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Thursday, March 31, 2011

Junk & Jonathan: Part 1—Getting the History Correct

This is the first in a series of postings about a new book by Jonathan Wells: The Myth of Junk DNA. The book is published by Discovery Institute Press and it should go on sale on May 31 2011. I'm responding to an interview with Jonathan Wells on Uncommon Descent [Jonathan Wells on his book, The Myth of Junk DNA – yes, it is a Darwinist myth and he nails it as such].

The first question is "what is junk/noncoding DNA?" And the answer is,
“Non-coding” in this context means “non-protein-coding.” An important function of our DNA is to specific the sequences of subunits (amino acids) in the proteins that (along with other types of molecules) make up our bodies. When molecular biologists discovered in the 1970s that about 98% of our DNA does not code for proteins, some biologists called non-protein- coding DNA “junk.”
This is misleading. You can consult the excellent article by Ryan Gregory on the origin of the term "junk DNA" to see what it meant in 1972: A word about "junk DNA". The bottom line is that the original meaning of the term "junk DNA" was much closer to what we now call pseudogenes. "Non-coding DNA" is that portion of the genome that does not encode amino acids. In the original paper by Susumu Ohno (1972) there was plenty of discussion about functional noncoding DNA (centromeres, regulatory sequences, spacer DNA). In addition, every scientist in 1972 knew that there were functional genes for tRNAs and ribosomal RNAs in the noncoding DNA.

There was never a time when knowledgeable molecular biologists equated "junk" DNA and "noncoding" DNA. That doesn't mean that there weren't slip-ups from time to time as less knowledgeable scientists published articles on genome organization. There are even modern scientists (and science writers) who make the mistake of confusing "noncoding" with "junk."

My point is that if you are going to answer the question accurately then you should represent the consensus view of most scientists who know that lots of noncoding DNA has a function. You should also attempt to present the modern view of junk DNA instead of implying that forty year old concepts still hold sway. The modern view is that junk DNA is that part of our genome that has no known function. It does not include noncoding regions like regulatory sequences, RNA genes, centromeres. telomeres, origins of replication, recombination hotspots, splice sites, minimal intron length, and scaffold attachment regions (SARs).

The interviewer is Denyse O'Leary and her sympathies are clear in the followup question, "Why was it called “junk” in the first place? And why does all this remind me of one of those auction program episodes where someone is storing leftover carpet nails in what turns out to be a Ming dynasty vase? My mom loves those."

Jonathan Wells answers,
According to Charles Darwin’s theory, all living things are descendants of common ancestors that have been modified solely by unguided natural processes that include variation and selection. In the modern version of his theory—neo-Darwinism— genes control embryo development, variations are due to differences in genes, and new variations originate in genetic mutations. In the 1950s, neo-Darwinists equated genes with DNA sequences (Francis Crick called DNA “the secret of life”) and assumed that their biological significance lay in the proteins they encoded. The 98% of our DNA that does not code for proteins was attributed to molecular accidents that have accumulated in the course of evolution.

“The amount of DNA in organisms,” neo-Darwinist Richard Dawkins wrote in 1976, “is more than is strictly necessary for building them: A large fraction of the DNA is never translated into protein. From the point of view of the individual organism this seems paradoxical. If the ‘purpose’ of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing. Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.” (The Selfish Gene, p. 47)

Since the 1980s, however, and especially after completion of the Human Genome Project in 2003, biologists have discovered many functions for non-protein-coding DNA. If the Ming vase is a living cell and the leftover carpet nails are “junk DNA,” it turns out that the nails are not only made of gold, but they also make an essential contribution to the beauty of the vase.
There's so much wrong with this answer that it's difficult to know where to begin. Maybe I'll just summarize in point form and elaborate in the comments if anyone wants to discuss it further.
  • Implying that junk DNA has anything to do with Darwin's theory of evolution by natural selection is totally wrong. No matter how you define "neo-Darwinism" the fact remains that most biologists who believed in adaptation were very skeptical of junk DNA precisely because it didn't fit with Darwin's view of evolution. The idea that as much as 90% of our genome could be junk was very much a minority view in the 1970s and it's probably still a minority view.
  • Dawkins was writing about selfish DNA when he wrote that passage in The Selfish Gene. Selfish DNA is not junk DNA. It has an adaptive purpose and a function. It is completely wrong to claim that Richard Dawkins was a big fan of junk DNA in the 1970s. Dawkins makes that very clear in The Extended Phenotype when he proposes various explanations for the extra DNA in our genome.1
  • The statement, "The 98% of our DNA that does not code for proteins was attributed to molecular accidents that have accumulated in the course of evolution" is wrong. There was never a group of knowledgeable scientists who thought that all noncoding DNA was due to accidents. Beginning in the 1970s, there were some who thought that a majority of our genome is junk and some (I am one) still think that as much as 90% could be junk. It's worth emphasizing that this view (that most of our genome is junk) was promoted by a relatively small number of scientists and never adopted as the consensus view of the majority of biologists.
  • It is misleading to imply that many functions of noncoding DNA have been recently discovered. The only discovery that could even remotely fall into that category would be additional categories of small RNAs that weren't known before. The well-characterized examples account for less than 2% of the genome. Everything else is speculative and controversial.
Denyse asks, "What caused the change of view about junk DNA? Can you suggest a couple of key findings?" And Wells replies,
In a word, evidence. The first to emerge was the fact that almost all of an organism’s DNA is transcribed into RNA. (So although most of it may be non-protein-coding, it codes for RNA.) From a Darwinian perspective, this is surprising: Why would an organism struggling to survive devote so many of its internal resources to producing supposedly useless RNA? Indeed, since 2003 it has become clear that non-protein-coding RNAs perform many essential functions in living cells.
Among those of us who advocate junk DNA there are very few who have changed their minds in the past decade. Why is that? It's because we simply don't believe that the "evidence" of widespread transcription is meaningful. Those scientists who oppose the concept of plentiful junk DNA may have taken comfort from the transcription data but their minds weren't changed either. The truth is that there was, and is, a genuine scientific controversy and it has not been settled in spite of what the Intelligent Design Creationists tell you.
Pseudogenes constitute one type of so-called “junk DNA.” These are segments of DNA that resemble segments that elsewhere (or in other organisms) code for protein. Yet RNAs transcribed from some pseudogenes have been found to function in regulating how much protein is produced by the DNA segments they resemble.
Even if you added up all of the known examples of this phenomenon from every investigated species and stuffed them into a single genome it wouldn't amount to more than 0.01% of the genome. And there's no reason to think that the phenomenon is anything more than an interesting exception.
Repetitive DNA, in which a non-protein-coding sequence is repeated many times, is another type of so-called “junk DNA.” Yet repetitive DNA is now known to regulate many essential functions, including embryo implantation in mammals.
Also misleading. A few examples from diverse species do not make a difference. Indeed these exceptions tend to "prove the rule" rather than overthrow it. Wells is deliberately misleading his audience but he's in good company since there are many scientists who do the same thing. In order to have a serious impact on the junk DNA debate it's not sufficient to show that a few bits of repetitive DNA have gained a function in some species. You have to show that this generalizes to the 50% of the genome that's made up of repeated DNA of various sorts.
There is also growing evidence that non-protein-coding DNA can perform functions that are independent of its sequence. One example is the region of a chromosome (called a “centromere”) that attaches it to other structures in the cell. Another example is the retina in the eyes of nocturnal mammals, in which non-protein-coding DNA acts like a liquid crystal to focus scarce rays of light.
There are many known functions of noncoding DNA. They've been known for decades. As a general rule, the proponents of junk DNA seem to be better informed about these regions of the genome than their opponents. It hasn't made a difference in the past and it doesn't now. (Centromeres account for about 2% of the genome. They fall into the 10% that's known not to be junk.)

