A physicist tries to understand junk DNA: Part II

Yesterday I posted some comments on a blog post by physicist Rob Sheldon [A physicist tries to understand junk DNA ]. My comments were based on what I had seen on Uncommon Descent but it turns out that was only a summary of a longer post that appeared on Evolution News & Views (sic): More on Junk DNA and the "Onion Test".

The longer post doesn't add very much to the argument but it does have something interesting at the bottom. Here's what Rob Sheldon says about the Onion Test and junk DNA.

A physicist tries to understand junk DNA

Rob Sheldon has a PhD. in physics and a M.A. in religion.¹ With two strikes against him already, he attempts to understand biology by discussing evolution, junk DNA, and the Onion Test [Physicist suggests: “Onion test” for junk DNA is challenge to Darwinism, not ID]. As you might imagine, posting on Uncommon Descent in support of Intelligent Design Creationism leads directly to strike three.

The Onion Test was created by Ryan Gregory in 2007 [The Onion Test] and published in the scientific literature by Palazzo and Gregory in 2014. It goes like this. Take your favorite hypothesis suggesting that most of the DNA in the human genome is functional and use it to explain why the onion, Allium cepa, needs a genome that is five times larger than the human genome. Then explain why closely related species of onion need twenty times more DNA than humans.

Learn to think like a scientist

There's a course at MIT (Boston, USA) called "7.00x Introduction to Biology - The Secret of Life." It's a very popular MOOC (online course). Here's the trailer for the course. In it, Eric Lander tells you that if you take his introductory biology course you will learn to think like a scientist and you will be able to understand the latest breakthroughs.


Here are the week one lectures that focus on biochemistry. I don't have time to go through it all but check out the description of ATP beginning at 2:13. This is not how good teachers explain the importance of ATP in the 21st century but it is how it was taught 40 years ago.

Get a job as a dissertation writer

Jerry Coyne has found a posting for a job in Toronto [see Dissertations for sale!]. You can see the original at: Dissertation Writers wanted for Work from Home Position. It's suitable for retired professors and post-docs who can't get any other job.

We are a medium sized, cloud-based consultancy headquartered in New York, but with consultants spread across the globe, from Asia to South America. We primarily handle Academic Consulting for Doctorate level clients, and we currently have several job openings in the Academic Research department.

Job responsibilities:
Your main responsibility will be to assist our clients in conducting the research needed needed to complete their theses, dissertations, or journal articles, and then writing drafts for portions of those documents, such as a Literature Review, Introduction or Discussion chapters.

The job will involve communicating with clients by email and by phone to understand their specific needs, provide suggestions on how to improve their research, and finally write a draft of the document itself. It will also involve engaging in ongoing discussions with clients after the first draft, and revising/rewriting the document to our clients' satisfaction.

*This is strictly a work-from-home position*, and any applicant should view this as a strong incentive.

Please note that this is a *full-time position*.

Requirements:
- Applicants must possess a meticulous nature and an extremely high attention to detail.
- A very positive and upbeat attitude (particularly as relates to phone calls and email communication with clients).
- Native English speakers only.
- A 4-year college degree is an absolute must, preferably from a well-known university.
- Ghostwriting or Technical Writing experience is desired, but not a must.
- Tutoring and/or research experience is also a bonus.

Compensation:
Compensation for the successful applicant is very generous. As we expect very few applicants to have directly applicable work experience in this field, there will be an extensive training program before the candidate is taken on in a more permanent capacity. Training will be paid, at USD 4,000/month, and is projected to last 3-4 months. Following successful training, pay will be USD 85,000 - USD 100,000/year.

I've chaired quite a few Ph.D. exams for humanities students and I reckon I could bang out a pretty good thesis in a few months.

As for journal articles, the ENCODE Consortium could hire me for $8000 per month.

