Now that one story is on pause, let's turn to another story and another set of blog entries. I'll begin with something I previously posted a few months ago.

Let's talk about receptor tyrosine kinases (RTKs). We can think of an RTK as a communication device, since these membrane proteins transmit signals from the cell's environment into the cell. Event X outside the cell is translated into Event Y inside the cell. Specifically, the signaling molecules (such as hormones) bind the extracellular portion of the receptor protein. This binding event is then somehow communicated to the contents inside the cell. But how?

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In their paper, "A Disconfirmation Bias in the Evaluation of Arguments," psychologists Kari Edwards and Edward Smith (Journal of Personality and Social Psychology, 1996, Vol. 71, No. 1, 5-24) explore this tendency. They begin their article as follows:

When evaluating an argument, can one assess its strength independently of one's prior belief in the conclusion? A good deal f evidence indicates the answer is an emphatic no. This phenomenon, which we refer to as the prior belief effect, has important implications. Given two people, or groups, with opposing beliefs about a social, political, or scientific issue, the degree to which they will view relevant evidence as strong will differ. This difference, in turn, may result in a failure of the opposing parties to converge on any kind of meaningful agreement, and, under some circumstances, they may become more extreme in their beliefs.

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A major short-coming of Intelligent Design Theory has been its reluctance to identify the designer. This study addresses this problem and firmly establishes the reality of Intelligent Design.

Most design theorists are uncomfortable talking about the designer. Wedgocentric analysis has demonstrated this reluctance to be part of a sinister plot to foist a theocracy on an unsuspecting, scientifically-illiterate, Bush-electing public. If intelligent design is to be recognized for the science that it is, it must eschew this deception and show the scientific community the designer.

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I came across an old textbook entitled, The Principles of Heredity. It was written by geneticist Laurence H. Snyder and published in 1935 (Boston, New York [etc.] D.C. Heath and company). The book was intended as a text for "the beginning student of heredity." The textbook has a chapter on Eugenics that provides us a glimpse of one portion of our American and scientific history. Given that this material was being taught to students, I've transcribed this chapter and offer it merely as a service for those interested in the history of eugenics.

Here

Behold the orange. Being perfectly round, it has no sharp edges with which to poke you in the eye if it happened to fall from the tree. Note how easily it fits into the palm of my hand. And it even comes with its own biodegradable wrapper! To open it, you"¦..hey wait, the thing doesn't have a tab! Where's the dagburnit tab?!

Ah, behold the thumbnail. Note how it so perfectly punctures the biodegradable wrapper and"¦.. Read the rest of this entry »

[I posted this about a year ago. Now that some of you have read The Design Matrix, you might appreciate a second look.]

Jason Rosenhouse provides a nice summary of the debate between Bill Demsbki and Michael Shermer. What I most appreciate is Rosenhouse's summary of Shermer's talk, which apparently was organized into five basic points.

Being a selfish Gene, I'm curious as to how Shermer's arguments would stack up against The Matrix. Would Shermer's arguments pose a pointed and deadly attack in the Matrix?

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[HT to Guts for putting together this truly outstanding video!]

Mike Gene. It's not his real name, and no one knows if he is a he or a she, but none of that matters, because it's his (or her) book in any case. And never underestimate the power of the arguments of a pseudonymous Internet persona – I know I don't.
"“ Douglas

According to the endosymbiotic theory, mitochondria are the descendents of bacteria. The theory postulates that a primitive cell engulfed some aerobic bacteria and rather than digest them, a symbiotic relationship was established, where each partner benefited from the new relationship. This relationship then set the stage for the ultimate stream-lining of the bacteria, such that they were transformed into mitochondria through the transfer of much of their gadgetry to the host nucleus.

In a nutshell, the essence of the argument for the endosymbiotic origin of mitochondria is that mitochondria look like they share a common ancestor with bacteria. The argument is quite convincing, as there are numerous mitochondrial genes whose sequences are much more similar to bacterial sequence than that which exists in the nucleus of the same cell. In fact, this is an example where no one piece of evidence carries the day, but instead it's the cumulative power of multiple lines of evidence.

There are some important lessons to be learned from the development of the endosymbiotic theory.

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[Here's an old posting about Richard Dawkins' argument concerning animal rights.]

Where is it? I've looked through the catalogs and web pages for an instrument that would measure "˜importance,' but I cannot find it. So I look to the peer-reviewed literature thinking someone has come up with a way to detect "˜importance' and find nothing. How can this be?

In the essay that probably explains Richard Dawkins reluctance to defend the practice of science against animal rights terrorists, Dawkins writes: "Most people take it for granted that humans are more important than apes. But this assumption has more to do with double standards than biology." When first reading this, I thought that maybe I missed the important development where biology can speak to whether humans are important. But alas, it turns out Dawkins is confusing his science and metaphysics again. Those of us who understand science realize that beliefs about the importance of humans cannot be addressed by science.

