Thursday, March 05, 2015

Don't misuse the word "homology"

Here's the latest science news from The Allium": Evolutionist Loses It As Colleague Conflates Homology and Similarity Yet Again.
Evolutionary biologist Dr. Constance Noring shot and killed her microbiology colleague and formerly good friend, Dr. Dan Deline when, for the umpteenth time he used the word homology when he really should have said similarity.
Read the rest. I sympathize with Professor Noring. This could have been me if Canadians were allowed to buy handguns.


C0nc0rdance reads from Dobzhansky defending accommondationism

Here's how COncOrdance explains his latest YouTube video.
To celebrate Darwin Day, Feb 12th, 2015, I offer the words of Dobzhansky, who was a central figure in the modern evolutionary synthesis with his 1937 book, "Genetics and the Origin of Species". Dobzhansky was also a deeply religious man who believed that God had a hand in the process of evolution, a view I don't share, but try to understand.

Dobzhansky cites Teilhard de Chardin, who was a biologist, a theistic evolutionist, and a controversial figure who described evolution as cosmic attainment of perfection, a concept I also strongly disagree with.

This is an excerpt from the original work:
The American Biology Teacher, Vol. 35, No. 3 (Mar., 1973), pp. 125-129. [Nothing in Biology Makes Sense except in the Light of Evolution]
I'm not sure what purpose is served by reading from Dobzhansky's book where he praises Pierre Teilhard de Chardin. Keep in mind that Teilhard's most famous book was reviewed by Peter Medawar who described it like this: "... the greater part of it, I shall show, is nonsense, tricked out with a variety of metaphysical conceits, and its author can be excused of dishonesty only on the grounds that before deceiving others he has taken great pains to deceive himself."

That's pretty much the consensus view of Teilhard these days. It's also pretty common to point out that science as a way of knowing conflicts with religion as a way of knowing in spite of what Dobzhansky said 46 years ago.

Here's the video ....



Is most of our DNA garbage?

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.


Wednesday, March 04, 2015

Does talk.origins still exist?

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.



Monday, March 02, 2015

Genomes and junk DNA

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?


Sunday, March 01, 2015

The University of Toronto explains why it hosted an alternative medicine conference

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.


Friday, February 27, 2015

Here's how an atheist discusses the problem of evil

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.


Thursday, February 26, 2015

Bacterial resistance to antibiotics has nothing to do with evolution according to Michael Egnor MD

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.


A quiz on Darwin's Theory of Evolution

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?
  1. What is a biological species? How does it differ from a variety? Give examples.
  2. How has Darwinian theory changed since Darwin? (Be specific.)
  3. Define the two criteria for "Darwinian fitness."
  4. What are "Darwin finches?" Where are they found?
  5. What is the function of HOX genes?
  6. What is meant by "ultra-conservation" in evolution? Give two examples.
  7. Give an example of a recent evolutionary change in humans, within the last 10,000 years.
  8. What is parallel evolution? Give an example.
  9. What is meant by "genetic drift"?
  10. 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?


Is the University of Toronto promoting quackery and pseudoscience?

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.


Wednesday, February 25, 2015

Watch what happens when a Canadian politician says he doesn't believe in evolution

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.


Tuesday, February 24, 2015

How do you explain the differences between chimpanzees. humans, and macaques?

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]

Monday, February 23, 2015

Should universities defend free speech and academic freedom?

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,

Sunday, February 22, 2015

What counts as "evidence"?

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.

Thursday, February 19, 2015

The top ten problems with evolution according to Intelligent Design Creationists

Most of Intelligent Design Creationism consists of whining about evolution. Their main goal seems to be to discredit scientists and evolution in order to lay the ground work for a new approach to science, one that demonstrates the existence of an intelligent designer.

Most of their criticisms of evolution are ridiculous but a few of them require a response. So far, after more than 25 years of whining, the creationists have utterly failed to make a convincing case against evolution.

Are they still trying? You bet. Casey Luskin has done us the favor of listing "The Top Ten Scientific Problems with Biological and Chemical Evolution" in a series of blog posts on Evolution News & Views (sic).

Here they are for your amusement.
  1. No Viable Mechanism to Generate a Primordial Soup. I think he's right about this one. But then, I don't think a primordial soup plays a role in the origin of life.
  2. Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code. This has nothing to do with the origin of the genetic code. It's an argument against "RNA world." Casey Luskin is correct. We don't know how the first information-containing molecules arose and how they came to be self-replicating.
  3. Step-by-Step Random Mutations Cannot Generate the Genetic Information Needed for Irreducible Complexity. Luskin is dead wrong about this one.
  4. Natural Selection Struggles to Fix Advantageous Traits in Populations. Casey Luskin doesn't understand modern evolutionary theory, and it shows.
  5. Abrupt Appearance of Species in the Fossil Record Does Not Support Darwinian Evolution. Casey Luskin doesn't understand modern evolutionary theory, and he doesn't understand the scientific literature. What else is new?
  6. Molecular Biology Has Failed to Yield a Grand "Tree of Life". Modern scientific discoveries have revealed that there may not be a universal tree of life common to all genes. Casey Luskin accepts the evidence but rejects the idea that scientific explanations can change when new data comes in.
  7. Convergent Evolution Challenges Darwinism and Destroys the Logic Behind Common Ancestry. This is nonsense compounded by wishful thinking.
  8. Differences Between Vertebrate Embryos Contradict the Predictions of Common Ancestry. Dead wrong.
  9. Neo-Darwinism Struggles to Explain the Biogeographical Distribution of Many Specie. What?
  10. Neo-Darwinism's Long History of Inaccurate Predictions about Junk Organs and Junk DNA. You'll have to read that post yourself to see how many different ways Casey Luskin can go wrong and the very few ways he can go right.