Sunday, December 25, 2011

And the Winner Is .....

 
I collected the names of all the undergraduates who got the right answer for Monday's Molecules. I put them on slips of paper and had my colleague, Alex Palazzo draw one of them from a small beaker.

Alex still has a blog on Scienceblogs called Transcription and Translation (formerly The Daily Transcript) but he hasn't blogged very much recently. He's too busy doing experiments.

What name did he draw out of the beaker?

The winner of a free autographed textbook is .....

Thursday, December 22, 2011

The Cambrian Conundrum: Fossils vs Genes

The earliest fossil examples of most animal classes and phyla appear in the fossil record at about the same time in the Cambrian (about 530 million year as ago (Ma)). This period of apparent rapid divergence is referred to as the "Cambrian Explosion."

It seemed unlikely that this disparity could have evolved in just a few million years so many scientists have been searching for fossil antecedents in the early Cambrian and Ediacaran (635-541 Ma). Many trace fossils have been found in the past few decades, indicating that the fossil animals of the Cambrian were preceded by small wormlike creatures.

The other approach has been sequence analysis. One can construct molecular phylogenies by comparing the sequences of genes in modern extant organisms. This approach has been highly successful over the past fifty years so that we now know a great deal about the relationship of the various animal phyla. The correspondence between the old morphological taxonomy and molecular evolution is the most powerful evidence we have that evolution explains the history of life [see Twin Nested Hierarchies].

The problem with sequence comparisons has always been getting accurate dates using the molecular clock. It is hard to get an accurate date when dealing with events that occurred 500 million years ago because there aren't very many calibration points. An accurate calibration point is a known time when two lineages diverge.

If there really was a rapid divergence in the Cambrian then one would expect the molecular tree to show this. But it never has. The molecular phylogeny shows that chordates diverged from invertebrates at least one hundred million years before their fossils appear in the Cambrian. Similarly other phyla and classes of animals have their origin long before the Cambrian, according to the molecular clock.

A recent paper in Science extends this comparison by calculating more a more accurate molecular phylogeny using seven housekeeping genes from 118 different species (Erwin et al. 2011). The result is shown in Figure 1 of the paper: "The origin and diversification of animals as inferred from the geologic and genetic fossil records." (Click on the figure to embiggen.)

Do the IDiots Understand Biochemistry and Molecular Biology?

 
We've been discussing whether Intelligent Design Creationists understand enough about biochemistry, molecular biology, and evolution to warrant their criticisms of these fields. The answer is clearly "no" as they demonstrate time and time again.

This time it's an anonymous posting on the premier IDC website, Evolution News & Views [Long Non-coding RNA Punches Another Hole in "Junk Genome" Myth]. The anonymous poster links to a recent paper in Genes & Development that shows a function for a particular long non-coding (lnc) RNA. The paper implies that many of these lncRNAs (up to 400) are expressed in mouse erythroid cells.

Regulatory RNA have been known and studied for at least four decades and various lncRNAs have been characterized over the past twenty years. The IDiot at Evolution News & Views seems to think that this is a new discovery proving that there's no junk in our genome. The facts are quite different.

As I pointed out in my review of The Myth of Junk DNA, the amount of the genome devoted to producing lncRNAs is about 0.1% [Junk & Jonathan: Part 6—Chapter 3]. So, not only have we known about regulatory RNAs for many years, we also know that their genes don't account for very much of the genome, I figure it can't be more than 2% even when you include all of the most optimistic estimates of regulatory RNAs [see What's in Your Genome?].

But the ignorance of the IDiots is much more profound than just being incapable of calculating percentages. The latest posting reveals the depth of their ignorance.
These findings have two important implications. First, non-coding regions of the genome were assumed to be leftover evolutionary relics that no longer play a functional role. The assumption was not due to extensive studies of non-coding regions of the genome, but rather to a commitment to what is known as the central dogma of molecular biology: DNA is transcribed into RNA and RNA is translated into amino acids to make proteins. This was considered the primary purpose of DNA. The non-coding regions were assumed to have no function, and were dismissed as the natural consequence of genetic "junk" accumulating over time. This paper is one among an accumulating corpus of papers discussing new and interesting functions of the non-coding regions of the genome. (See The Myth of Junk DNA by Jonathan Wells for a history of "junk" DNA and additional references describing the function of so-called "junk" DNA. See here for a discussion on the regulatory role of introns.)
There was never a time in the past fifty years when knowledgeable biochemists and molecular biologists thought that all non-coding DNA was nonfunctional junk. This was never an assumption of the Central Dogma of Molecular Biology which states that "... once (sequential) information has passed into protein it cannot get out again" [Basic Concepts: The Central Dogma of Molecular Biology]. There are many scientists who have misconceptions about the Central Dogma [The Central Dogma Strawman] but the IDiots go one step farther by misunderstanding the misconception!

We've known about functions in non-coding DNA since the early 1960s as anyone who has ever glanced at a textbook would know. It's hard to tell whether the IDiots are just butt-ignorant of basic science or whether they are lying. This is an especially tricky problem when the silly strawman argument is popularized by Jonathan Wells because he's supposed to know the science [Junk & Jonathan: Part 1—Getting the History Correct] [Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?].

We know that most of our genome is junk because we know a great deal about genomes, genes, biochemistry, molecular biology, and evolution. We know which parts are likely to be functional and which parts are likely to be broken genes and other kinds of junk. We know this because we understand the subject, not because we are covering up our ignorance.

The IDiots are ignorant of the science and they assume that everyone else is as well. That's a very bad assumption.


Wednesday, December 21, 2011

Center for Inquiry Canada: New Associate Members

 
The Board of Directors voted on accepting new Associate Members at its December 11th meeting. I have just received a letter from the Board signed by the new (?) Chair, Richard Thain.
Dear Professor Moran,

On December 11, 2011 one of the many important items on the agenda for the Board od Directors meeting was discussion of the applications for Associate Membership.

The goal is to have a diverse group of Associate Members which reflects our membership geographically. In order to achieve this, the Board recognizes that we must update our website and post the By-Laws which explain the governance of CFI Canada. We hope to attract more applications which will then be reviewed before the next CFI Canada AGM in March 2012.

We felt it was important to approve some of the applications at the December 11th board meeting, so we reviewed and accepted the following five people:

Iain Martel, Seanna Watson, Brian Eelhart, Craig Irving and Marlowe Filippov.

The other applications were put under review and will be considered with the next wave of applicants at a future board meeting.

The Board of Directors realizes you have made and are continuing to make significant contributions to our success. We would like to sincerely thank you for your continued support and committment to helping CFI build a better Canada through reason.

Richard Thain DDS
Chair, Board of Directors
CFI Canada
My application was rejected!

I wish I knew why the Board didn't accept my application but did accept some others. Iain Martel is the Chair of CASS and Seanna Watson is the Director of the Ottawa branch of CFI so I assume that the people filling these positions are a sort of ex officio Associate Members. That makes a lot of sense especially for Iain and Seanne who have devoted so much time and effort to CFI.

