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News updates

December 11, 2009

First, as a followup on my Ray Comfort post, I somehow failed to adequately highlight the role which the National Center for Science Education played in responding to Comfort’s release.  Not only did they play a role in publicizing Comfort’s “borrowing” of his biography of Darwin (here), but the organization also played a huge role in the organized response to Comfort’s release.  For example, Eugenie Scott did a pretty strong critique of Comfort’s introduction and editing job as part of a US News online debate (here, and here).  It’s also worth noting here that the organization has also developed a website, available here, dedicated to highlighting problems with the text.  These sources are well worth checking out!

Also worth noting is the recent leak of Kent Hovind’s PhD dissertation.  PZ Myers discusses it on his blog Pharyngula, here.  Myers even includes a link where it is possible to download a copy of the thing in pdf form.

Also, if you’re interested in seeing some of the original manuscript pages from Darwin’s On the Origin of Species, you can now, at least digitally!  If you’re interested, check it out here.

fossil of the week #2

November 12, 2009

glyptodon at AMNH


This week’s fossil of the week is Glyptotherium texanum, a large extinct relative of the armadillo.  This particular specimen is on display at the American Museum of Natural History in New York City.  These guys likely went extinct between 10,000 and 11,000 years ago.  Charles Darwin himself actually discovered some glyptodont remains similar to this species while traveling on the Beagle.

In other news, currently working through the newest sequel, this time authored by William Dembski and Jonathan Wells. Released in 2008 , the webpage set up for this book states that its key message is that: “[m]aterialistic science is bankrupt; intelligence acts in nature, and its activity must feature in our scientific understanding of the world“.  As is often the case with the Intelligent Design Movement, there appears to be a key focus on defeating “materialism”.  I haven’t pored very deeply through the online text sample yet (available here), but plan to comment on it in a post once I have. As a text initially intended as a new version of Pandas, I don’t have much hope for it as a strongly convincing read, but I’ll wait until I’ve thoroughly analyzed the sections dealing with material I have a background in before condemning (or if its actually compelling perhaps openly considering) it.


fossil of the week

November 1, 2009

Pikaia, on display at the Smithsonian National Museum of Natural History.  One of the oldest known chordates, Pikaia featured prominently in Stephen Jay Gould’s book “Wonderful Life” and can be seen as perhaps an extremely distant uncle to our species.  Picture presented in black and white to highlight the fossil itself (Burgess Shale specimens are notoriously difficult to photograph, and I’m not a professional photographer).


T-Rex Soft Tissue and Young Earth Creationists

October 31, 2009

Anyone who’s followed the Young Earth Creationist movement and paleontology lately should know about the 2005 discovery of T-Rex blood vessels by Mary Schweitzer et al.  Young Earth Creationists have jumped on the find (here for example).  Creationists claim that the proteins preserved were far too fragile to have survived for “millions of years” and therefore must be only a few thousand years old.  However, this claim is flawed.
First off, there is the possibility that the Schweitzer soft tissue is the result of replacement (see here for more information on that possibility) of the material by other biological entities (ie bacteria). Other possibilities include that the proteins in question actually are preserved dinosaur remains (recent findings suggest this is a strong possibility).  It is worth noting here that we are looking at proteins, and not full strands of DNA.  Proteins are much more durable than actual DNA strands. Recently, work has been done which suggests that fossils may commonly preserve soft material when trapped in hard sandstone (which blocks oxygen deterioration).

The actual process of extracting the soft material from the bones can lead to a basic misunderstanding of the nature of the find.  The bone that Schweitzer worked with was soaked in acid for analytical purposes (this is a standard practice when working with rocks or fossils).  After being soaked in acid, the remaining “soft material” appeared pliable (see picture on pharyngula here).  However, being soft and pliable after being soaked in acid does not mean that the entire bone appears to be very young.  In fact, the bone looks just like any fossil.  The bone is on display at Montana State University’s Museum of the Rockies, so I’ve been lucky enough to see it up close.  Here are some pictures of it:

