal cells contained in the lymph nodes.

Continue reading at the Chicago Tribune...
Ouch!

Over at Boyd Haley's OSR1 twitter feed, there hasn't been much action since their last exposure in the Chicago Tribune. Here's the feed as of June 25...

My BS meter tends to go crazy when someone responds to criticism with something like "the truth is at [my website]". Also, that earlier Chicago Tribune article Haley is referring to is this one, also written by Trine Tsouderos.

For more details on Boyd Haley and the autism community, jump over to Respectful Insolence and read Orac's post, Pumping autistic children full  of an industrial chelator (revisited).

Capturing a Record-breaking Burmese Python in Florida

Friday, June 18, 2010 at 3:28 PM Bookmark and Share
A couple of months ago, non-native Burmese Pythons (Python molurus bivittatus) began their breeding season in Florida -- at least the few who survived the large die-off this past winter.  By exploiting the breeding ecology and behavior of these hefty reptiles, wildlife managers use radio (or GPS?) tagged males to track down other pythons as part of their efforts to remove this invasive population.

In this post over at fieldherpforum.com, one member of a field crew has shared some photos and video from one such trip, where a tagged male lead the crew to a mating ball of five snakes:  the tagged male, three additional males, and one ginormous female. The big girl came in at a whopping 16'9" long and 134lbs!


Here's one photo of that tangled mass of snakes, plus some video just before and after the roundup.

Mid-week Reptilian #21: House Sparrow

Wednesday, June 16, 2010 at 10:15 AM Bookmark and Share
I'm writing this post in an airport as I wait for my very delayed flight (it's cool - I got a big juicy travel voucher and a couple meal vouchers, so Delta and I are still best buds). I had planned to get some work done, but as I sit here this week's reptilians are zipping around the terminal feasting on crumbs (practically begging me to write a blog post about them), trying to procreate, and all the while unknowingly flaunting their ability to coexist along side humans. It's that ability that has made the House Sparrow (Passer domesticus) one of the most successful bird species on the planet.

Figure 1: Male House Sparrow visiting a backyard in Toronto, Canada.

Software for Science & Math (part II): Getting started with R

Saturday, June 12, 2010 at 3:26 PM Bookmark and Share
A while back I wrote the first post in a series where I'll cover important concepts from Calculus, Probability and Statistics that (IMO) everyone should be familiar with. I wanted to occasionally involve two free software platforms (R and Maxima) in those posts, and I've finally gotten around to a post dedicated to getting started with R.

R is a handy computing platform and great way to learn basic programming skills. It can do basic statistics, plot data or mathematical functions, and provides access to a menagerie of advanced tools via R packages. And, it's all free. R's broad functionality and statistical capabilities makes familiarity with R a valuable skill in the natural sciences.

Getting Started with R

If you haven't already installed R on your computer you should check out this website on downloading and installing R or you can just pick your nearest CRAN mirror (e.g. at UCLA, NCI in Maryland, etc.) and download and install the appropriate version per their instructions.  If the install isn't working, feel free to post questions in the comments below.

Basic Interactive Examples

Craig Venter on the "synthetic cell"

 at 3:05 AM Bookmark and Share
I received an email a few weeks back from a reader suggesting I do a post or two on Craig Venter's recent accomplishment taking a bacterial cell and swapping in a fully synthetic genome, essentially making a new bacterial species.  It's a great suggestion, as I think what Venter and his colleagues have done qualifies as some smokin' hot, kick-ass science.  Unfortunately, I've not had much time to read up on the details, as I've been a bit busy with a conference and some pressing thesis work I need to get done (like yesterday).

As it happens, I just now stumbled across an opportunity to (at least briefly) touch on the subject. Check out  this gem of an interview with Craig Venter.


If you'd first like a sampler of what's in the video, below are a few selections that caught my attention (though I strongly recommend you watch it in it's entirety at least twice... maybe more!).

When I was first asked whether I found all this amazing, scary or both, I went with both, leaning more towards amazing than scary.  Now that I've looked into it further, I'm squarely at amazing and so far from scary it's almost scary! Venter and his colleagues seem to have put a great deal of effort into subjecting their research plans to serious ethical considerations, as mentioned briefly below, making sure their synthetic cell was too crippled and dependent on specialized media to thrive outside of the lab. Not at all surprising, but worth mentioning.

So what's the big deal here? I mean, yes it sounds cool - but what's the point? How will this impact my daily life in the coming years?  To answer that question we first need to be clear about what exactly they've done: very briefly, they've slapped together a genome sequence in a computer (yup, just a string of ...AGATCCACTAC... only it received a bit more forethought than my sequence) using the genome of a real organism as a starting point.  Then, they made the DNA using some advanced biochemistry and custom instrumentation (think of the expensive instruments used to read DNA sequences, but working in reverse). Next, they took that genome and used it to replace the genome of a bacterial cell. After that, they let their little unicellular Frankenstein go about doing it's own thing, happily reproducing itself in a lab somewhere.

While most of the media focus is on little Frankenstein, the real gem here are the techniques and technology that made it all possible.  As far as making a new cell goes, they didn't quite go there. They tweaked the genome a bit on the computer, made the genome (which really is an impressive accomplishment) and handed it off to an existing cell.  To use Venter's computer analogy, what they did was something like the cellular version of reformatting a computer running Debian linux, and replacing the operating system with a copy of Damn Small Linux.  Not a big change to say, Windows, and definitely not rebuilding a new computer from scratch.