Bryan Eelhart was the Financial Agent for the Green Party in the riding of Trinity-Spadina (Toronto) during the recent Ontario election. He's a member of the Board of Directors at Conscience Canada and he works for Science for Peace. Bryan has extensive expertise in website design and implementation.

Craig Irving is a freelance videographer from Toronto. He serves on the Multimedia Committee at Centre for Inquiry Canada.

Marlowe Filippov lives in Ottawa where she volunteers at the Centre for Inquiry. She's also an expert in websites. She's been helping out with membership problems and advising the National Director on other issues.

It appears that three two of the new Associate Members were chosen for their ability to help out with updating the CFI website.

There are currently three Associate Members who are CFI Advisory Fellows; Jeff Rosenthal from Toronto, Chris diCarlo from Guelph, and Ethan Clow from Vancouver. It's possible that the Board of Directors felt that only three CFI Canada Advisory Fellows should also be Associate Members, or maybe they felt that having two from the Toronto area was too much and that's why my application was rejected.

I'll try and find out more about the qualifications required for Associate Membership. It's clear that length of membership in CFI is not important since there are Associate Members who only joined CFI two years ago. I think that active volunteering on administrative tasks is an important criterion so if you are currently helping out in this area you will probably have a good chance of being appointed.

I'm a little unclear about the criterion of reflecting membership geographically. About half of all CFI Canada members are from the Toronto area but I don't think this means that half of the Associate Members will be from Toronto. I think it means that you're more likely to be chosen as an Associate Member if you are from one of the other centres that isn't already represented.

I'm not sure what the role of a CFI Canada Advisory Fellows is supposed to be. If we can't be Associate Members then who are we supposed to advise? :-)

Post a comment if your application was also rejected. That way we might be able to figure out what the Board of Directors is thinking when it comes to appointing new Associate Members. I'll let the Board know about this posting so they can comment, or at least see your comments.


A Torley Defense of Irreducible Complexity

Vincent Joseph Torley (vjtorley) has a Ph.D. in Philosophy (2007) from the University of Melbourne (Australia). He currently teaches English in Japan.

Torley hangs out at Uncommon Descent where he tries to defend Intelligent Design Creationism. He didn't like my recent posting on Irreducible Complexity [Barry Arrington Explains Irreducible Complexity] because I accused Barry Arrington of not understanding evolution. You might recall that Arrington began his defense of irreducible complexity by saying, "(1) By definition, evolution can work only in a stepwise fashion wherein each successive step is “selected for” because it has conferred a selective advantage on the organism."

This is not how evolution is defined and it's a particularly bad way to begin because the scientific understanding of many irreducibly complex systems involves the fixation of neutral or even detrimental alleles. Competency in evolution also requires an understanding of redundancy, contingency, and sloppiness.

Vincent Joseph Torley asks, "Will this do, Professor Moran?" He starts with ....
Let me state up-front that I am a philosopher, not a scientist. However, I believe in arguing rigorously, so I have attempted to state the argument from irreducible complexity in a rigorous fashion. I’d appreciate hearing from Professor Moran thinks of this argument, as a biologist.

Tuesday, December 20, 2011

These are not berries!

 

This is Juniperus communis from Botany Photograph of the Day. If you visit that website you'll learn two three things about juniper that you didn't know before: (1) juniper grows in lots of places, (2) the "berries" aren't berries, (3) gin comes from the French word for juniper.


The Mite Genome

 
The genome of the two-spotted spider mite, Tetranychus urticae has been sequenced and the results were published in Nature last month (Grbic et al. 2011).

Spider mites eat plants. They produce silk-like webs and that's why they're called "spider mites". They belong to the class Arachnida, which is the same group that contains spiders. The Arachnids are in the subphylum Chelicerata, a large group of arthropods distantly related to the insects and crustaceans. This is the first genome sequence of a chelicerate and that's why it's important.

Genome Size

The genome is only 90 Mb in size. It's the smallest arthropod genome that has been sequenced so far. Contrast this size with the human genome at 3,200 Mb or the genome of another tick, Ixodes scapularis, estimated to be 2,100 Mb. (Honeybee = 236 Mb, Drosophila = 140 Mb.) According to Ryan Gregory's animal genome size database this is the smallest known arachnid genome and the smallest known arthropod genome.

The authors estimate that there are 18,414 protein-encoding genes in the mite genome. This is about the same number of genes as most insects whose genomes have been sequenced and only slightly less than the number of genes in the human genome.

About 41% of the mite genome consists of exons (protein-encoding). Recall that less than 2% of our genome encodes proteins and in most insects the exon sequences make up less than 10% of the genome. (Honeybees and Drosophila also have smaller than average genome sizes.)

Introns

As you might imagine, the mite genome has a lot less junk DNA than other animals. This is partially reflected in the number and size of the introns. The average protein-encoding gene has less than three introns and the ones that are present are a lot smaller than the introns in species with larger genomes.

The figure on the right is a truncated version of a figure that appears in the supplemental information. It shows that the smallest introns are 40 bp and 70% of all introns are less that 150 bp in length (median = 96 bp). This is close to the smallest possible intron size allowing for slices sites and formation of a loop during splicing.

Transposons and Repetitive Sequences

Transposons (active and degenerate) make up less than 10% of the T. urticae genome and highly repetitive sequences (microsatellites) are almost absent. (The spider mite chromosomes don't have centromeres.)

Transposon sequences and highly repetitive sequences are a major component of the junk DNA found in large genomes so their absence in the mite genome is not a surprise.

Why Is the Mite Genome So Small?

The short answer is, we don't know. The long answer is much more complicated. As Michael Lynch points out (Lynch 2007 p.37), there's a balance between rates of insertion and deletion mutations. In species with small genomes the spontaneous rate of nucleotide deletion exceeds that of insertion so genome sizes shrink over time.

There may not be a selective advantage to having small or large genomes. It may just be that in some species the repair machinery tends to favor deletions while in closely related species the enzymes don't have this bias. Or maybe large genomes are slightly deleterious but the population size isn't large enough to allow natural selection to act. Some lineages may never have encountered significant bottlenecks so they've maintained a huge population size for millions of years allowing natural selection to operate on slightly deleterious mutations. This leads to smaller genomes.

Whatever the explanation, the small genome of mites shows us that most of the junk DNA present in other arthropod genomes is dispensable. That's why it's called "junk."



