Archive for May 2009

Archaeopteryx, cladistics, ghost taxa, and anti-evolution movements

May 18, 2009

Archaeopteryx is perhaps the best known “transitional fossil” in the sense of public recognition.  First discovered in Germany in 1861, 2 years after the publication of the first edition of Darwin’s Origin of Species, it has been hailed as a transitional phase between reptiles and birds ever sense.  Darwin himself was aware of the existence of Archaeopteryx, and addressed this fossil in later editions of the Origin.  Consider the following passage from the 6th edition of the book:

“[A]nd still more recently, that strange bird, the Archeopteryx [sic], with a long lizard-like tail, bearing a pair of feathers on each joint, and with its wings furnished with two free claws, has been discovered in the oolitic slates of Solenhofen.  Hardly any recent disc overy shows more forcibly than this , how little we as yet know of the former inhabitants of the world.” (Darwin 1859:444  see 6th edition here).

While Darwin at least mentions the existence of Archaeopteryx here, it is in a letter from paleontologist Hugh Falconer to Charles Darwin, from Jan. 3, 1863, where we begin to see the true significance of the find:

You were never more missed—at any rate by me—for there has been this grand Darwinian case of the Archaeopteryx for you and me to have a long jaw about…You are not to put your faith in the slip-shod and hasty accoutn of it given to the Royal Society.  It is a much more astounding creature—than has entered into the conception of the describer” (Falconer, 1863 in Correspondences vol. 11 p.5)

Falconer’s statements here tell us a number of things.  First, that he saw Archaeopteryx as a valid “transitional” fossil, or as evidence in favor of evolutionary theory.  Second, it is obvious here that Falconer had a large amount of respect for Charles Darwin as a scientist.  It is worth noting here that Falconer discovered stasis in the fossil record as a valid trend over a century before Eldredge and Gould’s 1972 work on Punctuated Equilibria, thus rendering Eldredge and Gould as a re-discovery, rather than a discovery, of stasis.  But I digress. 

Moving back to a discussion of Archaeopteryx, the genus was held as a transition between lagosuchids and birds for the first half of the 20th century.  This was largely due to a gappy lagosuchid and dinosaurian fossil record; upon more fossil discoveries, the Lagosuchid line was shown to be  too specialized to be ancestors of birds.  In fact, largely as a result of the work of John Ostrom on Deinonychus and Archaeopteryx, dinosaurs were suggested as the ancestors of birds (for more info on this, see Bakker 1986: 298-322).  With the discovery  of more fossils, especially feathered dinosaurs from China, the dinosaur-bird connection has become well-accepted among paleontologists (for more info, click here).

So why are dinosaurs accepted as bird ancestors by scientists today?  As early as the latter half of the 19th Century, TH Huxley noted similarities between dinosaurs and birds.  However, to fully appreciate the modern state of Archaeopteryx, one must look at recent publications.  While there is some debate as to the exact place of birds within the classification of Theropods (bipedal, often predatory, dinosaurs such as Tyrannosaurus Rex), birds are almost universally accepted among paleontologists as a form of derived theropod, generally within the maniraptorian segment of the group (see Benton 1992 p. 22). Looking specifically at Archaeopteryx, let’s consider some of the traits that suggest that birds evolved from dinosaurs.  The skeleton of Archaeopteryx is so similar to dinosaurs that the first specimen discovered was initially mistaken for a Compsognathus (a small type of theropod).  Archaeopteryx, as well as other theropods and birds, had a relatively unique mesotarsal joint (a part of the ankle), a half-moon shaped bone in the wrist (the semilunate carpal), gastralia, an s-shaped curve in the neck, and feathers.  Some more dinosaurian features of Archaeopteryx include conical teeth (similar to those of other early birds such as Hesperornis and Icthyornis), claws very similar in structure to those of dinosaurs such as Deinonychus, and a long bony tail (for more discussion, see Prothero 2007 p. 260). These similarities, among others (such as similarities in hip structure), suggest that birds did, in fact, evolve from dinosaurs.

