Carl Zimmer's article on junk DNA has appeared in the online edition of the New York Times magazine at: Is Most of Our DNA Garbage?.
Carl was in Toronto and Guelph last December gathering information for his article. You can see that Ryan Gregory is featured and my colleague Alex Palazzo gets quoted.
Here's a picture of us having dinner. That's Alex on the left, second from left is some old dude who everyone ignores, Ryan is next and Carl Zimmer is on the right.
Carl is still the best science journalist on the planet and I appreciate that he has alerted the public to a serious problem in genome studies. The general public has been snowed by the ENCODE publicity campaign and by naive journalists who have enthusiastically reported that junk DNA is dead.
It is not. The most knowledgeable scientists recognize that the issue is not settled. The very best ones (
) know that 90% of our genome is junk.
Several people have asked recently if talk.origins still exists and if the TalkOrigins Archive is still functional. As it turns out, the current king of the talk.origins newsgroup (David Greig) is going to be here (my office) either today or in the next few days to upgrade the talk.origins server. The name of the server is "Darwin" and here's what it looks like (right).
Here's a link to the newsgroup: talk.origins. Here's a description from the Wikipedia article on talk.origins.
The first post to talk.origins was a starter post by Mark Horton, dated 5 September 1986.
In the early 1990s, a number of FAQs on various topics were being periodically posted to the newsgroup. In 1994, Brett J. Vickers established an anonymous FTP site to host the collected FAQs of the newsgroup. In 1995, Vickers started the TalkOrigins Archive web site as another means of hosting the talk.origins FAQs. It maintains an extensive FAQ on topics in evolutionary biology, geology and astronomy, with the aim of representing the views of mainstream science. It has spawned other websites, notably TalkDesign "a response to the intelligent design movement", Evowiki, and the Panda's Thumb weblog.
The group was originally created as the unmoderated newsgroup net.origins as a 'dumping ground' for all the various flame threads 'polluting' other newsgroups, then renamed to talk.origins as part of the Great Renaming. Subsequently, after discussion on the newsgroup, the group was voted to be moderated in 1997 by the normal USENET RFD/CFV process, in which only spam and excessive crossposting are censored. The moderator for the newsgroup is David Iain Greig (and technically Jim Lippard as alternate/backup).
The group is characterized by a long list of in-crowd jokes like the fictitious University of Ediacara, the equally fictitious Evil Atheist Conspiracy which allegedly hides all the evidence supporting Creationism, a monthly election of the Chez Watt-award for "statements that make you go 'say what', or some such.", pun cascades, a strong predisposition to quoting Monty Python and a habit of calling penguins "the best birds".
Apart from the fun, the group includes rebuttals to creationist claims.There is an expectation that any claim is to be backed up by actual evidence, preferably in the form of a peer-reviewed publication in a reputable journal. The group as a whole votes for a PoTM-award (Post of The Month), which makes it into the annals of TalkOrigins Archive.
I forgot about penguins being the best bird. The article forgot to mention Howler monkeys.
The University of Ediacara consists of many faculty members named Chris plus some others. There's only one permanent student, me.
I won't try to name all the alumni who are still active on the newsgroup or on blogs. I'll let them confess identify themselves in the comments if they dare.
Here's the link to the TalkOrigins Archive. It contains all kinds of information on the evolution/creation debate including all the rebuttals to any argument the creationists have ever made.
Here's your chance to hear about genomes and junk DNA from one of the world's leading experts. The seminar is at the University of Toronto (Toronto, Canada) in the Medical Sciences Building. It's on Wednesday, March 4th—only two days form today! The seminar room (Rm 2172) is right around the corner from Tim Hortons. Ryan is from the University of Guelph. How Canadian can you get, eh?
I received a response from Bruce Kidd, the Principal of the University of Toronto at Scarborough on why his campus was hosting a conference on alternative medicine (see Is the University of Toronto promoting quackery and pseudoscience?). I had asked whether the university was officially involved in sponsoring the event.
Here is his complete response. He knows that I will post it on my blog.
Dear Professor Moran:
Thank you for your inquiry. The University encourages the fullest, critical investigation of scientific and social issues, including the bases of health and well-being and the various ways personal, community and environmental health can be maintained and strengthened. That is an essential part of our institutional mission. As you know, we have been debating whose knowledge counts, the methodological bases for such knowledge and the professional practices that have been developed as a result of such knowledge in the field of health for many years. That's how knowledge advances. The hosting of the Population Health and Policy Conference at UTSC yesterday was just one expression of that commitment to critical inquiry.
