Uncool Film Wins in Toronto

Denyse O'Leary is on to us. She reports that a religious film won the People's Choice Award at the Toronto film festival in September. O'Leary says, ...

Materialists, it seems, cannot count on the support of the public, not even in secular Toronto. Give the people a vote and everything’s lost. Hence the importance, to the materialist, of indoctrinating students at public expense in the school systems and suppressing dissent at the universities.

I apologize to all my materialist friends for letting you down. I tried to bribe as many film goers as I could by giving out free Tim Horton's gift certificates but I ran out. (And it was raining on two of the nights.) I warned them not to vote for Bella 'cause it would foil our attempts to keep the IDiots from getting tenure.

Alas, I failed. I've submitted my resignation to the The Grand Poobah of the World Materialist Conspiracy.

"So-called" RNA polymerase II???

The journal Cell has issued a press release announcing a paper from Roger Kornberg's lab in their Dec. 1st issue. [Nobel Laureate Finds “Elegant” Explanation for DNA Transcribing Enzyme’s High Fidelity, see Biology News Net for permanent link]

Last month, Roger Kornberg of Stanford University won the Nobel Prize in Chemistry for his efforts to unravel the molecular basis of eukaryotic transcription, in which enzymes give “voice” to DNA by copying it into the RNA molecules that serve as templates for protein in organisms from yeast to humans. Now, Kornberg and his colleagues report in the December 1, 2006 issue of the journal Cell, published by Cell Press, new structures that reveal another critical piece of the puzzle: how the so-called polymerase II enzyme [my emphasis] discriminates among potential RNA building blocks to ensure the characteristic accuracy of the process.

It's an interesting paper. That's not what I want to talk about.

I'm curious about Cell's use of the phrase "so-called polymerase II." This seems very strange to me. When I use the term "so-called" I intend to call into question the meaning of the words that follow. For example, if I refer to Bill Dembski as a "so-called" intellectual, it means I don't think he's an intellectual.

Are Americans in the process of changing the meaning of "so-called" in the same way that they're changing the meaning of "begs the question?" If so, it indicates an interesting trend toward strict literalism and away from more subtle meanings.

Should I avoid using "so-called" because Americans won't get the sarcasm?

Monty Python - The Galaxy Song

Watch the original below, and a cartoon version here.

I'm told by reliable sources that there are astrophysics professors who can sing the entire song.

Biochemists Have Songs Too

 
See the original below and hear the much better biochemist version here. (Thanks to Greg Crowther.)

Moran on Miller

Over at EVOLUTIONBLOG, Jason Rosenhouse has written a little essay criticizing my interpretation of Ken Miller's beliefs. [Moran on Miller]

I suggested that Miller's God can tweak evolution and John Rosenhouse replies,

I am not aware of any instance where Miller argued that God tweaks mutations to get what He wants. In fact, it seems to me that Miller's view of evolution is almost indistinguishable from that of Richard Dawkins. For example, in Finding Darwin's God Miller has nothing but praise for Dawkins' description of evolution in The Blind Watchmaker.

Miller lays out his case in Finding Darwin's God: A Scientist's Search for Common Ground between God and Evolution. Chapter 7 ("Beyond Materialism") sets the tone for the last half of the book. Here, Miller stresses the importance of the Heisenberg uncertainty principle (p.200). This is the basis for his statement that, materialism is wrong at its core (p.203).

Miller then goes on to his main point; namely, that ...

... the fact that mutation and variation are inherently unpredictable means that the course of evolution is, too. In other words, evolutionary history can turn on a very, very small dime—the quantum state of a single subatomic particle.

This is an important part of Miller's argument. Let's make sure everyone understands it. Miller is saying; (a) tiny changes can have profound effects, and (b) there is fundamentlal uncertainly at the subatomic level so we can never be sure of what caused something to happen. It's important for Miller's argument that evolution appear to be fundamentally a random process. I know from personal experience that Richard Dawkins does not agree.