T-Rex femur

bone that soft tissue was extracted from

close up of site of extraction

location in bone where soft tissue was extracted from

As you can see, the bone itself does not look like something that just died; in appearance, it is extremely similar to most T-Rex bones one could find.  While the presence of blood vessels and cells being preserved in this bone is a surprise, it is not detrimental to the scientific interpretation of the age of this fossil.  Sure, it’s weird from a paleontology perspective, but unlike “Creation Science”, which forces everything to fit within its preconceived Biblical framework, paleontologists adjusted their position.  They asked the tough questions, and came up with plausible explanations for the existence of this material.  Yet Creationists are quick to jump on the find as proof of a young Earth.  Judging from the fact that the geologic evidence in general supports a very old Earth, and some hypotheses about the preservation of proteins and such have been tested (and shown promise), the Creationists appear to not have as strong a case as one would initially think.  But for Young Earth Creationists, the mantra stays the same:

Don't stop believin'



Coelacanth at Smithsonian National Museum of Natural History

October 30, 2009

I visited the museum this summer, and after walking through the paleontology displays (which were phenomenal, especially the Burgess Shale displays), I ran across this thing:


Coelacanth at NMNH

It took me a minute to process the display.  I subconsciously knew what it was likely, since I became extremely excited and practically ran up to the display.  However, it took me a minute to fully realize that I was standing face to face with a taxidermy specimen of an actual coelacanth.  Not sure how many people have seen pictures of an actual coelacanth, so I figured it’d be worth sharing (sorry about the relatively crappy quality; had to work around kids and curious people to get the shot).  If you’re ever in DC, the Smithsonian Natural History Museum is well worth checking out; its free, and they have a decent amount of material on display. The building gets a bit crowded (after all it is a free museum), but its well worth the time spent.

Icons of Evolution?

August 24, 2009

I spent the day yesterday in New York City. On the ride from Albany to NYC, I pulled out an old copy of Jonathan Well’s Icons of Evolution.  I purchased the book as a high school student (10th grade, if I’m not mistaken), when I was first getting into paleontology and evolution.  The title of the book looked interesting, and glowing reviews from people who I once thought might be well-respected mainstream scientists (these “mainstream scientists” were Philip Johnson, Michael Behe, and Guillermo Gonzalez) due to lack of scientific background on my own part led me to purchase the book, hoping to see an exposure of big gaps in evolutionary theory.  As you can tell, the book did not convert me.  I read the book, although something about it seemed fishy (as I now know, there are major scientific inaccuracies within the book which I will not address here; for more on them, click here).  I wasn’t some dogmatic, atheistic Darwinist hoping to squash opposing views; I was a highschooler who engaged opposing views just in case there was something to them.  I still hold the same practice today; when faced with opposing views, I do what every truly curious person does…I look at the facts.

However, a book such as Icons of Evolution can be confusing to a highschooler or even an open-minded adult with little or no scientific background.  I picked up the book thinking, at least for a moment, that there must be some sort of “controversy” over evolution (I had the same initial reaction to Behe’s Darwin’s Black Box as an 11th grader).  After a deeper analysis of the books and also available refutations of them, I realized that the supposed “controversy” was really only skin-deep.  Evolution isn’t a “theory in crisis”, but a well-developed and well-supported scientific theory.   However, looking back to this youthful stage, it is entirely concievable that I could have walked away from Behe and Wells with the idea that evolution really is a scientifically controversial issue.  If I had not been deeply interested in paleontology and evolution already, perhaps I would have just read Behe and Wells and then concluded that evolution is indeed a “theory in crisis”.  After all, their books were found in the science section of a major bookstore. 

I think that this is an important issue with regards to public perceptions of evolution (or science in general).  Anyone with an interest in a scientific topic can walk into a bookstore and pick up the first book on a topic to catch their eye.  Unfortunately, not all books are of the same quality.  In popular writings, there is no peer-review process to make sure that books on science are scientifically sound.  Major errors can slip right through the editorial process into print, and also into the hands of readers.  Yet the popular realm is where pseudoscience makes its push for credibility.  The general public, relatively lacking in scientific literacy (as I was as a highschooler), is often perceptive to pseudoscientific ideas.   If you look at an issue such as climate change or evolution, you will find a much larger percentage of the general public in opposition to the idea than you will for scientists.  Pseudoscientific ideas are often presented side-by-side with valid science (in bookstores, newspaper articles, and so on), thus implying a sense of equality between them.  Often, people do not have the time (or interest) to do a background check on the ideas to distinguish between valid and invalid ideas.  Due to this phenomenon, I would suggest that some sort of philosophy of science course (one that deals with the science/pseudoscience divide as well as what science is and isn’t) has a place in high school curricula in America. While there are numerous complaints against the American educational system, a course such as this could at least expose the general public to the difference between science and pseudoscience and equip them with the tools to tell the difference.