Denyse's last question is about me. "Can you interpret this for me, from Larry Moran (University of Toronto evolutionary biologist): “I don’t demand civility, but I do demand accuracy. When Denyse and her friends say that Darwinists promoted junk DNA I have to draw the line.” But he must be referring to my observation that originated in Francis Collins’s (US government’s chief 2000 genome mapper’s [!]) statements in a well-received and widely read book. Are there two types of truths at work here? Evidence, and … what? "
When I use the term “Darwinist,” I mean someone who accepts and defends the theory I describe in my answer to Question 2. Crick and Orgel were Darwinists in this sense; so are Miller, Dawkins, Coyne, and Avise—all of whom have promoted the myth of junk DNA. When Collins published The Language of God in 2006, he not only promoted junk DNA but also wrote that “Darwin’s theory of evolution, that is, descent from a common ancestor with natural selection operating on randomly occurring variations” is “unquestionably correct” (pp. 127, 141). Sure sounds like a Darwinist to me.

Collins also wrote that intelligent design is a “God of the gaps” position that is doomed to collapse with further advances in science (p. 193). But Collins has it exactly backwards: He and other promoters of the myth of junk DNA have put their faith in a “Darwin of the gaps” argument that must now retreat in the face of new advances in genome research.
Several of these scientists have written about pseudogenes and the fact that their existence provides strong support for evolution and strong evidence against the existence of an intelligent designer. Most (all?) biologists understand that pseudogenes are an example of junk DNA. Wells has chosen the one example of junk DNA where there's an overwhelming consensus. They are junk.

But that's not what the scientific debate is about. Pseudogenes are not a myth. They are a fact, and they make up as much as 2% of the mammalian genome. The scientific debate is about whether most of our genome is really junk DNA. I think Francis Collins supports this idea, with some reservations, but I don't know about Jerry Coyne or Kenneth Miller or Richard Dawkins. John Avise is, of course, one the main proponents of junk DNA being a majority of our genome. His book Inside the Human Genome: A Case for Non-intelligent Design was published just last year (2010). It's for those needing an antidote after reading the upcoming train wreck by Jonathan Wells.

It is extremely misleading to claim that "Darwinists" promoted the idea that most of our genome is junk. Most biologists are skeptical of that claim and that's especially true of those who would be comfortable calling themselves "Darwinists."

Denyse closes with one of her characteristic comments.
Okay, everyone, back to work tomorrow in Darwinworld, where facts like these do not matter in the least.
That's why I call them "IDiots." Facts matter to real scientists. The tough part about being a scientist is deciding what's a fact and what's not. Well showed us that he was not up to the task of behaving like a real scientist when he wrote Icons of Evolution and I suspect he's about to provide us with another example of misinformation and selective reading of the scientific literature.

1. Dawkins recognizes that there is some junk in our genome—pseudogenes are a good example—but that does not mean he buys into the idea that a huge percentage of our genome is just junk.

Sunday, March 27, 2011

Stephen Harper on Coalitions

September 9, 2004

Her Excellency the Right Honourable Adrienne Clarkson,
C.C., C.M.M., C.O.M., C.D.
Governor General
Rideau Hall
1 Sussex Drive
Ottawa, Ontario K1A 0A1


As leaders of the opposition parties, we are well aware that, given the Liberal minority government, you could be asked by the Prime Minister to dissolve the 38th Parliament at any time should the House of Commons fail to support some part of the government’s program.

We respectfully point out that the opposition parties, who together constitute a majority in the House, have been in close consultation. We believe that, should a request for dissolution arise this should give you cause, as constitutional practice has determined, to consult the opposition leaders and consider all of your options before exercising your constitutional authority.

Your attention to this matter is appreciated.


Hon. Stephen Harper, P.C., M.P.
Leader of the Opposition
Leader of the Conservative Party of Canada

Gilles Duceppe, M.P.
Leader of the Bloc Quebecois

Jack Layton, M.P.
Leader of the New Democratic Party

[Hat Tip: Ryan Gregory]

Intelligent Design Creationism Isn't about God

David Klinghoffer, posting on the Discovery website, says that his worldview might be attractive to atheists [What Intelligent Design Offers to Agnostics].
Intelligent design has as much to offer to the unbeliever or the unorthodox searcher as to the confirmed traditional believer. It might even have more. Does that surprise you?

