Monday, February 25, 2008

Transitional fossils

Dear Discovery Institute,

Today we will talk about your stance on transitional fossils once again. As suggested in my earlier post on transitional fossils, at least some of your members think that there are no transitional fossils. However, when a transitional form such as Tiktaalik comes up, obviously falling right between phases that were supposed to have had not transitional phases, you seem compelled to comment. We will consider an attack on mainstream scientists and Tiktaalik linked on your site in this letter.

First, here is a link to the article being discussed:
http://www.evolutionnews.org/2006/04/one_step_forward_two_steps_bac.html

Now, for our first quote:

"I love it when new "missing links" are discovered, because it's then--and only then--that Darwinists admit how precious little evidence had previously existed for the evolutionary transition in question. When reports came out this week of an alleged example of a fossil representative of the stock that might have led from fish to tetrapods -- Tiktaalik roseae -- evolutionists finally came clean about the previous lack of fossil evidence for such a transition"

I don't see the major issue with scientists admitting to not having a transitional form. An argument of this type is about as valid as attacking a scientist's background by claiming that the individual did not have a strong background before recieving an education. Just because Tiktaalik was not known initially does nothing to undermine it's validity as a transitional form. In fact, it serves to support evolutionary theory; evolution predicts the presence of a transitional form, paleontologists find exactly that in the rock record, and then claiming that the transitional fossil is invalid because scientists don't have the transitional fossils that fall between this transitional fossil, less complex fossils, and more complex fossils. But I guess this is the sort of attack that the Intelligent Design movement must resort to when any "evidence" of a Designer in the fossil record is completely and totally insignificant. Attacking admissions of the lack of transitional fossil A when we have B, C, and F does nothing to undermine the scientific validity of evolution. Rather, it shows that scientists aren't making up transitional fossils. Scientists have the transitional fossils that they claim exist. I guess this is the type of attack that must be resorted to when there is no scientific validity behind the claims of the attacking party.

The general trend with this type of argument is as follows: First, mention a transitional fossil, then make some sort of weak attack against modern science (often selectively quoting from technical papers that appear to support their claims when in actuality the article itself doesn't; I suggest referring to the link posted and checking out the papers discussed for more on this). Then, we see the argument from personal incredulity...ie "well I can't see how this can be a transitional fossil, so it must not be", ignoring that the scientists who studied the fossil may actually know more about paleontology than the author of the article debunking the science does. Funny. Does the article linked in this blog use this type of end claim? Of course!! Let's see it!

"But only now that we have Tiktaalik will we hear evolutionists boast about the size of the previously large "gap" in this transition, and how Tiktaalik solves all these previously unanswered questions. I'm super skeptical that this new fossil is good evidence that a transition took place: Acanthostega was truly a tetrapod, but Tiktaalik is a fish. As Clack and Ahlberg write, there's still a large gap (and any usefulness a fin had for walking was the result of a lucky pre-adaptation)"

My advice, trust scientists who have worked on the fossils, and not some random person writing on a website that claims that Tiktaalik can't be a transitional fossil because of some preconcieved devotion to the "wrongness" of evolution. I'll link some of the articles here. Have fun Discovery Institute, they make the author's points in the linked article above look extremely weak.

http://www.nature.com/nature/journal/v440/n7085/abs/nature04637.html

http://homepages.wmich.edu/~karowe/tetrapod%20fish%20brief%20summary%20NAture%20April%202006.pdf

http://www.nature.com/nature/journal/v440/n7085/abs/nature04639.html

http://www.sciencemag.org/cgi/content/full/312/5770/33

There's 4 peer-reviewed, scientific journal articles that support Tiktaalik's validity as a transitional form. I challenge you to show me even one peer-reviewed article debunking this fact.

Sunday, February 17, 2008

Discovering Discovery Institute's science education policy

Dear Discovery Institute,

Today, I've been investigating your perspectives on science education. I have noticed some interesting trends, and would like to raise some questions as to the motives of your views. It appears that your view on science education is, like most of the articles and books your fellows publish, strongly consonant with Wedge Strategy.

To discuss your science education policy, we will consider the document on your website that explains it. First, let's take the beginning of the document:

"As a matter of public policy, Discovery Institute opposes any effort require the teaching of intelligent design by school districts or state boards of education. Attempts to mandate teaching about intelligent design only politicize the theory and will hinder fair and open discussion of the merits of the theory among scholars and within the scientific community. Furthermore, most teachers at the present time do not know enough about intelligent design to teach about it accurately and objectively.