Grbic, M. et al. (2011) The genome of Tetranychus urticae reveals herbivorus pest adaptations. Nature 479:487-492. [doi: 10.1038/nature10640] [PubMed]

Lynch, M. (2007) "The Origins of Genome Architecture" Sinauer Associates, Inc. Publishers, Sunderland, Massachusetts, United States

Monday, December 19, 2011

Jonathan McLatchie and Junk DNA

 
THEME

Genomes & Junk DNA
Jonathan McLatchie takes on PZ Myers in a spirited attack on junk DNA [Treasure in the Genetic Goldmine: PZ Myers Fails on "Junk DNA"]. The Intelligent Design Creationists are convinced that most of our genome is functional because that's what a good designer would create. They claim that junk DNA is a myth and their "evidence" is selective quotations from the scientific literature. They ignore the big picture, as they so often due.

I discussed most of the creationist arguments in my review of The Myth of Junk DNA.

Jonathan McLatchie analyzes three argument made by PZ Myers in his presentation at Skepticon IV. In that talk PZ said that introns are junk, telomeres are junk, and transposons are junk. I have already stated that I diasgree with PZ on these points [see PZ Myers Talks About Junk DNA]. Now I want to be clear on why Jonathan McLatchie is wrong.
  1. Introns are mostly junk. I think PZ exaggerated a bit when he dismissed all introns as junk. My position is that we should treat introns as functional elements of a gene even though many (but not all) of them could probably be deleted without affecting the survival of the species. Each intron has about 50-80 bp of essential information that's required for proper splicing [Junk in Your Genome: Protein-Encoding Genes]. The rest of the intron, which can be thousand of base pairs in length, is mostly junk [Junk in Your Genome: Intron Size and Distribution]. Some introns contain essential gene regulatory regions and some contain essential genes. That does not mean that all intron sequences are functional.
  2. Telomeres are not junk. I don't think telomeres are junk [Telomeres]. They are absolutely required for proper DNA replication. PZ Myers agrees that telomeres (and centromeres) are functional DNA (28 minutes into the talk). Jonathan McLatchie claims that PZ describes telomeres as junk DNA, "Myers departs from the facts, however, when he asserts that these telomeric repetitive elements are non-functional." McLatchie is not telling the truth.
  3. Defective Transposons are Junk. PZ Myers talks about transposons as mobile genetic elements and states that transposons make up more than half of our genome. That's all junk according to PZ Myers. My position is that the small number of active transposons are functional selfish genes and the real junk is the defective transposon sequences that make up most of the genome [Transposon Insertions in the Human Genome]. Thus, I differ a bit from PZ's position. Jonathan McLatchie, like Jonathan Wells, argues that because the occasional defective transposon in the odd species has acquired a function, this means that most of the defective transposon sequences (~50% of the genome) are functional. This is nonsense.

[Image Credit: The image shows human chromosomes labelled with a telomere probe (yellow), from Christoher Counter at Duke University.]

Monday's Molecule #154

 
Today's molecule is a bit more complicated than some of the others. You have to identify the molecule (common name only) and describe (briefly) its function. Can you name the precursor?

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment. This is your last chance to enter the Christmas draw for a free textbook!

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The molecule is thyrotropin-releasing hormone. It's derived from a long precursor protein containing multiple repeats of the tripeptide Glu-His-Pro.

The winner is Joseph C. Somody.

I'll announce the undergraduate winner of my textbook on Christmas day.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney


Friday, December 16, 2011

Key Figures in Intelligent Design Creationism

 
Here's a recording of interviews with three prominent Intelligent Design Creationists ....

Guillermo Gonzalez is a Senior Fellow at the Center for Science and Culture (Discovery Institute).
Douglas Axe, director of The Biologic Institute, which is largely funded by the Discovery Institute.
David Berlinski is a Senior Fellow at the Center for Science and Culture (Discovery Institute).

This is the best they have to offer. It gives you a very good idea of what Intelligent Design Creationism is all about. It's about nothing ... there's not a single mention of what IDC stands for and not a single bit of evidence for the existence of a designer. All you hear is whining about real science (evolution) and conspiracies.

Here's a quotation from Berlinski.
Nobody else is doing what the Discovery Institute has been able to do, and that is really put an entire scientific establishment on the defensive, forced for the first time to respond to some very significant criticism...




Christopher Hitchens (1949 - 2011 )

 
Christopher Hitchens died yesterday and everyone in the atheist community is going to pay tribute in their own special way. For me, the highlight of Hitchen's career was last year's debate with Tony Blair here in Toronto (Nov. 26, 2010). The subject was "Is religion a force for good or ill?"

This is his opening statement.




Wednesday, December 14, 2011

Centre for Inquiry Canada: Update

 
The Board of Directors of CFI Canada met with a few Associate members last Sunday (Dec. 11, 2011). The purpose of the meeting was to discuss the termination of Justin Trottier as national Executive Director. Ian Bushfield has put together a brief description of the meeting at: The Continuing Story at CFI Canada.

The Board of Directors has emailed a statement to interested parties (see below). You can find out who's on the Board of Directors and who's an Associate Member at: What's Happening at Centre for Inquiry Canada?.

It's difficult to know what the Board has in mind with respect to Justin. They have not given him a paying job but they seem to be holding out hope that he might take over when the acting National Executive Director leaves in March 2012.

According to their statement, the Board is committed to adding new associate members. They say they have made decisions on some of the applications that they have already received. I have not heard from them on the status of my application.

Meanwhile, the Chair of CFI Edmonton, Brent Kelley, has resigned [Resignation as Chair of CFI Edmonton].
On Sunday, December 11, the Associate Members of CFI Canada met in Toronto. This meeting was followed shortly thereafter by a meeting of the board of directors. We, the board, believe it is important to provide you with information about these meetings and the actions and decisions that took place at these meetings.

The meeting of Associate Members was scheduled pursuant to the by-laws of our organization, that is, it was scheduled after the requisite number of Associate Members requested the meeting. The request for the meeting indicated its purpose was to consider the separation of Justin Trottier from the position of National Executive Director (NED), so that topic was discussed. Justin Trottier, who was present at the meeting, was provided a summary of the concerns of some of the directors and he was provided an opportunity to address those concerns. Some Associate Members also expressed their views, as did some of the Regional Executive Directors who audited the meeting.

We believe there was a frank and candid discussion of Justin Trottier’s tenure and the circumstances that led to his separation. We also believe this frank, candid exchange of views was of benefit to the organization.