Could it be a trend, with critics of intelligent design and others outside the familiar world of ID's friends and advocates at last realizing that ID isn't merely NOT the same thing as creationism? More than that, a couple have noted lately, intelligent design isn't necessarily even theistic.
Wow! That's what I call real NEWS for evolution. The idea that intelligent design might actually have nothing to do with a creator is truly astonishing.

Let's see how this plays out later on in his posting ...
Every real solution to this problem of despair assumes a reality beyond our mundane, one-dimensional and material one. How could it not? We are in despair, or fear falling into it -- whether we're religious or otherwise -- over the limitations of our own lives.

The ultimate limit is imposed by death, which we fear as no generation in memory seems to have done despite the overwhelming safety of our existence. In the meantime, while we are still alive, the lack of a sense of ultimate purpose and meaning that goes with the culture of materialism feeds the anxiety that underlies so much of that culture.

Materialism corrodes the confidence we might otherwise have that any search for meaning that we undertake is not necessarily in vain. Intelligent design offers the hope, by the refutation of materialist science, that "something is out there," whatever it might be, capable of granting genuine purpose to our existence. An agnostic like James Kirk Wall or a -- I don't know what exactly -- like Jack Scanlan should easily appreciate this.
This is why philosophy is so confusing. Let's see if I've grasped the logic here. Intelligent design is anti-materialistic but not religious. It implies the existence of "something" that is out there that gives David Klinghoffer some sort of purpose in life and makes him feel less afraid of death. That "something" can't be God because intelligent design isn't necessarily theistic.

You can't make this stuff up. All you have to do is read what the IDiots, themselves, write on the leading Intelligent Design Creationist blogs.

Saturday, March 26, 2011

Creationism Attacked in the Canadian Parliament

Yesterday the Canadian government under Stephen Harper was defeated for contempt of parliament [Canadian Government Falls]. This is the first time that this has happened in the history of the British Commonwealth.

During the debate preceding the vote, the Leader of the Bloc Québécois party, Gilles Duceppe, had this to say about the government leaders, [Hansard]
This government is very transparent. When we look at the Conservatives, we know exactly what they are thinking. We can see right through them. Quite apart from the image they like to project, if you look closely, you can see right through them. The Minister of State for Science and Technology is a creationist and believes that dinosaurs walked the earth with humans. He thinks that The Flintstones was a documentary and Dino was the star. We can see their old Reform roots, which are likely what inspired the Tea Party.
This actually resonates within the House of Commons and with Canadians. Creationists don't get much respect in Canada.

I'd definitely vote for this guy if he wasn't a separatist.

Friday, March 25, 2011

Canadian Government Falls

This is how a parliamentary system of government works.

The following motion just passed in the Canadian House of Commons by a vote of 156-145.
Mr. Ignatieff (Etobicoke—Lakeshore) — That the House agree with the finding of the Standing Committee on Procedure and House Affairs that the government is in contempt of Parliament, which is unprecedented in Canadian parliamentary history, and consequently, the House has lost confidence in the government.
This was immediately followed by a motion from the Prime Minister to adjourn the House. That motion carried.

Michael Ignatieff, who moved lack of confidence, is the Leader of Her Majesty's Loyal Opposition (Leader of the Opposition) and the leader of the Liberal Party.

The defeat of the government on this confidence motion means that the Prime Minister (Stephen Harper) must resign. He will probably go to the Governor General (the de facto Head of State1) and seek permission to dissolve the House of Commons and call for a general election. In the absence of any party or coalition that could command the confidence of Parliament, that request will be granted.

1. Officially, the Governor General is the Canadian representative of the Queen of Canada who lives in the United Kingdom. The Governor General will not be phoning the Queen to ask her advice. The current Governor General is His Excellency the Right Honourable David Johnston.

Thursday, March 24, 2011

How Big Is the Human Genome?

The earliest direct estimates of the size of human genome clustered around 3,000 Mb (megabase pairs) or 3.0 ×109 bp (base pairs). The textbooks settled on about 3,200 Mb based mostly on reassociation kinetics. According to those results from the 1970s, roughly 10% of the genome consists of highly repetitive DNA, 25-30% is moderately repetitive and the rest is unique sequence DNA.

A study by Morton (1991) looked at all of the estimates of genome size that had been published to date and concluded that the average size of the haploid genome in females is 3,227 Mb. This includes a complete set of autosomes and one X chromosome. The sum of autosomes plus a Y chromosome comes to 3,122 Mb. The average is about 3,200 which corresonds to 3.5 pg (picograms) and that's the value on Ryan Gregory's Animal Genome Size Database.

In the past decade or so the common assumption about the size of the human genome has dropped to about 3,000 Mb. This is because the draft sequence of the human genome came in at 2,800 Mb and the so-called "finished" sequence was still considerably less than 3,200 Mb. Most people didn't realize that there were significant gaps in the draft sequence and in the "finished" sequence.

The latest information on the human genome from the human genome consortium is 3,156,105,057 bp (3,156 Mb) (Build 37 version 2, patch 2=GRCh37.p3 (November 2010)). I believe this build still has gaps around the centromeres of the chromosomes. That region consists of highly repetitive sequences that are almost impossible to clone and sequence. These regions, also known as heterochromatin, were not targets of the original sequencing project. Their total size was estimated at 198 Mb (International Human Genome Sequencing Consortium, 2004) corresponding to about 6% of the genome.

The estimate may have been too large to begin with and, in addition, I'm pretty sure that some of these heterochromatic regions are included in the total size of Build 37 v2. That means that the total size of the human genome is very likely to be ~3,200 Mb or 3.2 ×109 bp.

[Image Credit: Wikipedia: Creative Commons Attribution 2.0 Generic license]

Morton, N.E. (1991) Parameters of the Human Genome. Proc. Natl. Acad. Sci. (USA) 88:7474-7476 [free article on PubMed Central]

International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931-945 [doi:10.1038/nature03001]

Saturday, March 19, 2011

Punctuated Equilibria

This is an old video from 1991 but it does an excellent job of explaining punctuated equilibria. That's because it features Niles Eldridge and Stephen Jay Gould.