Also, on a relatively unrelated note, I recently read an interview on the ActionBioscience site with Philip Gingerich on the origin of whales.  It’s pretty good. If it’s an area you’re interested in, here’s a link to the interview.

Flushing a random tube #2

August 21, 2009

Continuing with posting random notes focusing on science, I’ve looked around for some interesting articles dealing with evolution with free online access.  Here’s a few to start:

First, the 1972 Eldredge and Gould Punctuated Equilibria article, available here in pdf format. This is the paper where Eldredge and Gould first describe the concept.  For a more basic explanation of Punctuated Equilibria, has a decent overview on the subject (available here).

Continuing with Gould, here’s his article titled “The Validation of Continental Drift”, focusing on some of the developments leading up to the modern theory of plate tectonics.  Good stuff! 

If you’re interested in origins, the 1858 Darwin and Wallace evolution paper is well worth checking out.  If you’ve read the Origin of Species, you owe your sanity to this paper presentation, which (along with Wallace initially contacting Darwin) led to the publication of Darwin’s “short abstract” that is the Origin of SpeciesHere’s the paper presentation from the University of Maryland website.

A final link of interest for this posting, the NCSE has a decent overview of all the major court cases dealing with evolution or anti-evolution movements.  If you’re interested in this topic, their site has an entire section focusing on it.  Available here.

Flushing a Random Tube #1

August 19, 2009

Trying a new approach on here.  I’m going to keep doing my more intense posts on a regular basis (ie longer posts focusing on one thing in detail), but also try to post other material of interest in shorter posts on a daily (or at least almost daily) basis, just to keep things interesting.  Today, as a result of inspiration from Stephen Colbert’s satirical wiki page, I’m flushing some random tubes, or looking around the internet for sites of interest.

First site in line is from Access Research Network, one of the major ID sites on the internet.  This is the ID Arts page.  From the page itself (available here):

“Our worldview impacts all areas of life including the arts. The arts also reflect philosophical and cultural trends in human societies. If philosophical and scientific concepts of intelligent design (ID) are valid, we believe they will both inspire, and be reflected in, our art, music, literature and film.”

So as we can see, ID is a social movement after all, regardless of the science.  This social aspect is reflected in the Wedge Document (although ARN is not part of the Discovery Institute, they are closely linked)(available here):

Discovery Institute’s Center for the Renewal of Science and Culture seeks nothing less than the overthrow of materialism and its cultural legacies. Bringing together leading scholars from the natural sciences and those from the humanities and social sciences, the Center explores how new developments in biology, physics and cognitive science raise serious doubts about scientific materialism and have re-opened the case for a broadly theistic understanding of nature. The Center awards fellowships for original research, holds conferences, and briefs policymakers about the opportunities for life after materialism.”

Now, stepping away from the Intelligent Movement, I want to highlight an extremely well-done paleontology website, the Oceans of Kansas project (available here).  If you’re interested in Mosasaurs and other aquatic reptiles from the Mesozoic (or paleontology in general), this site is well-worth checking out.

Also, in the world of Climate Change, the Hughen Falconer thing seems to be resolved.  In a comment on Chris Colose’s blog, it appears that someone sent an email to the people compiling the list asking to be added to it.  The people compiling the list apparently didn’t care enough to check the background of the the person in question though; apparently verifying a person’s credentials is not important.  Here’s the relevant part of the comment (available here; August 19th 2009 comment):

Further to this, I received an email reply from the site administrator and a person calling himself Hughen Falconer has had himself added via an email sent from a email address on 29th July.”

At least there’s some resolution there now; this “Hughen Falconer” guy seems like a hoaxter.

A Simple Truth

August 17, 2009

I put this post together in response to a conversation I got involved in dealing with science, pseudoscience, and religion.  Here it is in it’s unpolished, angry, and raw form:

What’s so terrifying about evolution?

While evolution is generally accepted among scientists, the public perception of evolutionary theory is mixed.  Many people perceive the existence of a “controversy” between advocates and opponents of evolution.  Some view evolution as an atheistic godless project that seeks to destroy all that is sacred to them.  Others sincerely believe that the science behind evolution is truly lacking, that competing ideas such as Intelligent Design or Creation Science (which are pseudoscientific in nature) are actually valid alternative ideas. 