Shortly after the Associate Members meeting, the board met. One of the issues considered was increasing the number of Associate Members. Among the decisions of the board on this issue were the following:
  • The board unanimously agreed to invite additional applications to the position of Associate Member, to ensure broader representation of the supporters of CFI Canada in this important class of membership;
  • Application forms can be obtained from the Interim NED, Michael Payton (mpayton@cficanada.ca), or from Kevin Smith, Secretary for the board;
  • Because the primary duty of the Associate Members is to elect directors at the organization’s annual meeting, applications will be reviewed carefully, and emphasis will be placed on the applicant’s prior work for and familiarity with the organization, as well as commitment to its mission;
  • The board concluded, consistent with the by-laws, that Associate Members should be a subset of the general membership and that the number of Associate Members should be kept at a manageable level;
  • The board resolved to act on applications in a timely manner so that applicants would be informed of their status prior to the March 11 annual meeting;
  • The board considered and acted on some of the applications it received prior to the December 11 meeting, and accepted applicants will be notified via email.
The board heard a report on the organization’s finances and the status of the organization from Interim NED Michael Payton. Although the organization has no cash crisis, and has sufficient assets to maintain operations in 2012, it was apparent that the organization needs to make efforts to increase donor support, and the board directed Mr. Payton to undertake fundraising. The Interim NED indicated he needed assistance in his new position to deal with the many tasks which require immediate attention.The board expressed appreciation for Mr. Payton’s willingness to step in quickly and assume the Interim NED position given the sudden departure of the prior NED. The board authorized Mr. Payton to seek volunteer assistance and stated it would consider a request to authorize
hiring of additional staff.

The board decided the branding initiative would continue, but that it would be put on hold given the current status of the organization. The organization’s first priorities are to ensure stability and reliable management, raise money, and begin to offer regular programming and services again as soon as possible.

After appropriate motions, the board resolved the following:
  • No final decision would be made on Justin Trottier’s possible reemployment in any position until the March 11 board meeting. In reaching this decision, the board carefully considered the views that had been offered concerning Mr. Trottier, both pro and con, as well as his record as NED. We also took into account the fact that we agreed to retain our current NED untill March at which time he will
    voluntarily step down.
  • The board would look favorably upon Mr. Trottier’s volunteering of his services to CFI Canada during the period prior to the March 11 board meeting.
    Lorne Trottier took no part in the voting on these motions. The motions carried 3-0, with Tom Flynn absent and Kevin Smith abstaining.
After the board meeting, the board was informed that Justin Trottier would volunteer to assist the organization. CFI Canada welcomes his willingness to volunteer, as it welcomes the willingness of all its volunteers to donate their valuable time and energy to furthering our mission.

One other item the board discussed at length was the perception that there is a lack of transparency and openness in board deliberations. To that end the board will be doing some renovations to the web site which will include, among other things, the posting of our by laws. We will also make available, the application to become an Associate Member along with the guidelines for applying. We will also have a dedicated email so CFI supporters can directly contact the board, the email directors@cficanada.ca
will be up by starting Thursday Dec 15th.

The board is committed to using its best efforts to ensuring not only the survival, but the success of CFI Canada and its important mission. We are well aware that many of the decisions we make are bound to be controversial. We cannot please everybody. At the end of the day we have to rely on our judgment. Our service as directors is not perpetual. Associate Members will be able to reelect or remove us at the March 11 meeting. In the meantime, we pledge to you that we will act in good faith, motivated by what we think is best for the organization and its missio

Thank you for your support.


Monday's Molecule #153

 
Today's1 molecule has a special significance for me since I "accidentally" purified the enzyme that catalyzes the last step in its synthesis. That was one of my first successful experiments as a graduate student (1969).

This is a complex molecule so I'm not going to insist on the IUPAC name. You can supply a common name as long as it is unambiguous (be careful!). This time it's not sufficient to just give me the name of the molecule. You also have to briefly explain what it does and where you can find it, including the "species." The functional explanation has to be a biochemical explanation.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

After today, you have only one more chance to win an autographed book.

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE:The molecule is β-D-glucopyranosyl-5-hydroxymethylcytosine. This is a modified base found in T4 bacteriophage and its relatives. The modification is required to protect phage DNA from E. coli host restriction endonucleases.

The winner is Bill Chaney.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)


1. Yes, I know it's Wednesday. I was too busy on Monday to post a molecule.

Tuesday, December 13, 2011

Barry Arrington Explains Irreducible Complexity

The Intelligent Design Creationists are feeling a little bit threatened these days. Some scientists are—believe it or not—actually addressing their main arguments head-on and showing them to be vacuous.

The IDiots don't like this because they are used to posting very silly arguments from amateurs on their blogs and then complaining that scientists are only picking the low-hanging fruit and not addressing the true "experts." Truth is, all of the so-called "expert" arguments have been refuted ages ago.

Here's an example from Barry Arrington who explains the real meaning of irreducible complexity and why it supports intelligent design [Denis Alexander’s Strawman Just as Silly].
No ID theorist has ever argued that evolution is impossible because complex biochemical systems cannot self assemble “all in one go.” This is an absurd caricature of the argument from irreducible complexity (IC).

The basic logic of IC goes like this: (1) By definition, evolution can work only in a stepwise fashion wherein each successive step is “selected for” because it has conferred a selective advantage on the organism. (2) an irreducibly complex system is a system which if one part is removed all function ceases. (3) by definition, therefore, an irreducibly complex system cannot be produced in a stepwise fashion. (4) therefore evolution is not capable of producing an irreducibly complex system.

Starting with this logic the ID proponent argues that certain systems are irreducibly complex and therefore could not have been produced by evolution. The bacterial flagellum and the blood clotting cascade are classic examples of such systems.
I have frequently accused Intelligent Design Creationists of not understanding evolution. For example, one of their heroes, Phillip Johnson, clearly thinks that natural selection is a synonym for evolution in spite of the fact that other mechanisms have been known for almost a century [see This Video Should Be Shown to all Biology Students and Phillip Johnson, One of the Very Best Intelligent Design Creationists].

Jonathan McLatchie defended his hero by saying [Maligning Phil Johnson, with Lots of Rhetoric but Little Substance] ...
This is the type of condescending rhetoric that is so prevalent in anti-ID writings. Does Shallit really think that we haven't heard of processes such as genetic drift and endosymbiosis?
We look forward to hearing again from Jonathan McLatchie about how IDiots like Barry Arrington understand evolution.

Arrington's false premise (#1) isn't the only thing wrong with his argument because one can quite easily construct plausible scenarios where each step in constructing an irreducibly complex system confers a selective advantage. All you have to do is postulate that the intermediate selective advantages are not the same as the final purpose of the system.

This is all been thoroughly debated over a decade ago. It's just not true that the concept of irreducible complexity has so flummoxed evolutionary biologists that they have abandoned evolution.

Barry Arrington also takes on one of my comments from somewhere. I don't remember the context but apparently I questioned whether the definition of "information" from computer science and philosophy could be applied to the "information" in DNA sequences. The problem is that, according to Intelligent Design Creationists, if the DNA information is the same as other kinds of information then it has to be created by an agent like some god or some space alien.

They don't seem to be troubled by such an explanation because they never ask the obvious question ... where did the information in the designer come from?1

Anyway, read Barry's defense of the idea that information in a DNA sequence is the same as other kinds of information that requires a designer [Upright Biped Replies to Dr. Moran on “Information”].

[UPDATE: Apparently that last posting was written by someone called "Upright Biped" and Barry Arrington just posted it under his own name on Uncommon Descent.]