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1. gather complete information – more than one source
2. understand and define terms (make others define terms, too)
3. question the methods by which results were derived
4. question the conclusion: do the facts support it? is there evidence of bias? remember correlation does not equal causation.
5. uncover assumptions and biases
6. question the source of information
7. don't expect all the answers
8. examine the big picture
9. look for multiple cause and effect
10. watch for thought stopping sensationalism
11. understand your own biases and values

From Human Biology: Health, Homeostasis, and The Environment, 3rd Edition, by Daniel D. Chiras.

HT: Dawgnotes

In my previous blog, I outlined ways in which my views of ID differ from mainstream views of ID. Let me now symmetrically balance this out by pointing to the areas where I disagree with the average ID critic.

Here are some ID critic positions I have commonly run across that I disagree with.

• ID is nothing more than religious belief and an attempt to sneak creationism into the public school curricula.
• ID is Complete Bunk and Total Nonsense.
• Irreducible complexity (IC) does not exist and if it did, it would always be explained (and predicted) by neo-Darwinian evolution.
• Complex specified information (CSI) does not exist in any biological system and if it did, it would be always be explained (and predicted) by neo-Darwinian evolution.
• Evolution is the result of an unguided, unplanned process of random variation and natural selection.
• ID is inherently anti-evolution. But if it is not, it is superfluous.
• All biological information has arisen by non-teleological processes.
• To detect design, one must first demonstrate the identity, methods, and psychology of the designer.

A couple of people in the comments section wanted me to distinguish my views about Intelligent Design from those that are commonly expressed (mainstream ID). So here's the short list:

• Mainstream ID argues that ID is indeed science. I do not think ID yet qualifies as science. I view ID more as a nascent proto-science and intellectual curiosity.
• Mainstream ID argues the evidence for design is strong and that we have identified systems that are best explained by design. I think the evidence for ID is weak yet there are examples where design is plausible. Thus, I am not out to convince skeptics and critics; I am interested in testing my own suspicions.
• Mainstream ID argues that irreducibly complex (IC) structures could not have evolved, while I think IC helps bring focus to candidates for design.
• Mainstream ID argues that biological systems demonstrate complex specified information (CSI), indicating design. While I think the method is a promising way of inferring design, I am not convinced that a true specification has been demonstrated.
• Mainstream ID seeks to challenge neo-Darwinian evolution. I think ID complements neo-Darwinian evolution.
• Many proponents of mainstream ID are anti-evolution. I am an ID evolutionist. There are a small number of cases where I tentatively propose design candidates that did not evolve (i.e., the flagellum), but I do not infer design by arguing they could not have evolved; I argue they did not evolve.
• Many proponents of mainstream ID argue that that information increase over evolutionary time cannot be explained by natural means. I don't agree.
• Mainstream ID seeks to detect design in a manner that is completely divorced from consideration of the designer. I am willing to make working assumptions (albeit, minimal) about the designer.

In the future, I will elaborate on some of this in much more detail.

A common technique among the critics of ID is to accuse their opponents of lying. Liar, liar, pants on fire, nose as long as a telephone wire! The problem is that more often than not, this is just a personal attack. Say the ID proponent argues X. If the critic thinks X is false, the critic immediately goes for the jugular and shouts "Lies!" Lies, lies, lies. But with the accusation of lying comes a very tall burden. If X is indeed false, then for the ID proponent to be lying, the ID proponent must know and agree that X is false. Otherwise, the problem is not quite as sinister.

For example, the ID proponent may simply be misinformed. She may simply be mistaken. He may be relying on a different point of view. She may be relying on a different point of emphasis. The critic should always remember that his perception of the ID proponent is not an observation of their mind. A critic may say, "But I have shown that X is false, yet the ID proponent continues to propose X. That makes him a liar!" No it does not. The proponent may not agree with the critic's presentation of X. The proponent may not trust the critic's presentation of X. The proponent may not understand the critic's presentation of X. Etc. Unless the proponent agrees and knows that X is false, he cannot be lying when he proposes X is true. And unless the critic can prove the proponent agrees and knows that X is false, it is irresponsible and inflammatory to publicly accuse the proponent of lying.

Of course, the "liar, liar, pants on fire" accusation is a sneaky and effective piece of political rhetoric. But the self-righteous accuser should remember it is also a double-edged sword. If errors and different interpretations of the world count as lies, what makes the accuser think he can escape his own judgmentalism?

Biologist Paul Myers is upset with President Bush, the Republicans, the Discovery Institute (proponents of Intelligent Design) and "the theocrats, faith-healers, and snake-oil artists." Dr. Myers feels that they have betrayed "the promise of the Enlightenment" and "the cause of civilized humanity." While Dr. Myers' intentions to defend the Enlightenment and Civilization are noble, I am concerned that he may have inadequatedly consulted with his enlightened colleagues in other departments. The reason I am troubled is found in his language of violence.

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