Lost in the wings of most public engagements of evolution lies the following line of inquiry:

“What if evolution is real? What does this imply for our destiny?”

Let’s consider the question for a moment.  The question in question cuts directly to the root of the human identity.  If evolutionary theory is even partially correct, then it has profound implications for our species.  Daniel Dennett (1995) describes the theoretical framework in question as a “universal acid” that intrinsically alters all that it touches.  Evolution is indeed such an acid.  When looking at ourselves as a species, what do we see? Are we somehow “above” nature, and immune to it’s carnal struggles, or are we a part of nature, subject to the rules that govern the natural world?

The most cutting aspect of evolutionary theory is also perhaps the most overlooked.   Let’s step away from transitional features, hox genes, phylogenies, radiometric dating techniques, and the plethora of other scientific lines of inquiry contributing to the study of evolution and deep time.  We’re looking for something much simpler, yet also much deeper.

This Simple Truth is stunningly obvious when considered.  If humans are the product of evolution, then our fate is intrinsically linked to that of our planet.  You may be preparing to question the validity of this statement, perhaps noting a possible re-definition with religious terms (perhaps a “Young-Earth-Creationist-friendly” re-statement of it).  However, at least to the depth necessary for this inquiry (although I am not an expert on theology or comparative religions), I feel that my statement holds true.  The God of the Young-Earth Creationists is one that can and does intervene often throughout Earth’s history, creating a global flood responsible for the fossil record and also able to remove the waters necessary for this flood (note that I am not in support of Flood Geology, a concept first developed by George McCready Price and later championed  by Whitcomb and Morris in The Genesis Flood; the scientific validity of Flood Geology is notably lacking).  This God could easily intervene if the human race leads itself towards the brink of extinction through nuclear proliferation, environmental destruction, global warming, or some other threat. On a slightly different note, Intelligent Design, with its strikingly anonymous designer, could present a similar situation.  Does the Magical Mystery Man (my preferred name for the Intelligent Designer, since we are given no name) intervene at the gaps in the fossil record, or after extinction events?  When does intelligent design take place?  And is the Magical Mystery Man able to intervene in other aspects of the universe?  We may never know.

However, if one accepts the validity of evolution, then we are on our own here.  I’m not claiming that evolution leads to atheism or agnosticism.  There are many theistic evolutionists, such as Roman Catholic scientist Kenneth Miller.  Miller’s 1999 book “Finding Darwin’s God: A Scientist’s Search for Common Ground Between God and Evolution” suggests that religious belief and an acceptance of evolution are not mutually exclusive.  Setting aside a discussion of whether evolution leads to atheism or not (as demonstrated, it need not), let us return to our discussion.  Evolutionary theory places us as a part of nature.  Our fate and the fate of the world around us is inextricably linked.  If we destroy the world in which we live, we can likely expect no divine intervention, no saving grace from above.  From a Christian perspective, God gave us free will, and is allowing us to exercise it (but expects us to face the consequences of our actions).  From an atheistic one, there is no God, and  besides, why would a non-existent entity intervene to save us from ourselves?

The heritage of our evolutionary history is visible on a global scale.  Like all organisms, everything we do impacts the world around us.  How can we be so naïve to think that we are invincible?  We have destroyed countless species in our own lust for growth, development, and opulence.  Judging from the fossil record, it is likely that our actions will catch up with us eventually.  Life is a precious thing, and the fossil record shows us that it can easily be extinguished (such as during the mass extinctions at the end of the Permian, Ordovician, and Devonian Periods, among others).  Are we on the path towards our own extinction? 

If evolution happens, then what about other “controversial” ideas such as climate change?  Are humans really able to alter global temperatures on a noticeable scale?  After all, there are lists of scientists who seem reputable that oppose climate change.  However, these lists are often relatively disreputable.  For example, a recent one lists a “Hughen Falconer” among its signees (as noted on Chris Colose’s blog.  Click here).  This “Hughen Falconer” appears to be none other than Hugh Falconer, the Victorian paleontologist.  Of course, nobody was talking about global warming in Falconer’s day!  The general scientific consensus tends to be a “positive” one: humans have had a noticeable impact on climate change.  This makes sense.  If one looks at the amount of energy used by people on a global scale per day, it is absolutely astounding.  Our mining ventures can easily destroy entire mountains and replace them with lakes (see LeCain 2009 [for more on this book, see here] for more on open pit mining); the human hunger for metals such as copper for industrialization has had huge environmental costs.  Why doubt the impact of other human activities?  Lowly stromatolites (Cyanobacteria, or “algae) were able to forever alter Earth’s early atmosphere.  Why wouldn’t humans be capable of causing alterations of a similar scale.  According to most reputable climatologists, the verdict is in.  Humans have accelerated global warming.