 However, Archaeopteryx’s status as a “transitional fossil” is often attacked by anti-evolutionists. One of the most popular approaches to Archaeopteryx from this angle is to denigrate Archaeopteryx as a “mosiac form”, and compare it to the platypus (see Johnson1993:80-81).  This approach assumes that the shared characteristics between Dinosaurs, Birds, and Archaeopteryx are of little consequence, just like the bill of a platypus (after all, a platypus has a bill and lays eggs, but nobody calls it a bird!).  However, this approach showcases a large-scale misunderstanding of how paleontology and comparative anatomy work.  Archaeopteryx is not considered a “transitional form” solely because it has some bird-like features and some dinosaur-like features.  It is significant because some of its features are shared ONLY by Theropod dinosaurs and Birds.  A cladistics-based approach to Archaeopteryx will place Archaeopteryx between other “birds” and “dinosaurs” as a “transitional form” (for more on cladistics, click here). This is due to the fact that many features are shared only by Archaeopteryx, Theropods, and other birds, not because Archaeopteryx just “shares some charisteristics” with birds and dinosaurs.  Anti-evolutionists (either ID advocates or Creationists) are fond of using this “mosiac form” approach to fossil proofs of evolution, even though (as demonstrated) it illustrates a misunderstanding of paleontology and cladistics. 

One other objection often raised to the status of Archaeopteryx is the argument that since the dinosaurs that are claimed to be Archaeopteryx’s closest relatives were contemporaries of Archaeopteryx in the Jurassic period, Archaeopteryx cannot be a valid “transitional form”.   However, this argument is also weak.  Using the concept of ghost taxa, or taxa inferred in a cladistic tree from unique shared characteristics, scientists can infer the characteristics of “transitional forms” between Archaeopteryx and the dinosaurs it evolved from, for example.  While this approach assumes the validity of evolutionary theory, this is not a problem, due to the fact that evolutionary theory is uniformly accepted by biologists and paleontologists.  Biologists see natural selection operating on a daily basis, and paleontologists continuously find an ordered, linear sequence within the fossil record.  Combining these two lines of evidence (among many others), one can infer that evolution does, in fact, work.  Therefore, the assumption of evolution as a scientific fact does not present a serious problem.

If Archaeopteryx’s status as a “transitional fossil” is so well-accepted by scientists (note that by saying Archaeopteryx is a traqnsitional form, I am not saying that it necessarily evolved into birds, but rather that it showcases features unique to birds and dinosaurs, which illustrates that dinosaur-bird evolution has taken place, either through Archaeopteryx or some other closely related group of early birds), then why are people still trying to destroy it’s status?  Archaeopteryx is not the problem here.  Evolution itself isn’t even necessarily the problem.  The problem is often that Archaeopteryx, evolution, and a 4.6 billion-year-old earth are seen, at least by some, to threaten the percieved “special place” of humanity in nature. This conflict is the root of the percieved conflict between science and religion.  What is at stake here, from the perspective of Creationists especially, is not science, but rather humanity’s special place, elevated above the rest of the natural world.

Works Cited:

Bakker, RT.  The Dinosaur Heresies: New Theories Unlocking the Mystery of the Dinosaurs and Their Extinction. Citadel Press Books, New York, 1986

Benton, MJ. Origin and Interrelationships of Dinosaurs, in The Dinosauria, edited by DB Weishampel, P. Dodson, and H. Osmolska.  University of California Press, Berkeley, 1992.  p. 11-30.

Darwin, C.  The Origin of Species. 6th edition, reprinted by Castle Books, Edison, 2004. First edition originally published 1859.

Falconer, H. letter of Jan. 3, 1863 to Charles Darwin.  In The Correspondence of Charles Darwin Vol. 11, edited by F. Furkhardt, DM Porter, SA Dean, JR Tophan, and S. Wilmot.  Cambridge University Press, Cambridge, 1999

Johnson, PE.  Darwin on Trial.InterVarsity Press, Downers Grove, 1993

Prothero, DR.  Evolution: What the Fossils Say and Why it Matters. Columbia University Press, New York, 2007.