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Here's a good example of a tenured professor who should be fired

I am a staunch defendant of academic freedom but tenure doesn't protect you from gross misconduct. Here's an example where a Professor of Philosophy at UNC faced dismissal hearings and, wisely, decided to resign. I'm betting that ethics wasn't her specialty.

Why did she resign? Read about it at: Jan Boxill, implicated in UNC scandal, resigns.

Apparently Boxill was counselor to the women’s basketball team and she participated in a scheme to give athletes decent grades in "courses" that didn't exist or required minimal work. Some of the courses were in African and Afro-American Studies (AFAM) and some were philosophy courses.

[The Provost's] letter to Boxill said there was "compelling evidence that over a period of several years you knowingly participated in grossly improper practices in your roles as a member of the faculty and an academic advisor to student athletes."

The letter, released Thursday, accused Boxill of several acts of misconduct:

▪ Requesting that AFAM employees provide specific grades to students.

▪ Steering athletes to AFAM courses that she knew were not overseen or taught by faculty, required only a paper and were graded by former office manager Deborah Crowder.

▪ Editing and writing portions of text inserted into the papers of the students she tutored.

▪ Allowing students to enroll in independent study classes in philosophy that required little academic work.

Bye-bye Boxhill.

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How to promote science according to new AAAS CEO Rush D. Holt

As the name implies, the American Association for the Advancement of Science (AAAS) is a group of American scientists dedicated to "advancing" science. It was formed in 1848 and over the years it has evolved into a sophisticated lobby for advocating and defending science funding as well as an organization that promotes science to the general public. It publishes several journals, including Science and Science: Translational Medicine.

The new CEO and Executive Publisher of Science is Rush D. Holt, Jr.. He is the son of a former United States Senator (Rush D. Holt Sr.). Rush D. Holt Jr. obtained a Ph.D. in physics in 1981 and taught courses in physics, public policy, and religion at Swarthmore College from 1980 to 1986. He is a Quaker.

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.

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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 ....

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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.

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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.

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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?

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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.

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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.

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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.

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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?

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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.

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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.

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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?

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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]

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,

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.

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.

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Who's to blame for bad science communication?

Most of us agree that there's a problem. A lot of what passes as science isn't being correctly communicated to the general public.

Lot's of people share the blame but I tend to focus on those people whose job is science communication. It must be true that science journalists aren't doing as good a job as they should.

A few years ago I attended a meeting on "The Two Cultures" in New York City. E.O. Wilson gave the plenary talk and he explained why everyone likes scenery that resembles the African savannah. It's because that's where humans originated [E.O. Wilson in New York]. The science journalists who were there applauded enthusiastically. I didn't.

Later on there was a session on science communication featuring a panel of science journalists. They insisted that the problems were not their fault. They can only rely on what scientists are telling them and that's what they report. Elizabeth Pennisi would be proud.

Carl Zimmer pointed out that it is important for science journalists to have a good source of scientists they can call on for advice whenever they are working on a new story. The other journalists didn't get it.

Richard Lenksi wonders who's to blame and he has created a poll [Science Communication: Where Does the Problem Lie?]. Go and vote.

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How many scientists does it take to screw ... ?

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?

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The null hypothesis of Darwinian evolution, again

I've read the paper by Schopf et al. (2015). Here's the entire section on Darwinian evolution.

How could the seemingly identical sulfur-cycling anoxic sediment-inhabiting biotas of the ∼1.8-Ga Duck Creek and ∼2.3-Ga Turee Creek cherts, like those of Proterozoic stromatolitic cyanobacteria (6, 8), have evidently remained fundamentally unchanged over billions of years?