The dénouement comes in Chapter 8 ("The Road Back Home"). The goal in that chapter is to find a way where God can be present and active in the world without being detectable by science. The solution is very ingenious,

Fortunately, in scientific terms, if there is a God, He has left Himself plenty of material to work with. To pick just one example, the indeterminate nature of quantum events would allow a clever and subtle God to influence events in way that are profound, but scientifically undetectable to us. Those events could include the appearance of mutations, the activation of individual neurons in the brain, and even the survival of individual cells and organsisms affected by the chance processes of radioactive decay. Chaos theory emphasizes the fact that enormous changes in physical systems can be brought about by unimaginably small changes in initial conditions; and this, too could serve as an undectable amplifier of divine action. (p.241)

So, God can guide evolution and perform miracles and we have no way of knowing it that he meddled. But meddle he does. That's an absolute requirement in Miller's religion.

Jason Rosenhouse continues,

It is likewise absurd to say that Miller's view of evolution is nearly indistinguishable from Behe's. Miller believes that God set up the initial conditions for making evolution possible, but then natural forces took over. He is quite clear in his book that the course of evolution was not foreordained by anything God did. This fact is crucial to Miller's view of Christian theology. He argues that a world in which God constantly intervenes, or one in which the course of evolution was foreordained by God, would also be a world that could not be viewed as truly separate from God Himself.

Miller's God has to perform miracles; that's an essential part of the Roman Catholic faith. What Miller is trying to do is explain how his God can do it while not conflicting with science. The passage that I just quoted is the answer. But let's be clear about one thing. Miller's religion is not deism, in spite of what you (John) might have thought.

Yes, it's true that Miller doesn't want a God who intervenes all the time. That's why he says that "God's miracles are not routine subversions of the laws of nature" (p.239). But that doesn't mean that miracles are forbidden—not by any reading of Miller than I can see. Instead, Miller argues that "when God does act in the world, He does so with care and subtlety."

Jason, the answering of prayer is another example of a God who is active in the present-day world. This is not consistent with your claim that Miller believes in a God who set up the initial conditions then stepped aside. Miller says,

... any traditional believer must agree that God is able to influence the thoughts and actions of individual beings. We pray for strength, we pray for patience, and we pray for understanding. Prayer is an element of faith, and bound within it is the conviction that God can affect us and those for whom we pray in positive ways.

That's not a deist God. That's not even the God of Michael Denton. At the risk of beating a dead horse, let's quote Miller once again to prove to you that he believes in an active God who intervenes in nature,

Remember, once again, that people of faith believe their God is active in the present world, where He works in concert with the naturalism of physics and chemistry. A God who achieves His will in the present by such means can hardly be threatened by the discovery that He might have worked the same way in the past.

According to Miller, the end result of evolution is to have "given the Creator exactly what He was looking for—a creature who would know Him and love Him ..." (p.239). Miller says that "... we can certainly see God's will emerging in the grand and improbable tree of life" (p.238). It's true, as you say, that Miller never explicitly states that God guided evolution. Instead, what he does is explain that there's a purpose behind the universe and that God is active in the world today and has been in the past. Miller then describes ways in which God could have undetectably guided things if He had wanted to, by fiddling with quantum indeterminacy. You are left to draw your own conclusions.

The most important difference between Behe and Miller is that Behe thinks you can actually detect God's handiwork while Miller thinks it is so well hidden that scientists can can never detect it. Miller recognizes it only through his faith.

The Atheist Delusion

In the interest of fairness, I present the other side of rationality. Check out The Atheist Delusion video by Eddie Current. It's hilarious.

Drop Cloning

New Scientist reports that biologists want to drop the word "cloning." Apparently, they want everyone to say "somatic cell nuclear transfer" instead.

It'll never fly. There are too many people who can't pronounce "nuclear."

Jason Rosenhouse on Science v Religion

Jason Rosenhouse has a lengthy posting over on EvolutionBlog. It's well worth reading. Here's a snippet ...

The situation is perfectly clear. Everyone cares about good science education and Ed can go climb a tree for suggesting otherwise. But some of us also believe that it does no good to pander and condescend to people's religious beliefs by telling them that there is no conflict between science and religion. There is a conflict, it is a big one, and most people find that obvious. Clever people like Miller and Collins can find imaginative ways of reconciling the two, but few people are buying it.

Yep. There's a conflict between science and religion, and ignoring it ain't gonna make it go away.

Psiphon Web censorship bypass tool

The University of Toronto announces the release of Psiphon, a software tool that bypasses internet censorship.