That being said, such hosting cannot be equated with endorsement of the various positions and points of view expressed at the conference. I have attended hundreds of conferences at U of T and other universities over the years and have never felt that the presentation of particular views meant that the hosting institution endorsed those particular views.
I hope that's helpful.
With best wishes,
Bruce Kidd, O.C., Ph.D., LL.D.
Vice-President and Principal
University of Toronto Scarborough
Professor, Faculty of Kinesiology and Physical Education
I'm all in favor of critical investigation of scientific issues and critical inquiry. I think it's a good idea for the University of Toronto to sponsored a conference where diverse points of view are presented and debated. That's how we learn to distinguish science from pseudoscience and "whose knowledge counts."
There is no possibility that this conference meets those minimal academic requirements.
Here's the welcome message from the Chair of Anthropology and the Associate Chair of Health Studies [see Population Health and Policy Conference].
Welcome to the second Population Health and Policy Conference at UTSC! This event demonstrates not only the energy and initiative of our student organizers, but also the enthusiasm of the students in the Health Studies programs at UTSC. The faculty in Health Studies are very proud of the commitment of our students.
The Health Studies programs promote an understanding of health across a spectrum of academic perspectives: from the clinical and biological health sciences, to social science and humanistic ways of knowing. What binds together these disciplinary approaches is a consciousness of the need for rigorous biological knowledge to be understood in tandem with the social milieu of human health and embodiment.
The programs are built around the bio-medical paradigm, to which the faculty in the program are unreservedly committed. This model has been spectacularly successful in increasing the life span and wellbeing of the majority of people around the world. At the same time Health Studies students learn how to view this paradigm critically through a variety of lenses, notably with respect to such issues as inequality of access, social factors that influence the prevalence of disease and the likelihood of cure, the impacts of government policy on health, and the perspectives of diverse practitioners and clients within the broad health care system. The theme of this year’s conference is Alternative Medicine and the ideas and practices it offers to complement standard health care and the biomedical model, including its emphasis on nutrition and lifestyle. As students and faculty we hold Alternative Health to the same standards of rigorous inquiry and critical appraisal that we apply to other aspects of our society.
The program covers much ground and promises to be stimulating and exciting. We look forward to seeing you there.
Prof. Michael Lambek, Chair, Department of Anthropology
Prof. John Scherk, Associate Chair, Health Studies
Apparently there are at least two ways of knowing the truth; science and the "humanistic way of knowing." I'm disturbed to see that students and faculty are holding alternative health to "the same standards of rigorous inquiry and critical appraisal that we apply to other aspects of our society." It suggests that we're in a lot more trouble than just alternative medicine.
Sophisticated Christian: My God exists and He is omnipotent, kind, and loving. He chooses to allow evil because X, Y, and Z.
Atheist: If your god exists (he doesn't) and if he is omnipotent, kind, and loving (he isn't) then he MUST create a perfect world where there is no evil. I reject your arguments X, Y, and Z for the following reasons. (Blah, blah, blah.) Because MY version of YOUR imaginary god requires that he create a world where there is no evil, and because there is evil in the world, god doesn't exist.
Discuss.
Sorry, I couldn't resist. Here's what Michael Egnor says on Evolution News & Views (sic): No, Despite Often-Heard Claims, Antibiotic Resistance in Bacteria Is Not Evolution.
This notion, however, is mistaken. Bacterial resistance to antibiotics has nothing to do with evolution. Evolution, in the Darwinian sense of undirected (unintelligent) process of random heritable variation and natural selection, is the process by which populations of living things change over time without intelligent agency causing or guiding the process. When the process of change in populations is guided by intelligence, it is called artificial selection -- breeding.
Of course I'm not the first to point this out. Charles Darwin, in the Origin of Species, made exactly the same argument. In his first chapter, he discussed artificial selection -- animal husbandry and breeding of plants. In subsequent chapters he developed an argument that in nature, changes in population are accomplished by natural selection, without intelligent agency. Darwin distinguished artificial selection from natural selection -- he distinguished breeding from evolution, and of course his theory of evolution is a theory of natural selection, not a theory of animal husbandry or plant breeding, which had been practiced for thousands of years and to which Darwin contributed nothing.