We suggest differing answers for these two early-evolved hypobradytelic lifestyles:

i) For cyanobacteria, the answer evidently lies in a genetically encoded ecological flexibility derived from their early adaptation to geologically exceedingly slow changes of the photiczone environment (e.g., of solar luminosity, UV flux, day length, and CO₂, O₂, and usable sulfur and nitrogen). Because of their large population sizes, global dispersal by ocean currents and hurricanes, and capability to generate oxygen toxic to anaerobic competitors for photosynthetic space, these ecologic generalists adapted to and survived in a wide range of habitats (6).

ii) Once subseafloor sulfur-cycling microbial communities had become established, however, there appears to have been little or no stimulus for them to adapt to changing conditions. In their morphology and community structure, such colorless sulfur bacteria—inhabitants of relatively cold physically quiescent anoxic sediments devoid of light-derived diel signals and a setting that has persisted since early in Earth history—have exhibited an exceedingly long-term lack of discernable change consistent with their asexual reproduction (6).

Given these observations, it might be tempting to interpret such sulfur-cycling communities as evidencing the “negative” null hypothesis of Darwinian evolution—if there is no change in the physical biological environment of a well-adapted ecosystem, there should be no speciation, no evolution of the form, function, or metabolic requirements of its biotic components—a confirmation of Darwin’s theory that seems likely to be provided only by ecosystems fossilized in an environment that has remained essentially unaltered over many hundreds of millions of years.

Although logically required, this aspect of evolutionary theory has yet to be established.

The null hypothesis of Darwinian evolution

In my last class we discussed the view that natural selection is the only mechanism of evolution (false). We then discussed the view that evolution only occurs when the environment changes (false). Finally, we tried to imagine how any species could become so perfectly adapted to it's current environment that further increases in fitness are impossible (silly).

Along comes a new paper by William Schopf whose earlier claim to fame was the discovery of 3.5 billion year old fossils. A claim that has been discredited. The "fossils" weren't fossils [Did Life Arise 3.5 Billion Years Ago?]. The latest study was funded by the NASA Astrobiology Institute.

I can't read the paper right now because I don't have access but here's the summary from PNAS.

Happy 50th birthday to Canada's flag

Americans have changed their flag many times¹ but Canada did it only once, on Feb. 15, 1965 [Flag of Canada]. Today is the 50th anniversary.

Even Goggle celebrates.

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1. The last time was in 1960.

Vincent Torley and the evidence for god(s)

Vincent Joseph Torley (vjtorley) didn't like my recent post where I said there was no evidence for the existence of god(s) [Evidence for the existence of god(s)]. The reason this is important is because I define science as a way of knowing that, among other things, relies on evidence. If you believe in something without supporting evidence then that conflicts with science as a way of knowing. There may be other ways of knowing that do not rely on, or conflict with, evidence but you first have to convince me that the knowledge produced by this other method is actually true knowledge.

Here's what I said in that post ...

I am always on the lookout for evidence that some sort of god actually exists. The reason I'm an atheist is because I've never seen any evidence that's the least bit convincing. I keep asking for evidence but nobody ever supplies any.

Vincent Torley ctiiticizes me for not making a clear distinction between "evidence" and "convincing evidence" and he is correct [see No evidence for God’s existence, you say? A response to Larry Moran]. When I say there's no evidence for the existence of god(s) I mean that there is no "evidence" that stands up to close scrutiny. That's not quite the same thing as saying that there's no "evidence" that others might believe or no potential facts that are presented as possible evidence.

It's an important distinction to keep in mind but It think it quite clear that when I say there's no evidence for the existence of god(s) I mean that there's no valid evidence. That brings up the question of what defines "valid evidence." The short answer is "I don't know" but I know it when I see it.

Let's look at one of Vincent Torley's claims that there's evidence for god(s); namely, the evidence of miracles. Note that he accepts the process of science. In other words, he is willing to defend his belief that god(s) exist by pointing to "valid evidence" that his belief is correct. What that means is that we discuss his claim using the ground rules of science according to my view of what science is.¹

Professor Moran will want to see good evidence of miracles, so I’ll confine myself to one case: the 17th century Italian saint, Joseph of Cupertino, who was seen levitating well above the ground and even flying for some distance through the air, on literally thousands of occasions, by believers and skeptics alike. The saint was the phenomenon of the 17th century. Those who are curious might like to have a look at his biography by D. Bernini (Vita Del Giuseppe da Copertino, 1752, Roma: Ludovico Tinassi and Girolamo Mainardi). The philosopher David Hume, who was notoriously skeptical of miracle claims, never even mentions St. Joseph of Cupertino in his writings. Funny, that.