Remember that Barry Arrington is a lawyer from Colorado and one of the regular bloggers on Uncommon Descent. Most IDiots consider him an expert on Intelligent Design Creationism. In other words, this is as good as it gets.


1. It's turtles all the way down, right?

Friday, December 09, 2011

The Top 50 Atheists

 
A website called The Best Schools has published a list of the top 50 atheists in the world today.
Atheists deny that God exists. Yet for an atheist to make our ranking of the 50 top atheists in the world—given in ascending order—it is not enough merely to deny that God exists. More is required.

Certainty. To make our list, someone has to be very sure of him- or herself. No mere agnostics will do. To make the cut, one has to do more than merely question God’s existence or even deny that knowledge of God’s existence is possible.

Celebrity is another requirement. To make our list, the atheist must have a public identification with atheism and must have made some public impact by challenging religion and/or promoting atheism, either in print or on the Internet. In other words, our ranking is a list of people who are well known because they are atheists, among other things—as opposed to people who are mainly famous for some other reason (like Jodie Foster or Bruce Willis). In a few cases, a person has made the list mainly on the basis of his or her attack on free will and morality—the foundation of the traditional religious view of human beings—so long as the person has also publicly identified as an atheist.
I know for a fact that some people on the list do not agree with the definition of atheist that the website promotes.

The ranking seems to be based largely on the production of books about atheism so it's heavily tilted toward philosophers. In fact, the top five are all philosophers. The top scientist, at number 6, is E.O. Wilson.

I'm surprised that there are philosophers who deny that gods exists as opposed to just not believing in them.

I'm not a very good atheist 'cause I've never heard of most of the top 50 atheists.


Ricky Gervais is not on the list.

Carnival of Evolution #42

 
This month's Carnival of Evolution (42nd version) is hosted by Psi Wavefunction, a researcher at Indiana University, Bloomington. He/she blogs at The Ocelloid : The Carnival of Evolution #42: Answers to life, the universe and everything.
Don’t panic — welcome to the forty-second Carnival of Evolution! Please bear with me and pretend it’s still Dec 1st — I had just recently emerged from a wormhole in time, caused by being in a protistologist’s heaven: Dalhousie University in Halifax, with about 30-40 dedicated protist geeks milling about. It was distracting and a pleasant contrast to being the only one in an entire state…

But now I’m back in a very evolution-ey place, just in time for a collection of equally evolution-ey posts from all four corners of the internet! (tubes have corners, right? No? Oh…)

Apologies if I missed any; there are a lot of submissions this month… will correct noted omissions and errors!

The next Carnival of Evolution will be hosted by the group at THE EBB AND FLOW. You can submit your articles for next month's carnival at Carnival of Evolution. Here's the website: Carnival of Evolution.


Thursday, December 08, 2011

What's Happening at Centre for Inquiry Canada?

 
The short answer is, "I don't know." The long answer is, "I don't think anyone else does."

Here's what I know.

Committee for the Advancement of Scientific Skepticism (CASS)
CASS continues to meet and there are many projects under way. One of the co-directors, Michael Kruse, resigned because he wasn't happy with the direction that CFI was headed. The other co-director, Iain Martel is carrying on.

Centre for Inquiry Ontario
Right now this branch doesn't exist as far as I can tell. There's no leader and no volunteers are working.

National Executive Director
The acting National Executive Director is Michael Payton. He is struggling to get a grip on the organization after the abrupt departure of Derek Pert a few weeks ago. (Derek was forced to resign when the Board of Directors failed to support him.) The former National Executive Director, Justin Trottier, was fired last September.)

Michael could use a lot of help but there's no room for anyone else in the new office. Don't expect the website to be updated in the near future. Don't expect any memberships to be renewed—and certainly don't expect to be notified if your expires. Don't even expect any email messages from the head office.

Michael is leaving for Singapore in a few months and there's nobody who looks like they could step into his job.

Board of Directors/Associate Members

Three members of the Board of Directors resigned two weeks ago (Carol Parlow, Ian McCuaig, and Michael Gardnier). The remaining Canadian members are: Kevin Smith, Lorne Trottier, Pat O'Brian, and Richard Thain. The representatives from CFI Transnational are Ron Lindsay and Tom Flynn.

The Associate Members elect the Board of Directors. In addition to the current directors and the three who resigned there are six Associate Members: Chris DiCarlo, Jeffrey Rosenthal, Zak Fiddes, Ethan Clow, Bisi Bashorun, and Barry Karr. (Barry Karr is from CFI Transnational.)

As far as I know, only three of these are active: Chris DiCarlo, Jeffrey Rosenthal, and Zak Fiddes.

Sunday Meeting
There's going to be a meeting this Sunday. It was called by a group of Associate Members. The first part of the meeting is between the Board of Directors and the three active Associate Members. The second part of the meeting is a Board meeting.

The main item on the agenda is whether the firing of Justin Trottier was fair. I believe Justin will be at the meeting. There's talk of a plan to re-hire him in some capacity. It's clear that some members of the Board are sympathetic and it's clear that some are adamantly opposed. It doesn't look like the dissention within the Board has gone away after three resignations.

Some of us tried to make the Sunday meeting an open meeting for all members of CFI but that plan met with firm resistance from the Directors.

New Associate Members
There's general agreement that we need new Associate Members. Several people have sent in applications. New members have to be approved by the Board of Directors. They will discuss this at the Sunday meeting.

Rebranding
The rebranding exercise is on hold, and so is everything else.

Homology

 
There's an interesting discussion about homology going on in the comments section of Fishing for Creationists. The creationists are claiming that homology disproves evolution.


Wednesday, December 07, 2011

Fishing for Creationists

Fishing for creationists is not a sport. All you need to do is dangle a bit of bait and dozens of creationists will fight for the right to impale themselves on the hook. The latest victim is Jonathan McLatchie who responded to criticism of Phillip Johnson [Maligning Phil Johnson, with Lots of Rhetoric but Little Substance]. I'm sure the other bloggers on Evolution News & Views don't see him as a fishy victim, they probably think of him as the designated hitter. (You could use "sacrificial lamb" if you want a Biblical metaphor.)

Jonathan M, as he prefers to be known, is studying in Scotland for a Master's degree in evolutionary biology. He's upset with Jeffrey Shallit for criticizing Phillip Johnson's 1993 video (see This Video Should Be Shown to all Biology Students). He's also upset with my critiques of the same video (see Phillip Johnson, One of the Very Best Intelligent Design Creationists).

Tuesday, December 06, 2011

PZ Myers Talks About Junk DNA

 
PZ Myers has a blog called Pharyngula—perhaps you've heard of it?