Instead of mandating intelligent design, Discovery Institute seeks to increase the coverage of evolution in textbooks. It believes that evolution should be fully and completely presented to students, and they should learn more about evolutionary theory, including its unresolved issues. In other words, evolution should be taught as a scientific theory that is open to critical scrutiny, not as a sacred dogma that can't be questioned

Discovery Institute believes that a curriculum that aims to provide students with an understanding of the strengths and weaknesses of neo-Darwinian and chemical evolutionary theories (rather than teaching an alternative theory, such as intelligent design) represents a common ground approach that all reasonable citizens can agree on."


At this point, we appear to be between phase 1 and 2 of Wedge strategy. There is the hesitance to teach Intelligent Design in the classrooms yet, but we are currently in a phase where there is a desire to undermine the validity of evolutionary theory in schools. As the opposition, with strong support from Discovery Institute yearns to "teach the controversy", they also deny any desire to teach Intelligent Design in the classroom. This is perhaps because we haven't reached that phase in the Wedge Document yet. Eventually, the Discovery Institute does, of course, wish to have Intelligent Design taught in classrooms; after all, the Wedge Document showcases a yearning to undermine the definition of science and the validity of evolutionary theory (and replace it with Intelligent Design).

"Four states (Minnesota, New Mexico, Pennsylvania, and South Carolina) have science standards that require learning about some of the scientific controversies relating to evolution.

Although Discovery Institute does not advocate requiring the teaching of intelligent design in public schools, it does believe there is nothing unconstitutional about voluntarily discussing the scientific theory of design in the classroom. In addition, the Institute opposes efforts to persecute individual teachers who may wish to discuss the scientific debate over design in an objective and pedagogically appropriate manner"


This statement should be revised to "Although Discovery Institute does not yet advocate requiring the teaching of intelligent design in public schools". As mentioned above (and also in my Wedge Document blog), the Discovery Institute does support replacing evolutionary theory with Intelligent Design in the scientific realm, and also by default the classroom, eventually. Teach the controversy now, teach Intelligent Design 5 or 10 or 15 years down the road. This way, students will be raised to doubt evolution first, and thus will become more receptive to the teaching of Intelligent Design. With luck, in a few generations, you'll succeed in raising students who will easily accept Intelligent Design. This strategy is perhaps Discovery Institute's best chance to gain some sort of scientific legitimacy. By slowly wedging their way into the scientific curriculum, they would theoretically succeed in raising America's children to accept Intelligent Design. A nation of people open to Intelligent Design would most definitely be an asset to Discovery Institute's attempt to undermine scientific materialism and redefine society. Scary thought.

"The U.S. Supreme Court in Edwards v. Aguillard strongly affirmed the individual teacher’s right to academic freedom. It also recognized that, while the statute requiring the teaching of creationism in that case was unconstitutional, “…teaching a variety of scientific theories about the origins of humankind to schoolchildren might be validly done with the clear secular intent of enhancing the effectiveness of science instruction.”

Here's an attempt to gain legal validity by the Discovery Institute. They can't legally teach Intelligent Design in the classroom because, as shown in a previous blog, Intelligent Design is inseparable from Creationism. However, by slowly wedging into the curriculum by teaching "a variety of scientific theories" (hey, here's a new scientific theory called "Intelligent Design"?), the Discovery Institute appears to see a possible way to infilitrate America's education system. Whether or not they succeed remains to be seen.

Works Cited:

Discovery Institute's Science Education Policy. Discovery Institute. 9/10/2007

Quick news update

Dear Discovery Institute,

Just thought you'd enjoy seeing a recent publication that yet again proves Behe's "irreducible complexity" argument for the bacterial flagellum wrong. Here's the links, hope you enjoy!!

http://www.newscientist.com/channel/life/mg19726431.900-uncovering-the-evolution-of-the-bacterial-flagellum.html

http://pandasthumb.org/archives/2008/02/flagellum-evolu-4.html#more

http://psom.blogspot.com/2008/02/evolutions-engine.html

As I have already touched upon this subject in a previous blog, I will not burden you with a full discussion of this information. The links above will be sufficient to show you some of the implications of the work.