If the implications of evolution and climate change are so profound, then why do so many people question the validity of these ideas?  I have implied that both evolution and climate change are well established scientific concepts. But if scientists accept them, then why does the general public often perceive them to be controversial ideas? Why evolution and climate change instead of quantum physics and advanced calculus?  Do the scientists have something to hide?

Luckily for scientists, it appears that they aren’t hiding anything.  Deniers of global warming or evolution often use out-dated or false arguments to further their point.  For example, in his book “Evolution: The Fossils Say No!”, Young Earth Creationist Duane T. Gish states that if we had “five or six” transitional forms from the evolutionary transition between fish and amphibians, it would be sufficient to prove evolution (52).  However, Gish was apparently not familiar with Icthyostega, Acanthostega, Tiktaalik, Panderichthys, Eusthenopteron, or other “transitional forms” (I will use the old term, which can be translated loosely to an organism that showcases lots of transitional features).  Even if he was, it he would likely make the same argument.  Scientific credibility is often not important to these people. 

What is important is public perception.  Raise objections that the average person, with little background in the subject in question, would see as reasonable.  Appeal to his sense of reason and fairness.   Show a list of scientists who doubt climate change or evolution, and claim that that list represents a sizeable portion of reputable scientists.  It’s ok if they are people with PhDs in Business and no scientific credentials, or have been dead for 200 years, or have little or no credibility within their own field of study.  You have their name on a list of people that deny climate change or evolution.  You can claim that they’re being oppressed for their views. Remind your reader that this is a democratic society, and that this oppression is unfair and un-American.  Heck, you can even appeal to your reader’s sense of patriotism if you want! Show your reader surveys of the American public that illustrate public doubts about evolution or climate change against surveys of scientists who overwhelmingly accept evolution or climate change, and then ask “why should the minority govern the majority?”

But most important of all, don’t worry about the facts.  Forget the fact that science is not a democracy.  Forget that science is governed by cold, hard data and not feelings, sympathy, and fairness.  Forget  (or rather exploit the fact) that the general public knows little about science, and do not attempt to educate the public.  Rather, use this lack of knowledge as a weapon to further your own goals.  Forget to try to publish your ideas in reputable journals, and focus on winning public opinion rather than scientific credibility.

But judging from the implications of evolution and climate change, should we let you succeed?  I say NO.  We should strive to educate the public about the nature of science, how it is done, the real meaning of the word “theory” in science (hint: it doesn’t mean “an unsupported guess”!!).  Point out the unscientific nature of religious attacks on evolution, but remain respectful of religion. Critically examine lists of “scientists who accept Creationism”, or “scientists who doubt climate change”, or “scientists who have doubts about Darwin”.  But most importantly, we must strive to expose pseudoscience and misinformation campaigns for what they are:


The cards are on the table, and the stakes are high.  We can embrace our place within nature and fight the threats to our existence, or we can deny it, and blindly hope for the Magic Mystery Man (our old friend the “intelligent designer) to ride in and save us.  What’s it going to be?

Works Cited:
Dennett, D.  Darwin’s Dangerous Idea: Evolution and the Meanings of Life. Simon & Schuster Paperbacks, New York, 1995
Gish, DT.  Evolution: The Fossils Say No!. Creation-Life Publishers, San Diego, 1979.
LeCain, T.  Mass Destruction: The Men and giant Mines That Wired America and Scarred the Planet.  Rutgers University Press, New Brunswick, 2009.
Miller, K.  Finding Darwin’s God: A Scientist’s Search for Common Ground Between God and Evolution. HarpersCollins Publishers, New York, 1999

Also, thanks to everyone involved in organizing The Giants Shoulders, a monthy collection of posts focusing on history of science.  My Hugh Falconer post has been included in this month’s edition.  For this month’s edition, click here.