Bacterial resistance to antibiotics is artificial selection. Antibiotics are intelligently designed by medical researchers, deliberately administered to patients by doctors, who understand that there are some bacteria that are not sensitive to the antibiotic and that have the potential to proliferate. Actually, the administration of antibiotics that kill some but not all of the bacteria in the patient is quite deliberate, because there are huge populations of beneficial bacteria (e.g. in the gut) that should not be killed since they are necessary for health.
Shhhh. Don't tell Michael Behe who wrote a whole book based on resistance to antimalarial drugs.
Someone named James Lewis at a blog named American Thinker seems to be upset about journalists who question politicians about evolution. He wrote a little quiz for journalists. There are ten questions. He claims that "Any biology student should ace it." Denyse O'Leary liked the questions [Quiz for media on Darwin’s theory of evolution]. She's a journalist but she didn't give us her answers. I can't imagine why.
I think I can give reasonable answers to most of the questions except #3 and #6. Question #10 is hard and so is question #1. I'm not sure if James Lewis would like my answers. What do you think?
- What is a biological species? How does it differ from a variety? Give examples.
- How has Darwinian theory changed since Darwin? (Be specific.)
- Define the two criteria for "Darwinian fitness."
- What are "Darwin finches?" Where are they found?
- What is the function of HOX genes?
- What is meant by "ultra-conservation" in evolution? Give two examples.
- Give an example of a recent evolutionary change in humans, within the last 10,000 years.
- What is parallel evolution? Give an example.
- What is meant by "genetic drift"?
- Why are there two sexes in most species?
Notice that random genetic drift has recently penetrated the thick sculls of many creationists. That's pretty amazing. I wonder if they can explain it?
There's a conference this Saturday at the University of Toronto on the Scarborough campus. It features presentations by a number of leading homeopaths and naturopaths. You may not be familiar with them so if you want a brief summary of their quackery check out Scott Gavura's post at Science-Based Medicine: Pseudoscience North: What’s happening to the University of Toronto?.
That post documents a number of very troubling things going on at my university.
The conference is organized by an outside a student group who pays to hold the event on the university campus. This is very common and it does not mean the the university endorses the conference. I believe the contract specifies that such an endorsement must not be implied or stated.
The poster contains a prominent sign using the University of Toronto logo and crest. That certainly looks to me like the university is sponsoring and endorsing the event. I am trying to contact Bruce Kidd, Principal of the University of Toronto, Scarborough to clarify the situation.
Rick Nicholls is the Progressive Conservative Member of the Ontario legislature representing the riding of Chatham-Kent-Essex. (Ontario, is a province in Canada. Each province has it's own provincial government. The members of provincial parliaments are called MPP's.)
Watch the video where he says he doesn't believe in evolution and listen to the questions that the reporters ask.
The Globe & Mail reports that Rick Nicholls was quickly reigned in by party leaders [Ontario PCs distance themselves from MPP who denies evolution].
On Wednesday, Mr. Nicholls stood behind his comments.
“[Ms. Sandals] was very flippant in her response to my colleague and I gave a flippant response back to her,” he said, adding that evolution “is one’s personal belief set.”
Within an hour, he followed up with an emailed statement saying he’d been given a talking-to by PC House Leader Steve Clark: “I acknowledge that my comment is not reflective of Ontario PC Party policy,” he said of his anti-evolution remarks.
Here's how the views of Rick Nicholls are covered in the Toronto Star: Tory MPP Rick Nicholls says he doesn’t believe in evolution .
And here's how it is covered in Huffington Post Canada: Rick Nicholls Says He Doesn't Believe In Evolution, PC Colleagues Distance Themselves.
In Canada, it's pretty much political suicide to admit that you don't believe in evolution.
In other news, there's a debate going on in Ontario's House of Commons on introducing a new sex education curriculum into public schools (including the Roman Catholic schools). Another Progressive Conservative MPP, Monte McNaughton, said "it’s not the Premier of Ontario’s job, especially Kathleen Wynne, to tell parents what’s age-appropriate for their children."
Our Premier, Kathleen Wynne, is openly gay. She was a bit puzzled by the comments so she addressed Mr. McNaughton with the following questions.
"What is it that especially disqualifies me for the job that I’m doing? Is it that I’m a woman? Is it that I’m a mother? Is it that I have a master’s of education? Is it that I was a school council chair? Is it that I was the minister of education?" Ms. Wynne thundered. "What is it exactly that the member opposite thinks disqualifies me from doing the job that I’m doing? What is that?"
