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.)


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


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.

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 (, 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
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.

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.

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


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.

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.