Saturday, February 16, 2008

Stephen Meyer teaches Wedge Strategy

Dear Discovery Institute,

Haven't written in a while. How have you been? I've been good, but am growing intriqued by the work of Stephen C Meyer, one of your Vice Presidents. As you know, Stephen Meyer is a proponent of the "teach the controversy" approach to evolution and Intelligent Design, and also a supporter of "On Pandas and People", which we have experienced in an earlier discussion. Lets investigate his article titled "The Origin of Life and the Death of Materialism".

First, we will return to a common theme in these blogs. Does this article remain consonant with Wedge Strategy? The answer is a resounding "yes", and as the following quote seems to imply, Intelligent Design is essentially a way to promote Wedge Strategy:

"Thus, for scientific materialists at the end of the nineteenth century, the whole history of the universe and life could be told as a seamless‚ or nearly seamless, unfolding of the potentiality of matter and energy. No longer could it be held that a pre-existent mind shaped matter. Rather, modern science showed that matter shaped and created the capacities of mind (and not the reverse). God did not create "the heavens and the earth." The heavens and the earth (i.e., matter) created (via evolution) the minds that created the concept of God.

By the turn of the twentieth century, this once shockingly materialistic approach to science had become the norm. Most twentieth century scientists have assumed no limits to the explanatory power of materialistic forces. Materialistic modes of thought and assumptions have spread from physics and biology to psychology, sociology, criminology, economics, educational theory, and even theology. Thus, Whitehead would in the end attempt to reconcile science and religion by asserting that even God himself evolves.

Yet now at the end of the twentieth century after many wars and genocidal policies pursued in the name of materialistic "science-based" ideologies, the scientific picture of the world is rapidly changing. From the microcosm of the cell and the quantum world, to the macrocosm of an expanding and finely-tuned universe, the materialistic vision of nature now seems incomplete. Even in biology where Darwin's theory, perhaps more than any other, inspired the possibility of a fully materialistic world view, materialism now seems to be failing as scientists have uncovered an awe-inspiring complexity in even the simplest of living cells. Indeed, nowhere is the inadequacy of materialistic science more evident than in the contemporary discussion of how life in its very "simplest" form might have first originated."
(Meyer 1996)

So, as implied by this statement, the materialistic worldview is destined to fall; for those who haven't read my other blogs, in laymen's terms, the implication here is that the very definition of science is supposed to be due to be overthrown (or at least according to Meyer's comments here). But is this truly the case? As I have shown previously, the very structures paraded as "irreducibly complex" by the Intelligent Design movement have been shown to be evolvable. Therefore, this statement by Meyer is obviously outdated, and currently inaccurate. While
most groups would give up an argument once it becomes untenable, however, Discovery Institute still holds onto the "irreducibly complex" argument. Therefore, besides the point that this constitutes an extremely poor attempt at science, it is possible to still use Meyer's 1996 statement to day as a good explanation of Discovery Institute's views, mainly because it is still an accurate representation.

Next, Meyer goes on to attempt to deny the evolvability of DNA (after discussing origin-of-life research, which is not my area of expertise). See, for example, the following quote:

"Second, in nature every amino acid has a distinct mirror image of itself, one left-handed version or L-form and one right-handed version or D-form. These mirror-image forms are called optical isomers. Functioning proteins tolerate only left-handed amino acids, yet the right-handed and left-handed isomers occurs in nature with roughly equal frequency. Taking this into consideration compounds the improbability of attaining a biologically functioning protein. The probability of attaining at random only L-amino acids in a hypothetical peptide chain 100 amino acids long is again (1/2)100 or roughly 1 chance in 10^30. The probability of building a 100 amino acid length chain at random in which all bonds are peptide bonds and all amino acids are L-form would be (1/4)100 or roughly 1 chance in 10^60(zero for all practical purposes given the time available on the early earth). " (Meyer 1996).

While to some readers, this may seem like a valid argument, it is not. In April 2001, Robert Hazen published an article titled "Life's Rocky Start", which discusses geology-based research that accounts for the left-handed bias in amino acids. In this article, Hazen shows that if mineral facies are used as a point of growth for amino acids, then biases in "handedness" will occur. One of the most "useful" minerals for a left-handed bias is Calcite. While research is still ongoing on this possibility, it shows promising results thus far.