He gave a talk on junk DNA at Skepticon IV in Sringfield, Missouri (USA) a few weeks ago. I disagree with a few thing he said,

1. Some intron sequences are essential for splicing whereas PZ implies that they are all junk.
2. Regulatory sequences make up less than 1% of your genome and not more than exons as PZ says [What's in Your Genome?].
3. Half or your genome is DEFECTIVE transposon, not active transposons. Active transposons are not junk. Defective transposons are a form of pseduogene and they are definitely junk. The distinction is important.

But the main point is that the IDiots predicted there wouldn't be any significant amount of junk in your genome and that prediction has been refuted.




Monday, December 05, 2011

Monday's Molecule #152

 
This is a simple molecule so I'm going to insist on the IUPAC name as well as the common name. This time it's not sufficient to just give me the name of the molecule. You also have to briefly explain what it does and why it's important to some humans. The functional explanation has to be a biochemical explanation, not a physiological one.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The molecule is chlorothiazide of hydrochlorothiazide or 6-chloro-1,1-dioxo-3,4-dihydro-2H-1,2,4-benzothiadiazine-7-sulfonamide. It's a drug commonly used to treat high blood pressure. Chlorothiazide belongs to a class of drugs that function as diuretics—they decrease blood volume by preventing reabsorption of water from the urine.

The winner is 凌嘉誠 (Alex Ling). His answer emphasizes the role of the drug in inhibiting carbonic anhydrase and that's a valid property. However, the most important immediate effect is probably the inhibition of the Na+/Cl- transporter in the kidneys. As far as I can tell the effects of the drug at the molecular level are not as clear-cut as one would like. The decrease in blood volume appears to be temporary and the long-term effect in lowering blood pressure is probabably due to some unknown effect on veins and arteries.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger


Earth to Rick: The Debate Is Over and You Lost!

 
Rick Santorum is a former United States Senator. He is running for the Republican nomination for President of the United States. In this video he is explaining why creationism should be taught in schools.

The Discover Institute blog, Evolution News & Views, posted this video [Santorum on Evolution: "It's Worth a Debate." Yeah, It is]. It obvious that the IDiots consider Santorum to be a credible supporter of Intelligent Design Creationism.

I suppose that's understandable given the quality of their other supportersl




William Dembski Disproves Evolution

 
Bill Dembski is another one of the "big guns" of Intelligent Design Creationism. He has a Ph.D. in mathematics (University of Chicago, 1988), a Ph.D. in philosophy (University of Illinois (Chicago), 1993) and a Master's of Divinity (Princeton Theological Seminary, 1996).

Here's a video explaining how Dembski can mathematically disprove evolution. Somehow this leads to proof of god. It may be difficult to follow the logic but that's probably because you and I don't have Ph.D.'s in mathematics or philosophy.

Keep in mind that this is no amateur. Dembski is among the very best of the best in Intelligent Design Creationism. His speculations have been thoroughly refuted by prominent mathematicians, scientists, and philosophers. Under normal circumstances, this would be enough to cause his supporters to abandon him but he's still a fellow of the Center for Science and Culture and he's still promoted as one of the leading supporters of Intelligent Design Creationism.




Phillip Johnson, One of the Very Best Intelligent Design Creationists

 

The IDiots have been complaining of late that we aren't addressing their very best arguments in favor of Intelligent Design Creationism. They think we're just picking off the low-hanging fruit by attacking amateurs and Young Earth Creationists. This isn't true, but that's not a surprise since much of what they say isn't true.

The Intelligent Design Creationists are celebrating the 20th anniversary of the publication of Phillip Johnson's Darwin on Trial [Phillip Johnson on the Scientific Nature of Opposition to Darwinian Theory] [Christian Post: Darwin on Trial Still Resonates 20 Years Later] [Why Phillip Johnson Matters: A Biography]. It's clear that they think of Phillip Johnson as one of the leading proponents of Intelligent Design Creationism and that's quite reasonable since he was one of the key players at the beginning of the movement. I'm going to assume that Phillip Johnson is not low-hanging fruit. He's among the very best that Intelligent Design Creationism has to offer or else they wouldn't be making such a big deal of this anniversary.

Thursday, December 01, 2011

I Don't Understand the Spammers

 
There are people somewhere who scour the blogs posting comments containing links to various websites. The object, I think, is to boost their scores on the search engines but I'm not sure this actually works. I imagine that these people are being paid to post comments.

I get about 20 of these spam comments per day. Since I moderate comments they never get posted and you, dear readers, never see them. The Blogger spam catcher puts most of them in the spam bucket.

So what's the point? The people posting these comments are wasting their time, and wasting my time as well. Is that the goal? I don't get it.


One Problem with Intelligent Design Creationism

 
There are many different ideas about creators but they all share one common feature; namely, they postulate the existence of a supernatural creator who is directly responsible for creating some parts of the universe (usually the whole thing!).

Intelligent Design Creationism is a version of creationism that focuses on the creation of life. Proponents of this version claim that god played a direct role in creating some parts of living organisms. They concentrate on biochemical structures like bacterial flagella and folded proteins but they're also interested in things like speciation and the Cambrian explosion.

Evolution can explain most of the things that the Intelligent Design Creationists worry about so their main overt activities are concentrated on discrediting evolution and discrediting those scientists who support scientific explanations of biology. Given this necessity, you'd think that the leading proponents of IDC would be quite knowledgeable about biology and evolution.

Wednesday, November 30, 2011

Joseph Hoffmann Responds

 
Joseph Hoffmann thinks he knows a lot about modern atheism so he wrote an insulting and rather stupid attack: Atheism’s Little Idea. A lot of atheists were offended and took the time to try and educate Hoffmann. My own contribution was: On Being a Sophisticated Atheist.

Hoffmann noticed that there was less than unanimous agreement with his position so he replied on his blog The New Oxonian: The Sure-Fire Atheist Rapid Response Manual.

You really have to read it to see just what a sophisticated response from a Harvard/Oxford intellectual looks like. I think he's a bit annoyed at all the attention he's getting.


How to Fix CFI Canada

 
In my opinion, there are two immediate things we need to do to fix CFI.

The first is more openness. To that end I think the December 11th meeting in Toronto should be open to any member of the Centre for Inquiry. The meeting is at 10 am (Sunday). I assume it's at the CFI offices in Toronto.

I expect that several people, including Justin Trottier and the Directors, will want to speak at that meeting. The objective is to explain exactly what's going on and how we got into this mess.

The second thing we need to do is add more Associate Members. Candidates for Associate Membership can send an application to the Board of Directors.1 The Board must approve these applications. Associate Members elect the Directors. There are only a dozen or so Associate Members and it's not clear how many of them are active in the Centre.

If you have any ideas about what should, or should not, happen next, please bring them up in the comments below.