Still, there are many reasons why their accomplishment is darn cool.  First, here's Venter with the big picture....
Interviewer: What do you ultimately hope to do with a method like this?
Venter: Well, this is an important step we think both scientifically and philosophically. It's certainly changed my views of definitions of life, and how life works. It's pretty stunning when you just replace the DNA software in a cell and the cell instantly starts reading that new software -- starts making a whole different set of proteins -- and within a short while all the characteristics of the first species disappear and a new species emerges from this software that controls that cell going forward. When we look at lifeforms we see them as sort of fixed entities. But this shows in fact how dynamic they are, that they change from second to second. And, that life is basically a result of an information process -- a software process -- our genetic code is our software. Our cells are dynamically, constantly reading that genetic code making new proteins, the proteins make the other cellular components, and that's what we see.

From a more practical perspective, our own success as a species has been in large part due to our ability to mix and match the DNA of different organisms for our benefit.  We've advanced from simple selective breeding of livestock and crops, interspecific hybridization, and basic artificial selection up through the relatively recent discovery of DNA and the ability to alter genetic material directly.  Venter et al's new techniques are another big step in that same direction.  This may have many implications, such as this example mentioned by Venter:
Perhaps the most important, immediate application is ... we're already working at the Venter Institute and working with Novartis to try and make new vaccines very quickly. We think we can shorten the process by 99% for making the flu vaccine each year by using these new synthetic techniques.
For flu and other pathogens with relatively high rates of evolution, and for some newly emerging infectious disease, we're limited in how quickly we can mass produce vaccines. This is perhaps common knowledge following last years swine flu pandemic, but increasing our response time to vaccinate against emerging infectious disease by an order of magnitude or two could literally save millions of human lives.

Finally, they've also done some pretty cool things that have little to do with the frontiers of science and technology.  Nothing wrong with having a little fun while you work, right?
We've developed a new code for writing english language, other languages, with punctuation and numbers into the genetic code. In the first watermark [in the new genome] we actually have this code that needs to be decoded for people to read the rest. We even have a website built into the genetic code that if people solve it they can let us know that they've been able to read it.

Stephen Prothero's book "God Is Not One", LA Times Review

Thursday, June 10, 2010 at 7:10 AM Bookmark and Share
There's a book review in the LA Times of Stephen Prothero's latest book God Is Not One (that's Stephen Prothero the author and professor of religion, not Donald Prothero the paleontologist who wrote this great book).

I won't be picking up the book until my thesis work gets finished, but I thought you might appreciate the reviewer's summary of religious differences that exist in the world today...
And how different are they?

Christians regard sin as the problem and see salvation as the solution. Muslims define the problem as pride that can only be conquered by submission. Buddhists seek to overcome suffering while Christians regard suffering as ennobling, which is why Christians aren't trying to achieve nirvana. Buddhists, unlike Christians, aren't looking for salvation since they don't believe in sin. Neither do Confucians. And while Jews and Muslims speak of sin, they are not all that interested in salvation from their sins.

And there's more.

Jews believe in one God, Buddhists believe in no God, Hindus believe in many gods. Christ is regarded as a God among Christians, whereas for Muslims, Muhammad is very much a man who achieved perfection as a prophet, political leader, military general and family patriarch. And when it comes to the diversity in denominations among the world's religions, Christianity is king.

Got all that?

[Hat tip to Ophelia Benson @ Butterflies and Wheels]

The Great Textbook Wars

Wednesday, June 9, 2010 at 4:57 PM Bookmark and Share
Texas (among other states) has made news in recent years whenever fundamentalist Christians wage campaigns to replace the content of  public school text books wherever they conflict with their particular brand of religious dogma.  Because states like Texas are large consumers of school books, those changes end up affecting other states and thus affecting the rest of the nation.

In light of that old aphorism "those who cannot remember the past are condemned to repeat it," you should check out The Great Texbook Wars -- an American RadioWorks documentary on the history of cultural and religious battles over what should and should not be taught in public schools.

While returning from a conference last week, I heard a local NPR station advertise The Great Texbook Wars for this coming Friday, June 9th.  You can check your local NPR listings to see if and when it's airing in your neck of the woods.

In the mean time, click on over to the website and check out the three short essays and many great photos available there.  It looks like a great program, one not to be missed!

Monday Mammal #8: Bill Nye the Science Guy?

Tuesday, June 8, 2010 at 1:17 AM Bookmark and Share
Oh, come on - he won the 2010 Humanist of the Year award!  I say that totally earns him some spotlight time as a noteworthy mammal (...plus I've been a bit busy lately).

Video of his acceptance speech are up over at Hemant's Blog.

Neil DeGrasse Tyson on the value of scientific literacy

Sunday, June 6, 2010 at 1:14 PM Bookmark and Share
I've often heard students question the day-to-day value of science: "Yeah, but how is knowing <insert scientific claim> going to impact my life if I'm not a scientist?" In my experience, these individuals almost always confuse a particular scientific claim with the scientific process that lead to acceptance of that claim.

Often times they're right - some scientific facts are simply useless for most people - but any decent response to their question should always bring them back to science as a process, not a fact. 
"Science literacy empowers you to know when someone else is just basically full of it. Because you understand... how the world works and what the limitations are, then you can judge whether someone is trying to exploit your scientific ignorance."
In the clip below, American astrophysicist (and kick-ass public speaker) Neil DeGrasse Tyson explains.

Steve Martin, Atheism, and The Age Of The Universe

Wednesday, June 2, 2010 at 12:36 AM Bookmark and Share
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

To The Pope: "Quick, Man! Cling Tenaciously To My Buttocks!!"

Tuesday, June 1, 2010 at 1:39 PM Bookmark and Share
To Powdered Toast Man:  "... Both of them?"


[Hat tip to Skepchick]