There are two important lessons for creationists in this video. Let's hope they learn them.

1. The evidence for punctuated equilibria is based on thousands and thousands of fossils covering millions of years. It required a complete fossil record. It has nothing whatsoever to do with gaps in the fossil record. It's the exact opposite of gaps!

2. Evolution is observed when a single species splits into two species and that takes place over a relatively short period of time. "Relatively short period of time" does not mean that the new species poofs into existence. It means 50,000-100,000 years.

Whenever your creationist friends start lying to you about punctuated equilibria you can ask them to watch this video. You'd think that would stop them from spreading misinformation but then you realize that this video is 20 years old.

Facts don't seem to matter to creationists.1

1. In the interests of fairness, I should note that there are a great many evolutionists who also don't understand punctuated equilibria. I'm really posting this video for them and not for the creationists.

[Hat Tip: Greg Laden]

Thursday, March 17, 2011

Happy St. Patrick's Day!

One of the cool things about studying your genealogy is that you can find connections to almost everyone. This means you can celebrate dozens of special days. In my case it was easy to find ancestors from England, Scotland, Netherlands, Germany, France, Spain, Poland, Lithuania, Belgium, Ukraine, Russia, United States, and, of course, Ireland.

We will be celebrating St. Patrick's Day tomorrow at the pub. It's rather hectic keeping up with all the national holidays but somebody has to keep the traditions alive!

Here's my Irish connection.1 The shortest connection is to the parents of my grandmother. My great-grandfather was Thomas (Keys) Foster, born in County Tyrone on September 5, 1852. He immigrated to Canada in 1876. Thomas married Eliza Ann Job, born in Fintona, County Tyrone on August 18, 1852. She immigrated to Canada in 1877.

Thomas and Eliza settled in Saskatchewan in 1883 and that's where my grandmother was born. Other ancestors in this line came from the adjacent counties of Donegal (surname Foster) and Fermanagh (surnames Keys, Emerson, Moore) and possibly Londonderry (surname Job).

Happy St. Patrick's Day 2010
Happy St. Patrick's Day (2009)
Happy St. Patrick's Day (2008)
Happy St. Patrick's Day (2007)
Niall Nóigiallach - Niall of the Nine Hostages

1. You don't have to be Irish or have Irish ancestors to celebrate St. Patrick's Day.

Monday, March 14, 2011

Five Things that Cannot Be Justified by Science

Bill Dembski thinks that in this video William Lane Craig makes a very good case against science. This is from 1998. (The other two people are atheist Peter Atkins and William F. Buckley.) Posted on Uncommon Descent: Oldie but goodie: William Lane Craig vs. Peter Atkins. Craig list five things science cannot account for. Do you believe him?

I'd probably have the same look on my face as Peter Atkins. It's not that these five things are devastating arguments against the power of science, it's that each one would take at least an hour to explain. The audience isn't going to wait that long so you know you're going to have to pass and leave Craig (and Dembski) to smugly assume that he's won.

It's typical anti-science trickery and Atkins probably wasn't expecting such a cheap shot in that environment.

Who is Omar Alghabra?

This is the Liberal candidate for Federal Parliament in my riding. I've gotten to know him over the past few years and I can affirm that he really does support education and world peace. I'm not so sure about the blind puppies ...

Saturday, March 12, 2011

The Lost Art of Wit and Sarcasm

PZ Myers on Salon reviews a book that I'm never going to read [David Brooks' dream world for the trust-fund set]. Unfortunately he uses language and style that's probably far above the heads of those who need convincing. But it's loads of fun.
I made it almost a third of the way through the arid wasteland of David Brooks' didactic novel, "The Social Animal: The Hidden Sources of Love, Character, and Achievement," before I succumbed. I had begun reading it determined to be dispassionate and analytic and fair, but I couldn't bear it for long: I learned to loathe Harold and Erica, the two upscale avatars of upper-middle-class values that Brooks marches through life in the story. And then I began to resent the omniscient narrator who narrates this exercise in unthinking consumption and privilege that is, supposedly, the ideal of happiness; it's like watching a creepy middle-aged man fuss over his Barbie and Ken dolls, posing them in their expensive accessories and cars and houses and occasionally wiggling them in simulated carnal relations (have no worries, though: Like Barbie and Ken, no genitals appear anywhere in the book), while periodically pausing to tell his audience how cool it all is, and what is going on inside his dolls' soft plastic heads.

I did manage to work my way through the whole book, however, by an expediency that I recommend to anyone else who must suffer through it. I simply chanted to myself, "Die, yuppie scum, die," when I reached the end of each page, and it made the time fly by marvelously well. In addition, there is a blissful moment of catharsis when you reach the last page and one of the characters does die, although it isn't in a tragic explosion involving a tennis racket, an overdose of organic fair-trade coffee, and an assassination squad of rogue economists at Davos, as I was hoping. That's not a spoiler, by the way; the book is supposed to be all about the happy, productive life histories of Harold and Erica, from birth to death, so it's no surprise that at least one dies. It is incomplete, in that the other one survives ... an unsatisfying ending that I could happily resolve with one more bloody page, and that represents the only case I can imagine in which I'd ever ask David Brooks to write another word.

Friday, March 11, 2011

One School System and Abortion

Ontario has two schools systems—both publicly funded. The "public schools" are open to all comers but the "Roman Catholic" ("Separate") school system isn't.

I support the One School System Network.
The organizations represented by the One School System Network [OSSN] are united in the conviction that:

Ontario's publicly funded school system bring students of all backgrounds together in an environment that fosters mutual respect and understanding while respecting their fundamental equality and helping them to realize their full potential as citizens.

To realize that vision, OSSN seeks the establishment of a single secular school system for each official language, namely English and French public school boards.

Furthermore, OSSN seeks the elimination of costly duplication in the Ontario school system in order to minimize infrastructure costs and to maximize opportunities for student development.

