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.

Linux Commands

 

Here's a list of the top 200 Linux commands. Some of them are very useful, especially for us old fogies. For example, I use "whoami" at least once a day.

Some of them will drive you crazy. Don't even think about typing "vi" unless you're prepared to throw the keyboard into the monitor. "Format" is lots of fun, try it with every letter of the alphabet.

"Grep" isn't what you think it is.

The computer is "Darwin." It's owned by David Greig (DIG) and lives in my office. "Darwin" is the server for the newsgroups talk.origins and sci.bio.evolution. DIG moderates talk.origins with a lot of help from Darwin. Josh Hayes attempts to control sci.bio.evolution—it's a losing battle.

I think I'll try out some of the more unusual Linux commands on Darwin. I wonder what "kill" does? ....

Something to be Proud of?

 

Gene Expression has a new icon in the sidebar. Apparently the author is proud to be an appeaser.

For the record, here's what it means to be a Neville Chamberlain Atheist. It means you're happy to attack Intelligent Design Creationists like Micheal Denton (Nature's Destiny) and Michael Behe (Darwin's Black Box) for mixing science and religion. But, you don't say a word when Ken Miller (Finding Darwin's God), Francis Collins (The Language of God: A Scientist Presents Evidence for Belief) and the Rev. Ted Peters (Evolution from Creation to New Creation) spout equally bad religious nonsense in the name of science.

The Neville Chamberlain Atheists object when Behe talks about intelligent design but mum's the word when Ken Miller talks about how God tweaks mutations to get what He wants. Hypocrisy is a strange thing to be proud of.

He must be joking, right?

An Inconvenient Truth

If you haven't seen it, get yourself to a video store tomorrow. Then read the debate about whether the National Science Teachers Association should accept 50,000 free DVD's [What's up NSTA?].

I don't agree with PZ on this one. The science is good but Al Gore is exploring the possibility of a run for the Democratic nomination in 2008. I saw him in action for three days at Chautauqua last summer. If it were Carl Sagan I'd say NSTA should show the DVDs in every classroom but it's silly to pretend that Al Gore isn't a politician.

Who Let Him Out on his Own?

Depak Chopra demonstrates, once again, why we call them IDiots. PZ Myers has pointed out the foolishness in his posting on Pharyngula, "Oh, no...not more Chopra!". The thrust of the rant has something to do with seeing things in your mind. (I didn't pay much attention, it's kindergarten stuff.) Apparently, the fact that you can create an image of a yellow flower means that God exists. PZ tells it like it is but he stops short of the important part of Chorpa's article where Chopra says,

Yet you assume--as do all who fall for the superstition of materialism--that flowers and the color yellow exist 'out there' in the world and are photographically reproduced by the brain, acting as a camera made of organic tissue. In fact, existence of flowers shifts mysteriously once it is closely examined. The experience of sight, sound, touch, taste, and smell is created in consciousness. Molecules don't assemble in your head to make the sound of a trumpet blaring in a brass band, for example. The brain is silent. So where does the world of sights and sounds come from?

Materialists cannot offer any reasonable explanation. The fact is that an enormous gap exists between any physical, measurable event and our perception. If I talk to you, all I am doing is vibrating air with my vocal cords. Every aspect of that event can be seen and measured, but turning those vibrating air molecules into meaningful words has never been seen or measured. It can't be.

I can't resist. Yes, Depak, turning the vibrating air molecules that come out of your mouth into meaningful words has never been seen or measured. And your point is?

Why does the Huffington Post put up with this IDiot?

Recording Lectures

Every time I give a lecture there’s a bunch of recorders in front of me. Following the lecture, there’s an active trade in lecture recordings on our student newsgroups.

I have mixed feeling about this. On the one hand, I understand why students would want to take advantage of cheap technology to make a permanent record of my words of wisdom. :-)

On the other hand, my words aren’t always wise and I don’t want students to memorize everything I say without checking it against the textbook and other sources. Lecture recordings should be supplements to learning and not the only source. (Don’t get me started about podcasts!)

This point was brought home in one of the threads on our student forums. The students in one of our biochemistry courses had just finished a midterm exam. One of the multiple choice questions was about cholesterol. For those of you who haven’t committed the structure of cholesterol to memory—I am one—I’m including a picture. The description in the textbook (it happens to be my textbook) is ....

Steroids are a third class of lipids found in the membranes of eukaryotes, and, very rarely, in bacteria. Steroids, along with lipid vitamins and terpenes, are classified as isoprenoids because their structures are related to the five carbon molecule isoprene. Steroids contain four fused rings: three six-carbon rings designated A, B, and C and a five-carbon D ring.

I then go on to describe cholesterol, an important steroid.

Choice “C” in the multiple choice question referred to the 4-ring structure of cholesterol. It was a correct choice and the students were supposed to choose another response, which happened to be an obvious incorrect choice. Cholesterol certainly has four rings, so what’s the problem?

The day after the exam, students started complaining on the newsgroup. Apparently Prof. X (no, it wasn’t me, this isn’t my course) said in lecture that cholesterol has only three rings and students have the recording to prove it! Several students demanded that they be given a mark for choosing response C. The complaints quickly escalated with some highly indignant students demanding an extra mark on the exam. According to their logic, it is unfair for students to be penalized because the Professor made a mistake in the lecture.

Other students chimed in. They pointed out that the Professor’s notes referred to four rings and the textbook clearly shows four rings; A, B, C, and D. They suggested that their fellow students have a responsibility to study from the notes and textbook as well as the recording. If there was a discrepancy, then it was up to the student to resolve it, including asking the Professor if necessary.

One of the best responses was from student “YYZ,” who has given me permission to quote him.

I’m saying you can’t only listen to the lecture and that’s it. You have to analyze what he says, look at the slides, think over if things make sense, etc. Studying isn’t mindlessly memorizing words coming out of a professors mouth ...

By Jove, I think he’s got it! It’s refreshing to see that some students understand how to study and it’s refreshing to see them take on the whiners. That’s how things are going to change in the universities. Professors are the enemy and nothing they say has any credibility (at least in the first two years). Responsible students have to speak up.

World AIDS Day

The Faculty of Medicine and the University of Toronto are hosting a series of events this week in association with World AIDS Day (Friday, Dec. 1). Check the flyers around the campus for events near you. There will be a student presentation in my class on Wednesday prior to the symposium on Promoting Evidence-based ART in Resource-poor Settings.

Light a Candle

 
Light a candle and Bristol-Myers Squibb will donate $1, up to a total of $100,000, to the national AIDs fund (USA). I'm usually not a fan of big PHARMA but .... why not?