In the Footsteps of Giants

May 7, 2009
Helderberg Escarpment

Helderberg Escarpment

In a hidden corner of Upstate NY, near Voorheesville, and just outside of Albany, lies John Boyd Thatcher State Park.  The major feature of this park is the Helderberg Escarpment, a cliff face consisting of Silurian and Devonian limestone.  The most prominent units are the Manlius and Coeymans limestone, consisting of Silurian deposits in the lower Manlius, and early Devonian deposits in the upper Manlius and Coeymans (click here for more information).  The landscape is dynamic, with caves and waterfalls, rockfalls, and gorgeous views from the cliffs.  The topography is pleasing to the eye.

waterfall, with Coeymans Limestone on top, and Manlius below it (the lower layers that have eroded more)

waterfall, with Coeymans Limestone on top, and Manlius below it (the lower layers that have eroded more)

The geology of the Helderberg Escarpment is intriguing, both for the strata itself and also for the fossils present, which consist of tentaculites and other small shells in the Manlius and more diverse brachiopods, bryzoans, trilobites, crinoids, and horn coral in the upper units (mainly the Coeymans and New Scotland Beds).  However, the historical significance of the location is perhaps even more intriguing.  The period of time from 1819 to 1850 saw visits to the escarpment by the likes of Charles Lyell, Louis Agassiz, James Hall, James Dwight Dana, and Benjamin Silliman, among others.  These scientists were all extremely influential geologists.  Let’s take a look at what they accomplished in their scientific careers.
Lower Devonian Brachiopods (from New Scotland beds)

Lower Devonian Brachiopods (from New Scotland beds)

Upper Silurian tentaculites from Manlius beds

Upper Silurian tentaculites from Manlius beds

Plaque at JBT State Park

Plaque at JBT State Park

Charles Lyell is perhaps the best known geologist on this list.  His book “Principles of Geology” was extremely influential, both to the geologic community and to Charles Darwin (Darwin read it while travelling on the HMS Beagle).  While James Hutton is credited with laying the foundation for modern geology (most famously, through his visit to Siccar Point), Lyell is the scientist most responsible for making geology popular as a science to the general public.  He was on friendly terms with Darwin, and encouraged a young Charles Darwin to present his theory of natural selection jointly with Alfred Russel Wallace in 1858.  Charles Lyell is best known for his work on the concept of uniformitarianism.  While a strict form of uniformitarianism is rejected by today’s geologists (in some instances, we know that catastrophic events have occurred on  a global scale, such as the asteroid impact that formed Meteor Crater in Arizona), Lyell’s contributions to geology are still extremely important to geology as a science.-
Louis Agassiz is remembered as one of the last great Creationist scientists; he still embraced a Biblical view of geology, even after the publication of Darwin’s Origin of Species. However, Agassiz did other things besides argue for a Biblical view of geology.  Agassiz did significant work on glaciers, which he saw as forming instantaneously.  While partially wrong, his work on glaciers helped to seal the end of Flood Geology as a scientific mindset. The Helderberg Escarpment and surrounding areas showcase some pretty interesting glacial features, thus perhaps leading to Agassiz’s interest in the region.  Agassiz is also remembered for his research on fossil fish. —
James Hall is the least recognized scientist that will be discussed here.  He studied under Amos Eaton at Rensselaer Polytecnic Institute in New York, and became the first state paleontologist of New York in 1841. James Hall helped bring the New York State Museum to national prominence as a paleontology institute for a number of years, and also discovered that fossil stromatolites were once living organisms.  Hall was Lyell’s guide to upstate NY, the Helderberg Escarpment, and is remembered as a decent scientist with an often flamboyant and short-tempered personality, as evidenced here:-                                                                                                                                                                                                                                                                             
“In one notable instance in 1849, Hall became outraged at discovering that James T. Foster, a school teacher in Greenbush, New York, had ordered the publication of a popularized—though by Hall’s standards, vague and inaccurate—geological chart for distribution in public schools. When he learned that copies of the map were to be shipped via the Hudson River Night Line to New York City, Hall stole aboard and threw the entire printing into the Hudson River!”-                                                                                                                                                                                                                
James Dwight Dana should be a familiar name to anyone who has ever taken a minerology course.  Dana was born in Utica, NY in 1813. Like Darwin, Dana participated in a scientific voyage, the American Wilkes Expedition.  Dana, like Darwin, also did some research on coral reefs.  While on the Wilkes Expedition, Dana read Darwin’s Voyage of the Beagle, ironically enough.  Dana also corresponded with Darwin, ran the American Journal of Science, and laid the foundation for modern minerology.  Darwin respected Dana as an intellectual, and sent him a copy of the Origin of Species in 1859 for feedback. The two men eventually developed a close relationship.-                                                                                                                                                   
Benjamin Silliman, while forgotten by many, is responsible for some relatively influential research.  Dana was a chemist and geologist, and was the first person to distill petroleum. Silliman’s father was a general in the Revolutionary War, and was taken prisoner by the British in 1779. Benjamin Silliman’s collections helped to lay the foundation for Yale’s Peabody Museum.  Silliman also was extremely influential in the development of science programs at Yale.-                                                                                                                                                                                                         
While the Helderberg Escarpment is unknown to most people today, it was known to many of the most prominent geologists of the 1800s. The historical players that visited this locality in Upstate New York helped to formulate the basic framework of modern geology.  Their research lies at the core of what we know about the geologic record. Some of the scientists that visited this location (James Dana, James Hall) corresponded with Darwin.  Charles Lyell often saw Darwin in person.  Perhaps Darwin learned about the Helderberg Escarpment through discussion with Lyell (although this is pure speculation). Locations such as this one are fascinating to visit, especially with the awareness that one is walking in the footsteps of some of the most important scientists of the 19th Century. 