Publicly funded schools in Ontario shall not discriminate on the basis of religion in any form including: school environment, enrolment of students, opportunities for all students, evaluation of students, employment and advancement of teachers and all other school board personnel, adherence to Ministry of Education curriculum guidelines including courses in World and Comparative Religions.

Publicly funded school boards may, where appropriate, permit voluntary religious programs for students provided by local faith groups outside regular instructional hours.
Here's one of the reasons why we need to merge the Roman Catholic schools into a single, secular, public school system: Students sent home.

Alexandria Szeglet added a strip of green tape to her St. Patrick High School uniform Thursday with the word “choice” written on it and was sent home for the day after refusing to take it off.

The Grade 10 student wore the green tape in response to a pro-life event at the school, where some students wore a red piece of tape with “life” written on it and didn’t talk for the day to display their belief in the injustice of abortion.
Alexandria and about 35 other students were send home for wearing the green tape. None of the students who wore red tape with the word "life" were sent home or asked to remove the tape.

Two of the comments below the article deserve more publicity.
Ann says:
Alexandria is my daughter. Her father and I are raising and guiding her and her sister into formulating independent thought and opinion. Alex went to school today wearing a green piece of tape in response to a pro-life scheduled event that she knew was already happening. It was JUST a piece of tape. Very quickly, she was informed that she wasn't allowed to imply her opinion ~ but others wearing "red" were. "Pro-choicers", like Alex, believe in simply that. If a woman chooses abortion, then Alex would support that. If a woman chooses to have the child, Alex would support that too. I know for a fact that she did this not expecting the out pouring of support she has been receiving, but to just put her opinion out there like all the rest. This IS a very touchy subject with a lot of people, and knowing that the School Board allows this in their halls ... I'm speechless. We're very proud of you, Alex.

Kerri says:
Alexandria is my niece and we are very proud of her ability to speak her own mind. This demonstration was done peacefully and without malice unlike some of the pro life demonstrations that have happened in the past. I am born and raised a Catholic woman, am well educated. Having attended a Catholic school myself, I am appaled at the ridiculousness of this situation and the stand that the school and school board have taken on this subject when Alex simply held true to her beliefs. Isn't that what we teach our children? To have independence, a mind of their own and to be secure in all the decisions they make?
Ask yourself this question: Would you want to be the person to explain who your childs dad was if you were a victim of rape or incest? OR What if your life was in mortal danger? PRO CHOICE means just that...a woman's choice. It's not a form of birth control nor is it a decision any woman would want to make. I know in my heart and in my wonderful niece's heart that she is intelligent enough to know what is right or wrong for her own self. We are proud of her if every sense and we will continue to support her throughout her life. It's a shame that the world is still stuck in the dark ages and that a woman still does not have the right to choose...This is a touchy subject that someone thought was ok for high schoolers to demonstrate...with the advent of Facebook and social media, what did they think would happen when people caught wind of today's events?
John de Faveri is the director of education for the Thunder Bay Catholic District School Board.
“On the issue, pro-life is part of the Catholic stand,” said de Faveri during a phone interview with Dougall Media Thursday afternoon. “The pro-choice students were not appropriate in the context of a Catholic school.”
That's exactly why we need to convert all these schools into secular schools.

It will be interesting to see what happens in Catholic high schools over the next few days. I expect that many Principals and Vice-Principals are in for a hard time.

[Hat Tip: Canadian Atheist: The easiest way to get kicked out of Catholic school…]

Thursday, March 10, 2011

Intelligent Design Creationism is not religious

Sometimes it's a good idea to let the other side have a say. It can be very revealing. This is from The Epistemological Deficiencies of Barbara Forrest. It's written by DonaldM.
Denyse O’Leary writes about Barbara Forrest’s fact-free attack on Frank Beckwith, which recently appeared in Synthese. While Denyse focused more on Beckwith’s response to Forrest’s scholarly article diatribe, it might be worth taking a closer look not only at Forrest’s article, but the entire issue of Synthese in which it is found. First Forrest. In the abstract for her article with the breathtaking title “The non-epistemology of intelligent design: its implications for public policy”, Bar writes:
Intelligent design creationism (ID) is a religious belief requiring a supernatural creator’s interventions in the natural order. ID thus brings with it, as does supernatural theism by its nature, intractable epistemological difficulties.
Okay, so we’re only 2 sentences into the abstract and we can already see that Bar has no clue what ID is about. I don’t know what ID books or articles she’s actually read, but claiming that ID is a “religious belief requiring a supernatural creator’s intervention” demonstrates how little she understands ID. Perhaps Bar could enlighten us as to what religion ID adheres. Since ID advocates come from a broad range of faith traditions as well as no faith tradition at all, it would seem a bit problematic for her to identify exactly which religion we’re talking about here. Further, I know of no ID advocate that makes the claim that ID “requires” a “supernatural” creator. While ID may be compatible with certain theistic beliefs, it by no means requires it. If Forrest has done even a cursory review of any ID literature she’d know that. (Actually, I suspect she does know that, but because she has a clear agenda, she fudges on the truth.)

Whenever I see the phrase “Intelligent Design creationism”, red flags go up all over the place. This traces back to Intelligent Design Creationism and Its Critics, a ponderous tome from 2001 edited by Robert Pennock, and in which Forrest herself had a chapter. The clever illusion of the title is to give the appearance of an unbreakable link between Intelligent Design and Creationism, no doubt because the term “creationism” carries with it the allusions to young earth creationism and all that goes with that. To Pennock and Forrest, Intelligent Design is just a modifier for Creationism. But any informed reader already knows something is amiss when we see that phrase.
So now you know. The intelligent designer doesn't have to be God. It could be the Wizard of Oz or aliens from Betelgeuse.

And intelligent design does not require a creator so it isn't a form of creationism. The universe could have sprung into existence spontaneously and the intelligent designer only started meddling when life got interesting. And his meddling didn't involve any "creation," just a little tweaking here and there.

In case anyone's really interested in Barbara Forrest's expertise you can read the transcript of her testimony in Kitzmiller v. Dover Area School District [Trial transcript: Day 6 (October 5), AM Session, Part 2]. You'll find an interesting explanation of why she knows that Intelligent Design Creationism is about God and why it's a form of creationism.