The evidence for St. Joseph’s flights is handily summarized in an article, The flying saint (The Messenger of Saint Anthony, January 2003), by Renzo Allegri.

If I were to accept the claim advanced by Vincent Torley then this would, indeed, constitute evidence that something very weird happened back in 1630. But I reject the claim. I simply don't believe that people actually witnessed Joseph of Cupertino flying through the air. It's not a fact. It's not evidence.

This is a case where an extraordinary claim requires extraordinary evidence. You can't just rely on what people say they saw because if that's all you need then there must be fairies at the bottom of the garden. And UFO abductions would be real.

Read Vincent Torley's other claims of "evidence" for the existence of god(s). Some of them are quite interesting but most of them are just wishful thinking. Take "fine tuning" for example. If the universe is really "fine tuned" for the existence of life—and that is disputed by many scientists—then why does that constitute evidence of gods? We could not possibly find ourselves in any universe that was not compatible with the existence of life. If this universe arose entirely by accident then we would still be here discussing the meaning of evidence.

Fine tuning is not evidence that gods exist. The best that could be said is that if you believe in gods then you can construct stories about supernatural beings who made the universe with the goal of producing life on one small insignificant planet near the edge of an otherwise unremarkable galaxy. If you don't believe in gods then it all looks pretty haphazard.

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1. If you believe that science cannot address any claim that involves the supernatural then, presumably, you will have to dispute Vincent Torley's claim using some other way of knowing. I don't know what that is. Perhaps one of you can describe it for me?

What did Judge Jones say in 2005? (Part III)

For those or you who are still interested in the debate over the nature of science and how it played out in Kitzmiller v. Dover Area School District back in 2005, I present to you ....

A Reading List
Science at the Bar—Cause for Concern by Larry Laudan

Is astrology science?

Many of you have heard stories about Micheal Behe's testimony in Kitzmiller v. Dover Area School District. Some of you have even made fun of him for saying that astrology is science.

The transcript of Behe's testimony is here. The important bits are when the lawyer for the plaintiffs is discussing the definition of "theory."

Q But the way you are using it is synonymous with the definition of hypothesis?

A No, I would disagree. It can be used to cover hypotheses, but it can also include ideas that are in fact well substantiated and so on. So while it does include ideas that are synonymous or in fact are hypotheses, it also includes stronger senses of that term.

Q And using your definition, intelligent design is a scientific theory, correct?

A Yes.

Q Under that same definition astrology is a scientific theory under your definition, correct?

A Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences. There are many things throughout the history of science which we now think to be incorrect which nonetheless would fit that -- which would fit that definition. Yes, astrology is in fact one, and so is the ether theory of the propagation of light, and many other -- many other theories as well.

Q The ether theory of light has been discarded, correct?

A That is correct.

Q But you are clear, under your definition, the definition that sweeps in intelligent design, astrology is also a scientific theory, correct?

A Yes, that's correct. And let me explain under my definition of the word "theory," it is -- a sense of the word "theory" does not include the theory being true, it means a proposition based on physical evidence to explain some facts by logical inferences. There have been many theories throughout the history of science which looked good at the time which further progress has shown to be incorrect. Nonetheless, we can't go back and say that because they were incorrect they were not theories. So many many things that we now realized to be incorrect, incorrect theories, are nonetheless theories.

Q Has there ever been a time when astrology has been accepted as a correct or valid scientific theory, Professor Behe?