Darwin and Owen

May 6, 2009

While Sir Richard Owen is best remembered today for coining the term “dinosaur” (or in the realm of the scientific historian, perhaps for his work on homology),  his personal affinities are often forgotten.  Richard Owen is remembered through the records we have of his life as a brilliant anatomist, but also as an arrogant jerk.  Here, we will look at Owen specifically through his relationship with Charles Darwin.  I choose Darwin here because he is both familiar to most people, and also because the historical record has preserved a large body of material on Darwin’s life, work, and interactions.

As Darwin began his work on the Beagle, he developed a professional relationship with Owen. This is evidenced by the fact that Darwin sent fossil specimens discovered while on the HMS Beagle (such as Toxodon; this letter is from their correspondence over the fossil) to Owen for study and description.  The working relationship between Darwin and Owen lasted at least into the early 1850s, as evidenced in this letter, written in 1850, where Darwin asks Owen for assistance in borrowing a specimen for study from a Mrs. Dixon.  This suggests that Darwin and Owen had at least a working relationship in 1850.

However, great discoveries often lead to hurt feelings.  In 1858, Darwin’s idea of natural selection was presented to the Linaean Society, along with a paper by Alfred Russel Wallace presenting an extremely similar concept.  The material presented by Darwin would soon be utilized in his best known work, On the Origin of Species (which you can read here).  While the work of Darwin and Wallace provided a working mechanism for evolution, Owen never embraced Darwin’s concept of natural selection, as evidenced by this review of On the Origin of Species from 1860.

Thus, Owen disagreed with Darwin on a scientific level.  This disagreement also helped fuel tensions between the two men.  In a letter from Darwin to Charles Lyell, dated 10 December, 1859, Darwin states the following about Owen:

I have [had a] very long interview with Owen, which perhaps you would like to hear about, but please repeat nothing. Under garb of great civility, he was inclined to be most bitter & sneering against me. Yet I infer from several expressions, that at bottom he goes immense way with us. — He was quite savage & crimson at my having put his name with defenders of immutability

This passage should turn some heads, as it makes me sound like a hypocrite.  Initially, I stated that Owen disagreed with Darwin on natural selection.  But here, we have Darwin relating (to Lyell) criticism from Owen for a statement claiming that Owen defended “immutability”.  This sounds like Owen supports evolution, and by Victorian standards, he occasionally did.  Owen vaccilated  between accepting and denying some sort of evolutionary process throughout his career.  However, Owen never accepted natural selection.  This dichotomy sounds strange today, where the sole working model of evolution that we have is based on natural selection, but in the mid-1800s, natural selection was not yet an acceptable paradigm.  Thus, in light of this fact, it is perhaps easier to understand Owen’s position. 