Psiphon is a downloadable program (available at http://psiphon.civisec.org/) that essentially lets someone turn a home computer into a server. Once psiphon is installed, the operator of the host computer sends a unique web address to friends or family members living in one of the 40 countries worldwide where Internet use is censored. Those in the censored country can then connect to the “server” and use it as a “host computer” to surf the Net and gain access to websites censored or blocked in their own country.

“Their connection is encrypted, so no one can eavesdrop on it,” [Professor Ronald] Deibert said. “It’s an encrypted communication link between two computers. So authorities wouldn’t be able to spot what websites are being visited by the user at risk.”

This means they'll be able to read Sandwalk and Pharyngula!
            
 

National Science Teachers Association

The original kurfluffle over the donation of "An Inconvenient Truth" DVDs to the National Teachers Association was prompted by an article in The Washington Post by Laurie David, one of the show's producers. Several bloggers were highly critical of NSTA, based on the "facts" in the newspaper article.

NSTA has now posted a press release on the NSTA Website.

Over the past few days, NSTA and film producer Laurie David have been discussing her offer to provide NSTA with copies of the DVD "An Inconvenient Truth" to mass distribute to our members. On November 29, 2006, NSTA's Board of Directors held a telephone conference to review Ms. David's request. In an effort to accommodate her request without violating the Board's 2001 policy prohibiting product endorsement, and to provide science educators with the opportunity to take advantage of the educational opportunities presented by films such as this, NSTA has offered to greatly expand the scope of the potential target audience identified in her initial request.

NSTA established its non-endorsement policy to formalize our position that the association would not send third-party materials to our members without their consent or request. NSTA looks forward to working with Ms. David to ensure that there are many options for publicizing the availability of the DVD to the national science education community, and to broaden the conversation on the important topic of global warming.

There appears to be more to this story than we originally thought. Several bloggers have commented [BadAstronomy, No Se Nada, A Blog Around the Clock, Discovering Biology in a Digital World].

The Three Domain Hypothesis (part 4)

[Part 1][Part 2][Part 3]
Ludwig and Schleifer question the reliability of the SSU tree. They begin by comparing trees constructed from the small ribosomal RNA subunit (SSU) and the large ribosomal RNA subunit (LSU). The example they use is 18 species of Enterococcus and they show that there are significant differences between the two trees. Surprisingly, they dismiss these differences as “minor local differences.” These authors are convinced that “SSU and LSU rRNA genes fulfill the requirements of ideal phylogenetic markers to an extent far greater than do protein coding genes.”

In spite of this bias, they compiled a database of protein trees from conserved genes that are found in all three of the proposed Domains. According to them, the Three Domain Hypothesis is supported by EF-Tu, the large subunits of RNA polymerase, Hsp60, and some aminoacyl-tRNA synthetases (aspartyl, leucyl, tryptophanyl, and tyrosyl).

The Three Domain Hypothesis is refuted by ATPase, DNA gyrase A, DNA gyrase B, Hsp70, RecA, and some aminoacyl-tRNA synthetases. Note the inclusion of ATPase in this list. The phylogeny of ATPase was one of the strongest bits of evidence for the Three Domain Hypothesis back in 1989 but further work has shown that these genes (proteins) now refute the hypothesis.

My own favorite is the HSP70 gene family, arguably the most highly conserved gene in all of biology and therefore an excellent candidate for studies of deep phylogeny. Hsp70 is the main chaperone in all species. It is responsible for the correct folding of proteins as they are synthesized. It forms a complex with DnaJ and GrpE in bacteria and similar proteins in eukaryotes. The complex associates with the translation machinery (ribomes etc.) during protein synthesis.

The conflict between trees constructed with HSP70 and the ribosomal RNA trees has been known for a long time. The actual pattern of the HSP70 tree can be interpreted in two different ways depending on where you place the root [see 1995] but neither one agrees with the Three Domain Hypothesis.

Here’s an example of an HSP70 tree that I just created using the latest sequences. It’s fairly typical of the trees that do not support the Three Domain Hypothesis. Eukaryotes cluster as a monophyletic group (lower left) and all prokaryotes form another distinct clade. The archaebacteria sequences (black dots) do not form a single clade, let alone a “domain.” Instead, they tend to be dispersed among the other bacterial groups.