Check out ...
Ian Bushfield (Vancouver): Beyond CFI Canada–Reasons for optimism


1. You can contact me for the application form.

Tuesday, November 29, 2011

IDiots and Incivility

 
This is just a heads-up to let you know that Casey Luskin is about to post a series of examples of bad behavior by ID critics [The Uncivil Style of Intelligent Design Critics]. Apparently it's going to be a long series ....
I'm going to let ENV readers in on a little secret: When many of us in the intelligent design (ID) movement read the arguments coming from our critics, we're surprised at their low quality and style. We don't rejoice at this -- we'd much rather see a robust, civil, and fruitful scientific debate over the relevant questions. But the incivility, basic inaccuracy, and unserious tone characteristic of so many criticisms of ID all make you wonder: If the critics had stronger rebuttals to offer, wouldn't we be hearing them?

...

There are so many examples of incivility among ID-critics that it's hard to know where to start. And I'm not just talking about the usual Internet suspects, like PZ Myers, Jerry Coyne, or Larry Moran.
On a completely unrelated topic that has nothing to do with Darwinist incivility ...

While you're checking out Evolution News & Views you might want to read a fascinating article by Richard Weikart defending his books From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Racism in Germany and Hitler's Ethic: The Nazi Pursuit of Evolutionary Progress [Robert J. Richards and the Historical Record]. It even has a photo to illustrate the point about Darwin (see below).


This is a follow-up to a very civil article posted last month: Can Darwinists Condemn Hitler and Remain Consistent with Their Darwinism?.
I threw down the gauntlet to many of my Darwinian opponents by telling her that if Darwinism is indeed a purposeless, non-teleological process, as many evolutionists and biology textbooks proclaim, and if morality is the product of these mindless evolutionary processes, as Darwin and many other prominent Darwinists maintain, then "I don't think [they] have any grounds to criticize Hitler."

According to Flam, these are "fighting words." However, I have spoken with intelligent Darwinists who admit point-blank that they do not have any grounds to condemn Hitler, so I am not just making this up. Many evolutionists believe that since evolution explains the origin of morality -- as Darwin himself argued -- then there is no objective morality. The famous evolutionary biologist and founder of sociobiology, E. O. Wilson, and the prominent philosopher of science Michael Ruse co-authored an article on evolutionary ethics in which they asserted, "Ethics as we understand it is an illusion fobbed off on us by our genes to get us to co-operate."
Anyway, let's not forget the important point and that's Casey Luskin's upcoming series on the incivility of ID critics.


David Berlinksi Prays for Me!!!!

 
Over at Evolution News & Views, Casey Luskin is ranting again about not getting no respect [The Uncivil Style of Intelligent Design Critics]. While checking out recent postings on that site to see whether the evil Darwinists were being treated respectfully, I came across a post by David Berlinski on Phillip Johnson. Imagine my surprise when I read this ....
At the Discovery Institute we often offer an inter-faith Prayer of Thanksgiving to the Almighty for the likes of P.Z. Myers, Larry Moran, Barbara Forrest, Rob Pennock and Jeffrey Shallit.
Thank-you to all the inmates at the institute. I really appreciate your thoughts and prayers.

Next time, could you ask him to send money?


Monday, November 28, 2011

On Being a Sophisticated Atheist

We atheists really have a hard time pleasing theists and philosophers who insist that we immerse ourselves in the study of gods before declining to believe in any of them. Apparently it's not sufficient to simply reject as unconvincing all of the arguments for the existence of god. We also have to study apologetics, which takes the existence of god as a premise!

As if that weren't bad enough, we now have a group of philosopher types who insist that we study every atheist who ever lived. One of those philosopher types is R. Joseph Hoffman, a graduate from Harvard Divinity School and the University of Oxford. He is mainly interested in early Christianity. Hoffman is a nonbeleiver who posts at The New Oxonian. His latest post is: Atheism’s Little Idea.

Is the Burzynski Clinic Full of Quacks?

The Burzynski Clinic is located in Houston, Texas, United States. It charges a lot of money to treat cancer patients and the treatment is probably not effective according to Andy Lewis at The Quackometer: The False Hope of the Burzynski Clinic.

Andy Lewis received a letter from someone named Marc Stephens who claims to represent the Burzynski Clinic. You have to read this letter to understand what's going on [The Burzynski Clinic Threatens My Family].
Le Canard Noir / Andy Lewis,

I represent the Burzynski Clinic, Burzynski Research Institute, and Dr. Stanislaw Burzynski. It has been brought to our attention that you have content on your websites http://www.quackometer.net/blog/2011/11/the-false-hope-of-the-burzynski-clinic.html that is in violation of multiple laws.

Please allow this correspondence to serve as notice to you that you published libelous and defamatory information. This correspondence constitutes a demand that you immediately cease and desist in your actions defaming and libeling my clients.

Please be advised that my clients consider the content of your posting to be legally actionable under numerous legal causes of action, including but not limited to: defamation Libel, defamation per se, and tortious interference with business contracts and business relationships. The information you assert in your article is factually incorrect, and posted with either actual knowledge, or reckless disregard for its falsity.

The various terms you use in your article connote dishonesty, untrustworthiness, illegality, and fraud. You, maliciously with the intent to harm my clients and to destroy his business, state information which is wholly without support, and which damages my clients’ reputations in the community. The purpose of your posting is to create in the public the belief that my clients are disreputable, are engaged in on-going criminal activity, and must be avoided by the public.

You have a right to freedom of speech, and you have a right to voice your opinion, but you do not have the right to post libelous statements regardless if you think its your opinion or not. You are highly aware of defamation laws. You actually wrote an article about defamation on your site. In addition, I have information linking you to a network of individuals that disseminate false information. So the courts will apparently see the context of your article, and your act as Malicious. You have multiple third parties that viewed and commented on your article, which clearly makes this matter defamation libel. Once I obtain a subpoena for your personal information, I will not settle this case with you. Shut the article down IMMEDIATELY.

GOVERN YOURSELF ACCORDINGLY.

Regards,

Marc Stephens
Burzynski Clinic
9432 Katy Freeway
Houston, Texas 77055
What would a normal person do after receiving such a letter? Ask for more information about the "defamatory" content. That's what Andy Lewis did and here's part of the response.
If you had no history of lying, and if you were not apart of a fraud network I would take the time to explain your article word for word, but you already know what defamation is. I’ve already recorded all of your articles from previous years as well as legal notice sent by other attorneys for different matters. As I mentioned, I am not playing games with you. You have a history of being stubborn which will play right into my hands. Be smart and considerate for your family and new child, and shut the article down..Immediately. FINAL WARNING.

Regards,

Marc Stephens
Yep, that's a threat you see in that paragraph.

Here's a few people who think that the Burzynski Clinic deserves more publicity.


"Yes," "No," and "I Don't Know"

John Wilkins has continued the discussion about agnosticism, atheism, and the meaning of debate [Once more into the fray, dear agnostics]. I'll try and respond to the specific points he makes in a minute or two, but first I need to make my own position (more) clear.