PC MPPs sat ashen-faced as Liberals heckled them and applauded Ms. Wynne.
Not a good day for the Progressive Conservative Party of Ontario.
Here's a figure from a paper by Marques-Bonet et al. (2009). It shows the differences between various human genomes (blue); between the human and chimp genomes (red); and between the human and macaque genomes (yellow).
The results are plotted a a fraction of sequence identity. (Convert to percent by multiplying by 100.) The window is 100 kbp (100,000 bp). Human chromosome 2 is on top and chromosome 7 is below.
Notice that the substitutions are pretty much randomly scattered over every part of the two chromosomes. The data is consistent with the idea that most of the DNA in those chromosomes is junk and most of the substitutions are nearly neutral mutations fixed by random genetic drift. The differences between each pair of species is consistent with an approximate molecular clock corresponding to a constant mutation rate over million of years. The absolute levels of sequence identity (i.e. 98-99% for chimp/human) is consistent with the time of divergence from a common ancestor based on the fossil record and other criteria.
Here are my questions. Is there any other explanation that accounts for the data? Is it possible to explain the results as adaptations—substitutions that are mostly fixed by natural selection? Is it possible to explain the results according to Intelligent Design Creationism?
I'm particularly interested in hearing from the creationists. What is your explanation?
Marques-Bonet, T., Ryder, O.A., and Eichler, E.E. (2009) Sequencing Primate Genomes: What Have We Learned? Ann. Rev. Genomics Hum. Genet. 10:355-386. [doi: 10.1146/annurev.genom.9.081307.164420]
This post was prompted by a discussion I'm having with Jerry Coyne on whether he should be trying to censor university professors who teach various forms of creationism.
I very much enjoyed Jerry Coyne's stance on free speech in his latest blog website post: The anti-free speech police ride again. Here's what he said,
This post is a response to a question posed by Vincent Torley, "Is Larry Moran a conspiracy theorist?"
A few weeks ago the Toronto Star (Toronto, Ontario, Canada) published a front page article on the dangers of Gardasil, a vaccine against human papillomavirus (HPV) that's recommended for adolescent girls. The article highlighted a number of anecdotal stories about girls who had developed various illnesses and disabilities that they attributed to the vaccine. The reporters thought this was evidence that the vaccine had serious side effects that were being covered up by the pharmaceutical industry.
Almost every scientist who read the story recognized that correlation does not mean causation and that the "evidence" promoted by David Bruser and Jesse McLean was no different than the claims of Jenny McCarthy and her supporters about the MMR vaccine and autism. There were dozens of health professionals and scientists who criticized the article in the Toronto Star culminating in a op-ed article that clearly pointed out all the flaws in the original piece [Science shows HPV vaccine has no dark side]. That article was signed by 63 scientists and physicians.
This morning I was flipping through the pages of the week's issue of Nature to see if there was anything interesting. There was. I'll tell you about it later, maybe.
I kept flipping. I found a paper with an intriguing title "New genetic loci link adipose and insulin biology to body fat distribution" [doi:10.1038/nature14132]. The authors found 68 loci in the human genome that are statistically correlated with excess body fat. That's not very interesting because very few of these association studies pan out in the long run. Most of those 68 loci are probably genetic noise.
The end of the paper was somewhat interesting. There seemed to be a lot of authors and affiliations. Let's count the authors 1,2,3,...401! There are 401 authors on this paper and they work at 300 different institutes and universities. The list of authors and affiliations take up three pages in the print edition of the journal!
The next paper has a similar title, "Genetic studies of body mass index yield new insights for obesity biology" [doi: 10.1038/nature14177]. The authors found 97 loci correlated with body mass index (BMI). These loci accounted for ~2.7% of BMI variation.
Not interesting.
There are a lot of authors on the second paper as well. Let's count them: 1,2,3,.....481! There are 481 authors from 347 institutes and universities. The list of authors and affiliations covers almost four pages (!) in the print edition of the journal. Is this a record?
It gets worse. In both lists of authors there are entries under "T" like "The PAGE Consortium" and others. They are marked with double daggers and the footnotes say "A list of authors and affiliations appears in Supplementary Information."
I checked it out. For the second paper there are about 800 additional scientists listed as members of the various consortia.
Am I the only one who thinks this is ridiculous?
) know that 90% of our genome is junk. 