The fun part of her testimony is when she shows that the word "creation" was replaced by "design" in the drafts of Of Pandas and People. This was in the 1980s. Maybe that's before DonaldM was born?

The surprise is not that the IDiots have dug themselves into a hole. We all know that. The real surprise is that they keep digging and digging.

Penis Spines

Most male mammals have spines on their penis. The spines are small keratinized projections that are connected to sensory receptors. We don't need to get into a discussion of their purpose—other blogs do that. The example shown here is a cat penis from Tom.

Humans don't have penis spines even though most other primates do. Part of the regulatory region of the relevant gene (androgen receptor, AR) has been deleted from our genome at some time after our lineage split from the chimpanzee lineage.

Is the loss of penis spines in humans an adaptation or is it an evolutionary accident? John Hawks discusses this: The real "junk" DNA. Read what he has to say on the matter. If you post comments here I'm sure he will see them.

The relevant paper was just published in Nature, McLean et al. (2011). Here's what the authors say,
Our results show that humans have lost an ancestral penile spine enhancer from the AR locus. Humans also fail to form the penile spines commonly found in other animals, including chimpanzees, macaques and mice (Fig. 2l). Simplified penile morphology tends to be associated with monogamous reproductive strategies in primates. Ablation of spines decreases tactile sensitivity and increases the duration of intromission, indicating their loss in the human lineage may be associated with the longer duration of copulation in our species relative to chimpanzees. This fits with an adaptive suite, including feminization of the male canine dentition, moderate-sized testes with low sperm motility, and concealed ovulation with permanently enlarged mammary glands, that suggests our ancestors evolved numerous morphological characteristics associated with pair-bonding and increased paternal care.

WARNING: I may be a little more selective about allowing comments in this thread. I know it violates Sandwalk policy but for this one time I'm not going to allow adolescent male humor to distract from the science. There's plenty of other opportunities for us to indulge our sense of humor in other postings.

McLean, C.Y., et al. (2011) Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471:216–219. [doi:10.1038/nature09774]

The Problem with Evolutionary Psychology

Jesse Bering is an evolutionary psychologist at Queen's University, Belfast, Northern Ireland (UK). He blogs at Bering in Mind on the Scientific American website. Read his latest post: Natural homophobes? Evolutionary psychology and antigay attitudes.

In that post, Bering takes seriously the idea that homophobia could be a character that evolved in our ancestors. The idea is that parents who were homophobic were more likely to be concerned about the sexual orientation of their children. If this led to more heterosexual children then the parents would have more grandchildren and the allele for homophobia would increase in the population.

To my mind this idea is so ridiculous it doesn't even merit discussion and it certainly should never be published in a "scientific" journal. Why is it that respected evolutionary psychologists think these just-so stories are an important part of their discipline? Does this mean that the entire discipline is suspect?1

Jesse Bering is the author of The God Instinct. I haven't read this book but I'm going to order a copy. Here's what he says on his website.
Why does even the most committed atheist turn to God when a family member falls seriously ill, or they find themselves in close personal danger? Using the latest scientific evidence, Jesse Bering explores how people's everyday thoughts, behaviours and emotions betray an innate tendency to reason as though God were deeply invested in their public lives and secret affairs.

In this entertaining and thought-provoking book, he argues that this religious reflex is not an irrational aberration, and that God is not a cultural invention or an existential band-aid, but an intrinsic human trait, developed over millennia, that carries powerful evolutionary benefits.

Breaking new ground, The God Instinct uses hard science to show that God is not a delusion, but a sophisticated cognitive illusion. Bering reveals the roots of religion in our ability to think beyond our immediate surroundings, and explains why this capacity for belief sets us apart from other animals.
Jesse Bering sounds like a complicated person with interesting perspectives on evolution and religion. Here's what he says about himself on the website.
Jesse Bering is Director of the Institute of Cognition and Culture at the Queen's University, Belfast. An evolutionary psychologist, he is one of the principal investigators on the Explaining Religion Project.

The Institute's research focuses primarily on human social behaviour, and current topics range from people's belief in the afterlife to moral disgust over social offences. Funded by the EU, the John F Templeton Foundation and the US Air Force, it has projects running all over the world, including India, Mali and Cyprus.

Jesse writes a weekly column for Scientific American, ‘Bering in Mind’. The members of The International Academy of Digital Arts and Sciences named the column an official 2010 Webby Honoree in the “blog­cultural” category.

As well as being an acknowledged expert in his field, Jesse Bering is well known for his approachable and engaging popular writing. Born in the USA, he now lives in Northern Ireland.

1. Perceptive readers will see a connection between evolutionary psychology and adaptationism.

[Hat Tip: Joe at Canadian Atheist]

Wednesday, March 09, 2011

Why Has this Bee Landed on this Flower?

This is a photo from Botany Photo of the Day. The flower is Crepis barbigera.

Why is the bee visiting this flower? What is the evolutionary advantage of attracting bees? You may think you know the answer but you will be surprised by the comment at the bottom of the posting on the Botany Photo of the Day website. Nothing in biology is simple.

Bacteria Fossils in Meteorites

When I first heard about the discovery of fossil bacteria in meteorites I immediately read the paper in the Journal of Cosmology [Fossils of Cyanobacteria in CI1 Carbonaceous Meteorites: Implications to Life on Comets, Europa, and Enceladus]. The first thing I noticed was that this "journal" seemed to be of very low quality. A little bit of digging revealed that it was some sort of online journal that publishes just about everything.

The second thing I noticed was that the evidence of fossils in these meteorites was not convincing. It seemed like the author, Richard B. Hoover, was not being very skeptical about what he was seeing. I dismissed the paper, it was almost certainly not true.

Lot's of other people reached the same conclusion.

Ian Musgrove at The Panda's Thumb [Life from Beyond Earth on a Meteorite, or Pareidolia?] [Commentaries posted at Journal of Cosmology]

Phil Plait at Bad Astronomy [Followup thoughts on the meteorite fossils claim]

PZ Myers at Pharyngula [Did scientists discover bacteria in meteorites?]