I teach a course on critical thinking about scientific issues such as evolution/creationism. Most (all?) of the "scientific" debates that enter the public realm can be divided into two groups: those where one side is right and the other side is wrong, and those where the issue is controversial. From a personal perspective, that means you can have three responses when asked if you agree with a scientific argument: "yes," "no," and "I don't know."

Monday's Molecule #151

 
This is a very complicated molecule so I'm not going to ask for the IUPAC name. You can win with the common name but be sure to get it right!

This molecule has played a very important role in elucidating some basic concepts in molecular biology but its structure is rarely shown in 21st century biochemistry textbooks.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

UPDATE: The molecule is rifampicin, an inhibitor of bacterial RNA polymerase. The winner is Philip Rodger. Congratulations Philip, please send me an email message so we can arrange lunch.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)


Sunday, November 27, 2011

NASA Confusion About the Origin of Life

NASA-funded researchers have evidence that some building blocks of DNA, the molecule that carries the genetic instructions for life, found in meteorites were likely created in space. The research gives support to the theory that a "kit" of ready-made parts created in space and delivered to Earth by meteorite and comet impacts assisted the origin of life. [NASA Researchers: DNA Building Blocks Can Be Made in Space]

Most scientists are not thinking critically about the origin of life. It is extremely improbable that asteroids could have delivered enough amino acids or purines to make a difference. Given the known stability of these molecules in the ocean, you would have to achieve an enormous delivery rate to make a concentration sufficient to drive polymerization. It's much more likely that the first complex amino acids, and the first purines and pyrimidines, were synthesized in special environments on Earth using simple inorganic precursors. This is the origin of life scenario promoted as "Metabolism First" [More Prebiotic Soup Nonsense].

I wish NASA astrobiologists would stop making the assumption that all they have to do is discover complex organic molecules in asteroids in order to solve the origin of life. There are a lot of steps between finding purines in asteroids and making a prebiotic soup that could contribute to the origin of life. Those steps need to be spelled out in their press releases so the public can evaluate the discovery.

Here's what I wrote a few years ago .... [Can watery asteroids explain why life is 'left-handed'?]
In order for extraterrestrial organic matter to have fueled the origin of life, a lot of meteorites carrying organic matter had to arrive on the primitive Earth. The problem of amino acid concentrations and stabiltity were discussed in a classic paper by Jeffrey Bada published in 1991.

Some of his calculations are worth remembering.

The current flux of extraterrestrial organic material is about 3 × 108 grams per year from cosmic dust and micrometeorites. About 1% of this is amino acids and most of them are not the ones found in living organisms. This should give rise over time to a concentration in the oceans of about 0.1 nM (10-10 M). That's not sufficient for life to have originated.

The flux in the past was almost certainly much greater and lots of organic material might have been delivered by large meteorites; however, it's unlikely that amino concentrations in the oceans could ever have been more than 10-100 pM for all amino acids combined.

Most amino acids will spontaneously degrade over time. There's a window of opportunity that only lasts about 10 million years because in that time all the water in the oceans will pass through hydrothermal vents and the high temperature will destroy most chemicals—including amino acids.
I don't know whether the NASA astronomers are aware of this problem but have developed a scenario to overcome it, or whether they just haven't thought about the problem.


Bada, J. (1991) Amino acid cosmogeochemistry. Phil trans. R. Soc. Lond. 333:349-358.

Saturday, November 26, 2011

The Implosion of CFI Canada

The Centre for Inquiry - Canada "... promotes and advances reason, science, secularism and freedom of inquiry in all areas of human endeavour." It is affiliated with the Center for Inquiry in the United States, headquartered in Amherst, New York (near Buffalo).

The Canadian Centre for Inquiry was founded in 2007 and the inaugural meeting was held in their rented facilities just south of the University of Toronto and a short walk from my office [Centre for Inquiry: March 10, 2007]. Justin Trottier was the new director.

CFI - Canada has now grown from the original Toronto (Ontario) branch to include branches in Vancouver, Okanagan, Calgary, Saskatchewan, Ottawa, Montreal, and Nova Scotia. There's paid staff in Toronto and there are now paid employees (usually part time) in several other centres.

Friday, November 25, 2011

Zoë Is Coming for Christmas

 
My granddaughter Zoë is coming for Christmas, from Los Angeles. She's bringing her parents. That means two of my little girls (mother and daughter) are coming home for Christmas.

Here's an atheist video from Australia. It's about Christmas, family, love, and a little baby girl who grows up. Can you get through it without shedding a tear? I couldn't.

TimMinchin the songwriter and singer in this video, grew up in Perth, Australia. He lives with his wife, daughter, and son in London, England. The song, White Wine in the Sun was first released in December, 2009.




[Hat Tip: Pharyngula]

De mortuis nil nisi bonum

De mortuis nil nisi bonum is a Latin phrase which indicates that it is socially inappropriate to say anything negative about a (recently) deceased person. Sometimes shortened to nil nisi bonum, the phrase derives from the sentence "de mortuis nil nisi bonum dicendum est" and is variously translated as "Speak no ill of the dead", "Of the dead, speak no evil", "Do not/ Don't speak ill of the dead" or, strictly literally, "Of the dead, nothing unless good".
There are times when social conventions need to be violated. This is one of those times.

Lynn Margulis died last Tuesday (November 22, 2011) at the age of only 73. Margulis is rightly famous for her endosymbiotic theory of the origins of mitochondria and chloroplasts. We known that she was right and she deserves credit for that part of her theory.

However, since then (about 1970) her record has not been stellar and it's only appropriate that we keep this in mind as we reflect on her contribution to science. Here's a video of Lynn Margulis "defending" science by promoting the idea that one of the buildings of the World Trade Center in New York was brought down on Sept. 11, 2001 by explosives that had been planted in the building months before.




[Hat Tip: Why Evolution Is True]

John Wilkins on Sandwalk

 
I like John Wilkins. If he lived in Toronto I would want to talk to him several times a week and I'd even pay for the the coffee and lunches. It's embarrassingly easy to teach me things I don't know, or correct my errors, but John has done way more than his fair share over the past twenty years.

I think he's mad at me [Prescriptions for atheists].
First, Larry points out that arguments about the existence of God require one to take a position on fairies. One can only be agnostic about gods to the extent one is agnostic about fairies. My previous argument that this is comparing unlikes has, in one fell swoop, been demolished! Of course, there must be other reasons for thinking that we can rule fairies out of contention (let us call them faeries to avoid confusion) which do exist but are undetectable. It cannot be the principle that “if it is unscientific it is irrational” for that would be the positivist presumption and that would be unscientific. I know I am wrong about positivism here, because Dan Hicks pointed out that some positivists weren’t positivists about everything. So positivism is never self-defeating, even when the positivist presumption is applied by some to everything.

Larry must have other reasons for showing that faeries do not exist – other than being uninterested in what some people claim; this, as Larry must appreciate, is not about what I the reasoner think is true, but about what others who make these claims must be called. I look forward to him enlightening me on this.