But I digress.  One other major component of the letter quoted above is the supposed anger that Owen showed towards Darwin.  While I hesitate to read too much into one letter, especially one between Darwin and a third party (Lyell) rather than Owen, this letter suggests that tensions between Owen and Darwin were at least building in 1859.  Judging from later sources, it is obvious that the professional relationship between Owen and Darwin would soon end.  Consider the following passage from Darwin’s autobiography:

I often saw Owen, whilst living in London, and admired him greatly, but was never able to understand his character and never became intimate with him.  After the publication of the Origin of Species he became my bitter enemy, not owing to any quarrel between us, but as far as I could judge out of jealousy at its success.  Poor dear Falconer….had a very bad opinion of him, being ocnvinced that he was not only ambitious, very envious and arrogant, but untruthful and dishonest.  His power of hatred was certainly unsurpassed.  When in former days I used to defend owen, Falconer often said, “You will find him out some day, and so it has proved.” (Darwin 1887)

This statement, perhaps more than any other, describes Darwin’s experiences with Owen.  Darwin admired Owen as a scientist, and sought assistance from Owen early in his career.  Darwin and Owen, while not necessarily friendly, worked well together for a period of time from the 1830s until the 1850s, until the publication of The Origin of Species.  Perhaps Owen truly did feel slighted when Darwin claimed that Owen accepted “immutability” rather than an evolutionary worldview.  Or perhaps Owen actually did become Darwin’s “bitter enemy” as a result of jealousy.  Personal feelings are difficult to pin down in situations such as this.  However, it is clear that Darwin, at least early on in his career, admired Owen and even defended him against attacks by Hugh Falconer (a Victorian paleontologist who Darwin also corresponded with).  After the publication of The Origin of Species, however, Darwin’s respect for Owen faltered, likely as a result of Owen’s attacks on Darwin. 

The relationship between Darwin and Owen can be instructive to anyone interested in science.  The dynamic nature of the relationship, one that started out as a working relationship between colleagues and ended with the two men being driven apart, serves as a reminder that scientists are people, not just brains that are stored somewhere in a box with no personal lives or relationships.  Science is a constructive process that requires the input of others in order to help with one’s own research, as evidenced by Darwin sending fossils to Owen for study in the 1830s.  Science, then, is a constructive enterprise.  If one scientist has a weak background in a subject area, they consult another scientist who is an expert in that subject.  Science is based not only on testable hypotheses but also on teamwork.

Teach the Controversy? Evolution, Creationism, and Intelligent Design in America

May 4, 2009

A few days ago, I was standing in line at a local bookstore waiting to buy a copy of Matthew Chapman’s 40 Days and 40 Nights: Darwin, Intelligent Design, God, OxyContin, and Other Oddities on Trial in Dover.[1]  It was a long line, so I soon found myself engaged in conversation with some of the other people waiting to buy books.  One woman saw the book I was carrying, and once she realized it discussed evolution at least partially, proceeded to instruct me that “evolution is just a theory; it isn’t proven yet.”  She seemed to be a well-meaning, intelligent person, but by implying that evolutionary theory is somehow weak since it is “just a theory”, it was clear that she had been misled.

She is not alone.  As evidenced by recent events, many Americans feel the same way about evolutionary theory.  In 2005, in Cobb County GA, for example, the local school board moved to place warning stickers in biology textbooks that read:

“This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully, and critically considered.”

Clearly the Cobb County school board also misunderstood the meaning of the term “theory” in a scientific sense.  But what is a scientific theory? Unlike the everday usage of the word “theory”, which generally refers to a guess or hunch, the scientific usage of the term “theory” means something along the lines of “a comprehensive explanation of some aspect of nature that is supported by a vast body of evidence,” according to an article by the National Academy of Sciences.  Luckily for science, the Cobb County stickers were eventually declared unconstitutional and removed from textbooks as a result of Selman v. Cobb County.  While the situation in Georgia has ended, the anti-evolution movement has kept going.

For example, Senate Bill 2396, which attempted to require a critical presentation of evolution in Florida schools, recently died in committee.  This bill sought to teach “the other side” as well, as stated by Stephen Wise, the senator who authored the bill.  Judging from NCSE and other sources, Wise also supports teaching intelligent design in schools, a practice strongly condemned in Kitzmiller v. Dover.  Bills such as Wise’s imply that there is some level of controversy in the scientific arena when evolution is considered.  However, as Stephen Jay Gould has argued, the only controversy surrounding evolutionary theory is a perceived controversy, fueled by rehashed Creationist arguments. 