A Well, I am not a historian of science. And certainly nobody -- well, not nobody, but certainly the educated community has not accepted astrology as a science for a long long time. But if you go back, you know, Middle Ages and before that, when people were struggling to describe the natural world, some people might indeed think that it is not a priori -- a priori ruled out that what we -- that motions in the earth could affect things on the earth, or motions in the sky could affect things on the earth.

I've seen lots of people mock Michael Behe for saying that astrology is science but I doubt they have read the actual transcript. Even if they have, I doubt that they appreciate the difficulties in deciding whether something is science or not.

These days, there is general agreement that astrology, homeopathy, etc, are examples of pseudoscience. Pseudoscience is something that masquerades as science. The proponents claim that their "theory" is supported by evidence and the conclusions are arrived at by a process of rational thinking. The reason we dismiss these views as pseudoscience is because they have been subjected to the rigors of scientific investigation and found to be false. The overwhelming majority of the scientific community agrees with this conclusion.

Bad science doesn't always become pseudoscience. Most bad hypotheses just die a quiet death when they are discredited. The transition to pseudoscience only happens when the proponents refuse to give up and insist that their theory is still valid science.

The point is, bad science and pseudoscience are science or at least they were accepted as possible scientific explanations until they were discredited. If they weren't within the realm of science then they could never have been falsified by science.

If you think you know how to define science in a way that eliminates all those ideas that you don't like then read: Is Astrology a Science?

You might not be so inclined to make fun of Michael Behe after that.

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Happy Darwin Day!

[Reposted from 2008.]

Charles Robert Darwin was born on this day in 1809. Darwin was the greatest scientist who ever lived.

In honor of his birthday, and given that this is a year of politics in America, I thought it would be fun to post something about Darwin's interactions with politicians. The historical account is from Janet Browne's excellent biography (Brown 2002).

William Gladstone (photo below) was an orthodox Christian. He was not a fan of evolution. In March 1877 Gladstone was leader of the Liberal party and a former Prime Minister of the most powerful country in the world. He was spending the weekend with John Lunnock—a well-known liberal—and a few other friends, including Thomas Huxley.

They decided to walk over to Darwin's House in Downe. This was 18 years after the publication of Origins and Darwin was a famous guy. The guests were cordially received by Darwin and his wife Emma. Darwin and Emma were life-long liberals and they were honored by Gladstone's visit. A few days later, Darwin wrote a note to his friend saying,

Our quiet, however, was broken a couple of days ago by Gladstone calling here.—I never saw him before & was much pleased with him: I expected a stern, overwhelming sort of man, but found him as soft & smooth as butter, & very pleasant. He asked me whether I thought that the United States would hereafter play a much greater part in the history of the world than Europe. I said that I thought it would, but why he asked me, I cannot conceive & I said that he ought to be able to form a far better opinion,—but what that was he did not at all let out.

A few years later Gladstone sent Darwin one of his essays on Homer. Darwin gratefully acknowledged the gesture.

In 1881, when Gladstone was Prime Minister again, Darwin and some of his friends petitioned Gladstone to award a pension to Alfred Russel Wallace, who was in dire financial straits at the time. Gladstone granted the request. Two months later Gladstone offered Darwin a position as trustee of the British Museum but Darwin declined. (Remember, Gladstone did not agree with Darwin about evolution, or religion.)

When Darwin died, Gladstone was instrumental in arranging for him to be buried in Westminster Abbey. The funeral was held on April 26, 1882. William Gladstone was too busy to attend. He went to a dinner at Windsor.

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Brown, J. (2002) Charles Darwin: The Power of Place (Vol. II). Alfred A. Knopf, New York (USA)

Patrick Ross, and the end of a very long road.

My friend, Robert Day, (Canadian Cynic) was subjected to a vicious and protracted serial defamation by Patrick Ross. Wanna know what happened?

Read: Patrick Ross, and the end of a very long road..

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What did Judge Jones say in 2005? (Part II)

We're discussing the nature of science by attempting to answer the question, "What is science?"