Note that this tree, like many others, shows numerous short branches at the bottom of the bacteria tree suggesting that the diversity among bacteria is ancient. Phillippe and Forterre (1999) were among the first to document the serious differences between conserved protein trees and rRNA trees in “The Rooting of the Universal Tree of Life Is Not Reliable” (J. Mol. Evol. 49:509-523). It’s worth quoting their abstract in order to emphasize the controversy since Ludwig and Schleifer don’t do a very good job.

Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria-Eukaryota sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides, for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome analysis.

The problem is obvious. All trees, RNA and protein, have potential problems of saturation and long branch attraction. Although Ludwig and Schleifer argue in favor of the ribosomal RNA tree, there is still serious debate over which sequences are revealing the “true” phylogeny. Are there good reasons for rejecting those trees that refute the Three Domain Hypothesis as it's supporters maintain?

---

Microbobial Phylogeny and Evolution: Concepts and Controversies Jan Sapp, ed., Oxford University Press, Oxford UK (2005)

Jan Sapp The Bacterium’s Place in Nature

Norman Pace The Large-Scale Structure of the Tree of Life.

Woflgang Ludwig and Karl-Heinz Schleifer The Molecular Phylogeny of Bacteria Based on Conserved Genes.

Carl Woese Evolving Biological Organization.

W. Ford Doolittle If the Tree of Life Fell, Would it Make a Sound?.

William Martin Woe Is the Tree of Life.

Radhey Gupta Molecular Sequences and the Early History of Life.

C. G. Kurland Paradigm Lost.

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Iraq: The Hidden Story

 
This show was broadcast on television in the UK. The Brits are better informed than we are.

Nobel Laureates: Dorothy Crowfoot Hodgkin

The Nobel Prize in Chemistry 1964.

"for her determinations by X-ray techniques of the structures of important biochemical substances"

Dorothy Crowfoot Hodgkin (1910-1994) was one of the pioneers of X-ray crystallography. Her many achievements include the first X-ray diffraction pattern of a protein in 1934 (with J.D. Bernal), and the structures of penicillin, vitamin B12, insulin, and tobacco mosaic virus. She did most of her work in Oxford from 1934 until her retirement in 1979.

Her Nobel Prize was in recognition of her enormous contributions to the field of X-ray crystallography, especially her work on the structure of vitamin B12. When she published the structure in 1954, it was the largest molecule whose three dimensional structure had been solved.

Neil deGrasse Tyson and Richard Dawkins

This is the video clip that so many of my colleagues are excited about. They think Neil deGrasse Tyson has hit the nail on the head. They agree with him that Dawkins is being "insensitive" when he criticizes religion.

I'm not familiar with Neil deGrasse Tyson. Is he famous in America? Is he a good educator? Is he effective? Has he been going around the country giving lectures where he gently and kindly urges his audiences to question their religious beliefs? Has he been softly pleading with Americans to respect atheists? Has he been speaking out, quietly, against the Ted Haggards and Jerry Falwells of this world? Is his strategy working?

Richard Dawkins has done more in the past two months to stimulate a dialogue on religion than all the rest of us have done in five decades. The blogs are full of excitement about atheism and religion. Dawkins has been at dozens of universities, appeared on dozens of TV shows, and been featured in major articles in most newspapers. The debate made the cover of Time magazine. There have been several symposia like the one Tyson was invited to. There wouldn't even have been a symposium without Dawkins.

People all over North America are questioning religion. I've seen it on the streets in my own neighborhood and overheard discussions in the restaurants. All of a sudden, people are realizing there are atheists in their midst—and they're not so bad after all. Ask yourself this: how does the Dawkins' form of education compare with the efforts of people like Neil deGrasse Tysons?

The Legend of Zelda

Check out the Nintendo site for cool videos documenting the history of The Legend of Zelda. Part 1 is included below.

I remember when we got out first game box back in 1988. We got it for the kids, it was very educational.

Of course we had to try one of the games just to see what all the excitement was about. My kids were only ten or eleven years old so I had to show them all the tricks of navigating the maze in Zelda. If I remember correctly, it was me who taught them everything they know about computer gaming. Well, almost everything ... Okay, so they whipped my butt. They got lucky.