While evolutionary theory is a vibrant theory, some groups still argue against evolution.  These arguments are often political or ideological (rather than scientific) in nature.  For example, many Young Earth Creationists argue that if we teach our kids that they came from monkeys, they will act like monkeys (to use an oft-repeated refrain). Answers in Genesis, a leading Young Earth Creationist website, alleges that “By definition, no apparent, perceived, or claimed evidence in any field, including history and chronology, can be valid if it contradicts the Scriptural record.” in their Statement of Faith.  The Discovery Institute, major backers of Intelligent Design, have stated in a fundraising memo that they seek “nothing less than the overthrow of materialism and its cultural legacies” (pdf p. 2). The author of the Wedge Strategy, the strategic plan laid out in the Wedge Document, is Philip Johnson.  Johnson seeks to attack the “naturalistic” philosophical underpinnings of evolutionary theory in an attempt to replace them with a framework that allows supernatural causation to become a key part of scientific investigations. Jonathan Wells, prominent Intelligent Design proponent, has implied that he is on a religious mission to “destroy Darwinism“.

Groups such as the Discovery Institute and Answers in Genesis provide the basic foundation for a percieved “controversy” within science over the validity of evolution.  While the scientific credibility of these groups is virtually nonexistent, they have touched a nerve within the American public.  They argue that science is “naturalistic” at its core, and therefore atheistic.  However, while science cannot use God as an explanation in its current form (God is supernatural, and therefore not scientifically testable.  Science can only test natural cause explanations), it also cannot refute the possibility of God existing.  Certain scientific facts may fly in the face of certain religious beliefs (such as the geologic timescale contradicting a specific interpretation of Genesis that proclaims a 6000 year old Earth), but this is not by design.  However, groups such as Answers in Genesis and the Discovery Institute have latched onto the idea that science is out to exclude God from the picture. In a relatively religious nation, it is easy to create an imagined controversy using this approach.  It is far easier for many people to accept a “scientific” idea that confirms their religious beliefs than one that refutes them.  While authors such as Stephen Jay Gould have argued that science and religion can coexist because they occupy “separate realms,” in some cases, this coexistence is impossible.  If a person believes that the Bible says that the Earth is 6000 years old, they are likely to accept ideas such as Flood Geology which, while being scientifically flawed, seem to confirm their belief system. This is why Answers in Genesis survives.  Not because they are a reputable scientific organization, but because they seem to provide people with confirmation for their beliefs.

So if anti-evolution arguments tend to operate on a political or religious playing field, why do they bother scientists?  According to Kevin Padian, the attempt to single out evolution in classrooms in Dover for special treatment (“evolution is only a theory”) has the effect of making kids stupid by confusing them about science (PDF p. 41). In the words of Theodosius Dobzhansky, “nothing in biology makes sense except in the light of evolution”.  Evolutionary theory is the keystone of biology in general, and is supported by mountains of evidence.  Teaching religious challenges to evolution not only will confuse students about the nature of science, but also violates the first ammendment establishment cause in the US Constitution.  Therefore, it is necessary to refrain from teaching “Creation Science” or “Intelligent Design” (which has been shown to have Creationist roots) in science classrooms, not only for religious reasons, but also for educational ones. People tend to accept the presence of a “controversy” surrounding evolution especially if evolution is perceived as a threat to their own religious beliefs.  However, the science classroom is not the place to provide religious guidance.  We need to embrace evolution, both in the science classroom and in the lab, if we hope to remain competitive as a nation in the scientific realm.  This is why anti-evolution movements are dangerous. Not because they somehow threaten evolution, but rather because they confuse the public about science, and also threaten the American scientific standing on an increasingly globalized playing field.

[1] An entertaining, irreverent, and all-around enjoyable text dealing with the 2005 Kitzmiller v. Dover trial, which struck down an attempt by a Dover, PA school board to have a paragraph read before science classes calling evolution a theory with major gaps, and referring students to copies of Of Pandas and People for another perspective (the intelligent design perspective).