Rosie Redfield at RRResearch [Is this claim of bacteria in a meteorite any better than the 1996 one?]

The Journal of Cosmology has now published 21 commentaries on the paper and only two of them are the least bit critical or skeptical of the results. That inspired the journal to insert this statement in the introduction to the article.
Official Statement The Journal of Cosmology,
Have the Terrorists Won?

Only a few crackpots and charlatans have denounced the Hoover study. NASA's chief scientist was charged with unprofessional conduct for lying publicly about the Journal of Cosmology and the Hoover paper. The same crackpots, self-promoters, liars, and failures, are quoted repeatedly in the media. However, where is the evidence the Hoover study is not accurate?

Few legitimate scientists have come forward to contest Hoover's findings. Why is that? Because the evidence is solid.

But why have so few scientists come forward to attest to the validity? The answer is: They are afraid. They are terrified. And for good reason.

The status quo and their "hand puppets" will stop at nothing to crush debate about important scientific issues, and this includes slander, defamation, trade libel... they will ruin you. Three hundred years ago, they would burn you for questioning orthodoxy. Has anything changed?

The scientific community must march according to the tune whistled by those who control the funding. If you don't do as you are told, if you dare to ask the wrong questions, they will destroy you.

JOC offered the scientific community a unique opportunity to debate an important paper, but for the most part they have declined.

The message is: Be afraid. Be very afraid. Or you will be destroyed.

Why is America in decline?

Maybe the terrorists have won.
Did you need convincing that this is not real science?

Now here's the tough question. Why did so many people immediately see that this paper was flawed while many others, including some journalists, were taken in? I think it's because many of us recognized this as an extraordinary claim that required extraordinary evidence. We also realized that if this was even close to being true it would be published as a front page story in Science or Nature. In addition, we have lived through many examples of exaggerated claims, including previous claims of meteorite fossils that proved to be untrue; not to mention the 3.5 billion year old fossils that weren't fossils [Did Life Arise 3.5 Billion Years Ago?].

It's a combination of skepticism and experience. Can that be taught?

Zombie Theories

According to Greg Laden there are certain "theories of everything" that "will generally evolve into a zombie that won’t die and can’t be killed, potentially eating the brains of science geeks and graduate students for decades." The classic example is Aquatic Ape Theory but theories of bipedalism in humans are a close second. [The Aquatic Ape Theory as a Zombie Theory]

Monday, March 07, 2011

When Did People First Start Knowing the One True God?

It's so easy to make fun of creationists and almost as easy to mock the so-called "theistic evolutionists" who have developed "sophisticated" ways of rationalizing Christianity and evolution. The accommodationists among us don't like to alienate the theistic evolutionists because their views are not in conflict with science—or so they say.

Let's take a look at the science behind theistic evolution. Here's an article from BioLogos that looks very interesting. It's written by Denis Alexander, Director of the Faraday Institute for Science and Religion at St. Edmund’s College, Cambridge and it's billed as A Response to Coyne, MacDonald, Ruse, and Wilkinson, Pt 2. Jerry Coyne brought it to my attention1 [It feels so good when it stops].

Remember that Denis Alexander is at Cambridge University (UK) so he's presumably one of the top intellectuals in his field. He says,
First, it should, I hope, be clear by now that I don’t think there is any problem with using the language of “data” and “models” in this context, providing that we don’t start thinking that we’re using the terms as they’re generally used in everyday science. Since such terms are used, as we have seen, in a wide range of disciplines, there seems no particular reason not to use them here. If pressed, then I would say that their use in our present context is somewhat akin to the various models posited to provide evolutionary explanations for the origin of music.1 In other words, it is quite possible to generate plausible models for things which are consistent with various kinds of data and argument, including in this case a good deal of aesthetic insight, yet without any realistic hope of deciding between different models in the foreseeable future. If someone would prefer to label the Retelling Model and the Homo divinus Model, ‘informed speculations’, then I have no problem with that at all, except to say that in the end even speculation A may be more plausible than speculation B, so it comes to the same thing in the end. Carrying out thought experiments is the way that human knowledge expands.

Speaking of knowledge takes me to a second point, this one for the positivists. In many ways this particular discussion is one internal to the Christian community, a point that will become even more apparent below. Clearly models that discuss the possible ways in which humans first came to know God are not going to gain much traction in the minds of those who do not believe that God exists. So I wouldn’t blame atheists at all for thinking that even discussing such models is a bit of a waste of time. If I was trying to present arguments to atheists for belief in God, then this is certainly not where I would start! But my intention here is not to present arguments for belief in God, but instead to present some reflections for the world-wide community of around two billion Christians, who do as a matter of fact believe in God and, in their various ways, do believe that God can be known, and who, one presumes, do believe that theological knowledge counts as real knowledge.


Instead I start with a somewhat different set of questions when thinking about models such as the Retelling and Homo divinus models. Taking the corpus of Biblical literature as a whole, here we have a ‘grand narrative’ of creation, alienation from God due to human sin and disobedience, redemption through Christ, and a new heavens and a new earth. We have the possibility of fellowship with God through freely willed choice. Our nearest cousins, chimps and bonobos, to the best of our knowledge, do not. So the curious Christian is likely to ask at least some time during their lives, “Well, when did that possibility first begin? When did people first start knowing the one true God in such a way that they could pray, walk with God, and be responsible to God? When could they first be judged by God because they had sinned?” It is those kinds of questions that the Retelling and Homo divinus type of models are interested in addressing. Did all this happen rather slowly, as in the first model, or rather fast, as in the second? Notice that the questions raised are not to do with the origins of religion (however defined), which is another kind of discussion altogether, but with the origins of spiritual life, knowledge of God, the time when humans first became answerable to God for their actions. Notice also that the questions would still be there even if we had in our hands only the New Testament. It is not Genesis that poses the questions, though Genesis is clearly relevant, but rather the Christian theology of creation, sin and redemption. The themes of creation, sin and redemption keep replaying like a musical répétitif through the biblical symphony. The early chapters of Genesis is where the répétitif is first introduced, and so attracts our attention, but let us not forget the répétitif in the rest of the biblical texts.
Here's one of many possible charts showing our fossil ancestors.