It is also worth noting that Meyer goes on to claim that Intelligent Design is the only known explanation for the creation of "information" in organic systems. Let's see the claim, however:

"since intelligent design is the only known cause of information-rich systems, the presence of information--including the information-rich nucleotide sequences in DNA--implies an intelligent source. Scientists in many fields recognize the connection between intelligence and information and make inferences accordingly. Archaeologists assume a mind produced the inscriptions on the Rosetta Stone. Evolutionary anthropologists try to demonstrate the intelligence of early hominids by arguing that certain chipped flints are too improbably specified to have been produced by natural causes. N.A.S.A.'s search for extra-terrestrial intelligence (S.E.T.I.) presupposed that information imbedded in electromagnetic signals from space would indicate an intelligent source. As yet, however, radio-astronomers have not found information-bearing signals coming from space. But closer to home, molecular biologists have identified encoded information in the cell. Consequently, a growing number of scientists now suggest that the information in DNA justifies making what probability theorist William Dembski and biochemist Michael Behe call "the design inference." (Meyer 1996).

To disprove this statement would severly undermine Meyer's credibility, and the credibility of the Discovery Institute as a whole. So, lets consider the following question: Is Intelligent Design the only explanation for the evolution of biological information? No. But don't take my word for it; let's see some of the technical literature!! First, here's an experiment showing the evolvability of information. I will quote the abstract, then link the entire article under works cited:

"How do genetic systems gain information by evolutionary processes? Answering this question precisely requires a robust, quantitative measure of information. Fortunately, 50 years ago Claude Shannon defined information as a decrease in the uncertainty of a receiver. For molecular systems, uncertainty is closely related to entropy and hence has clear connections to the Second Law of Thermodynamics. These aspects of information theory have allowed the development of a straightforward and practical method of measuring information in genetic control systems. Here this method is used to observe information gain in the binding sites for an artificial ‘protein’ in a computer simulation of evolution. The simulation begins with zero information and, as in naturally occurring genetic systems, the information measured in the fully evolved binding sites is close to that needed to locate the sites in the genome. The transition is rapid, demonstrating that information gain can occur by punctuated equilibrium. " (Schneider 2000)

There's one source showing that information is evolvable. Is this conclusion repeatable? Adami et al show that it is, in fact reproducable.

"To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural "Maxwell Demon," within a fixed environment, genomic complexity is forced to increase. " (Adami et al 2000)

Thus, the claim that Intelligent Design is the only explanation for biological complexity is proven false. Yet another blow to the coffin of Intelligent Design, and also the Discovery Institute's Wedge Strategy. Let us conclude with a final quote from Meyer's 1996 article:

"Other work promises to reshape our conception, not only of living things but of our science and ourselves. If the simplest life owes its origin to an intelligent Creator, then perhaps man is not the "cosmic orphan" that twentieth century scientific materialism has taught. Perhaps then, during the twenty first century, the traditional moral and spiritual foundations of the West will find support from the very sciences that once seemed to undermine them. " (Meyer 1996)

Here we see more of Discovery Institute's Wedge Strategy at work. This is a telling quote, because it shows that Intelligent Design advocates are appealing to religion as a source of legitimacy to some degree; see, for example, how the above quote attempts to show that Intelligent Design proves the validity of religion. As shown by the blogs on this site, however, Intelligent Design does not itself have scientific validity as a theory. However, ID proponents keep attempting to undermine the definition of modern science in attempt to give their "theory" scientific validity. Until they can provide compelling evidence in favor of this action, their attempts to gain scientific validity will consistently fail.

Works Cited:
Adami, C., Ofria, C., Collier, T. "Evolution of Biological Complexity". PNAS, April 25, 2000. Vol. 97, no. 9. 4463-4468. http://www.pnas.org/cgi/content/full/97/9/4463
Hazen, R. "Life's Rocky Start". Scientific American, April 2001.
Meyer, S.C. "The Origin of Life and the Death of Materialism". The Intercollegiate Review 31, no. 2. April 1, 1996.
http://www.discovery.org/a/98
Schneider, T. "Evolution of Biological Information" Nucleic Acids Research, 2000. Vol. 28 No 14. 2794-2799. http://nar.oxfordjournals.org/cgi/content/full/28/14/2794