So, what do you think, dear readers? When did our species first start knowing the "one true God"? Jerry Coyne is putting his money on Homo erectus but I'm thinking the correct answer is "not yet." It troubles me a bit that the majority of members of our species have never, ever, in their entire history believed in the Judeo-Christian God. That nasty little fact doesn't seem to trouble Denis Alexander. I guess that's because we rely on different ways of knowing. My way is scientific. David Alexander relies on "theological knowledge."

[Photo Credit: This is a photo of one of our ancestors from One Million Years B.C. I don't know if she knew about the one true God.

1. I don't usually read the articles posted on The BioLogos Forum.

Sunday, March 06, 2011

The Blue-footed Booby

The question of the week in New Scientist (Feb. 12-18, 2011) is, "The blue-footed booby is an extraordinary-looking bird. It has fairly dull plumage but strikingly coloured blue legs and feet. What could be the evolutionary benefit of such a conspicuous feature? Both sexes have blue feet so they don't seem to be for impressing potential mates."

This is bound to bring out the adaptationists. You can be almost certain that the answers will consist of various just-so stories based on the assumption that blue feet have to be an adaptation. Can you make up a good adaptationist story to explain the blue feet? It doesn't have to have any supporting evidence. Try and avoid explanations that rely on sexual selection—that's too easy.

The evolutionary relationship between the various booby species is shown below in a figure take from Friesen and Anderson (1997). The Peruvian and blue-footed boobies apparently diverged from a common ancestor about 200,000 years ago. The Blue-footed booby's range is northern Peru and the Peruvian booby lives in southern Peru. They do not form hybrids where their ranges overlap.

[Photo Credit: Wikipedia]

Friesen, V.L. and Abderson, D.J. (1997) Phylogeny and Evolution of the Sulidae (Aves: Pelecaniformes): A Test of Alternative Modes of Speciation. Molec. Phylo. Evol. 7:252-260 [doi:10.1006/mpev.1996.0397]

Saturday, March 05, 2011

A Creationist Objects

I get lots of email from theists and creationists. They remind me that the controversies over religion and evolution are complicated. Here's a recent letter that illustrates the problem. It's from a creationist who struggles to incorporate his understanding of evolution into a worldview that just can't accommodate it. The results are .... interesting.

I really don't know to respond to this letter.1 Where does one begin when trying to correct such a profound misunderstanding of science?
I love your new definition of evolution as "a change in the frequency of alleles in a population over time." What happened to spontaneous and random mutations? Epigenetics blew that out of the water. I find it amusing every time I hear some evolutionists claim evolution is fact and the evidence is "overwhelming." Evolutionists have given up on fruitless attempts to prove the impossible and have implemented a new strategy of just claiming evolution has been proved by mountains of evidence.

Epigenetics proves adaptation and nothing else. It controls gene expression driven by environmental stress. It, nor any of the other theories of evolution provide for mechanisms to increase information in genomes. Hence evolutionists are confined to wild extrapolation of adaptation to prove macro evolution. Why hasn't it occurred in experiments? 50,000 generations of bacteria and still no macro evolution nor even proof of a simple DNA change much less added information in the genome. Guess why? You can't get there from here. Evolutionists look like idiots trying to make a plausible explanation why provisions for adaptation reside in what they call "Junk DNA" for millions of years before the organism is exposed to environmental changes that calls upon for them to survive.

The next time you consider calling someone an idiot you might consider there are some reading your posts that are not impressed by your insane unfounded conclusions. Allele frequencies are not going to hide the obvious shortcomings of evolution theory. Proving allele frequencies change proves epigenetics and adaptation and nothing else unless you are an idiot.

Don Berry

I have the sense of the common cow who knows how to eat the grass and spit out the cockle burrs.

1. I do not publish email messages without first obtaining permission from the author.

Friday, March 04, 2011

Get a Job: in Victoria

From Faculty Position 2011.

University of Victoria
Biochemistry and Microbiology


The Department of Biochemistry and Microbiology leads in molecular biological research at the University of Victoria with strengths in structural biology, microbial pathogenesis, regulation of gene expression, and epigenetics.

The department is the academic home of the University of Victoria-Genome BC Proteomics Research Centre – an internationally recognized centre for proteomics research focused on structural proteomics, metabolomics, clinical proteomics, and protein imaging. The Centre also provides support for proteomics research in the areas of protein identification, quantitative proteomics, and biomarker discovery and validation.

Applications are invited for a tenure track position for a Biochemist at the rank of assistant or associate professor. The department is interested in applicants who intend to develop a hypothesis-driven research program that builds on a background of proteomics. The research program of the successful applicant is expected to complement the aims of the Proteomics Centre and the research strengths of the department. A strong commitment to teaching in the undergraduate and graduate programs of the department is required.

The deadline for application is 15 March, 2011. Applicants should provide electronic versions of a CV, a statement of research objectives, a statement on teaching objectives, and arrange for electronic letters from no more than 3 referees to be received by the application deadline.

The University of Victoria is an equity employer and encourages applications from women, persons with disabilities, visible minorities, Aboriginal Peoples, people of any sexual orientation and gender, and others who may contribute to the further diversification of the University.

All qualified candidates are encouraged to apply; however, in accordance with Canadian Immigration requirements, Canadians and permanent residents will be given priority.

Robert D. Burke, Chair
Department of Biochemistry and Microbiology
University of Victoria
Canada V8W 3P6

Thursday, March 03, 2011

Astronomy and Biology

This is a remarkable picture. Depending on your personal preferences, you may be attracted to the sky in the background or the beautiful blue color along the shoreline of the lake. Are you an astronomer or a biologist, or both?

Phil took the picture and he explains it at: Gippsland Lakes.

Hat Tip: another Phil at Bad Astronomy