The example I've chosen is the debate over intelligent design (ID) and whether it is science or not. Many people believe that the question was settled by Judge Jones in Kitzmiller v. Dover Area School District: Decision of the Court. His answer was "no," intelligent design is not science.

In my first post I went over part of his decision in order to show that the issue is a lot more complicated than most people think [What did Judge Jones say in 2005? (Part I)]. It turns out that there are many ways to define science and Judge Jones picked one in order to prove that ID is not science. But there are other definitions of science where ID would qualify as science.

A lot of my ideas come from a recent book called Philosophy of Pseudoscience: Reconsidering the Demarcation Problem. Much of that book is based on philosopher Larry Laudan's view of the demarcation problem. Here's a relevant passage (p. 111)...

What did Judge Jones say in 2005? (Part I)

It is generally recognized that we don't do a very good job of teaching the nature of science. We also don't do a good job of teaching students how to think critically. This issue is going to heat up in a few months when Jerry Coyne's new book comes out.

Let's light a few fires right now. We'll look at the decision in Kitzmiller v. Dover Area School District. It was written by Judge John E. Jones III and it reflects on the nature of science and whether intelligent design (ID) is science. You can find the complete transcript on the TalkOrigins Archive website at: Kitzmiller v. Dover Area School District: Decision of the Court. The decision was published in December 2005.

Let's look at Section E4: "Whether ID is Science." I'll put Judge Jones' statement in boldface italics and my comments in regular type.

How has teaching changed in the last five decades?

I've been trying to get my colleagues to change the way they teach university courses. So far, I haven't had much success.

Part of the problem is the culture of the university (University of Toronto, Toronto, Canada). Here's a description of the problem. It was sent to me by a former public school teacher (thanks, Helen) but it captures the essence of what's happening in higher education—especially the last decade.¹

1. Teaching Maths In 1950s

A logger sells a truckload of lumber for $100. His cost of production is 4/5 of the price. What is his profit?

2. Teaching Maths In 1970s

A logger sells a truckload of lumber for $100. His cost of production is 4/5 of the price, or $80. What is his profit?

3. Teaching Maths In 1980s

A logger sells a truckload of lumber for $100. His cost of production is $80. Did he make a profit ? Yes or No

4. Teaching Maths In 1990s

A logger sells a truckload of lumber for $100. His cost of production is $80 and his profit is $20 Your assignment: Underline the number 20.

5. Teaching Maths In 2000s

A logger cuts down a beautiful forest because he is selfish and inconsiderate and cares nothing for the habitat of animals or the preservation of our woodlands.

He does this so he can make a profit of $20. What do you think of this way of making a living? Topic for class participation after answering the question: How did the birds and squirrels feel as the logger cut down their homes? (There are no wrong answers, and if you feel like crying, it's ok).

I don't think the last part is quite accurate. In a real modern classroom we would refer to the logger as "she" or at least "he/she."

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1. Normally I don't reproduce these internet clips but this one is so relevant.

Nessa Carey and New Scientist don't understand the junk DNA debate

There's a new book on junk DNA due to be published at the end of March. It's called Junk DNA: A Journey through the Dark Matter of the Genome. The author is someone named Nessa Carey. Here's her bio ....

Nessa Carey has a virology PhD from the University of Edinburgh and is a former Senior Lecturer in Molecular Biology at Imperial College, London. She worked in the biotech and pharmaceutical industry for thirteen years and is now International Director for the UK's leading organisation for technology transfer professionals. She lives in Norfolk and is a Visiting Professor at Imperial College.

Pretty impressive.

Here's how she describes her view of the human genome.

Bill Maher debates vaccinations with three non-scientists ... what could possibly go wrong??

If you've ever had any doubts about Bill Maher then watch this video and read Orac's takedown at: After five years, Bill Maher lets his antivaccine freak flag fly again.

Bill Maher is a kook. Nobody should listen to him about anything because he's blown whatever credibility he ever had. Just look at the sycophants he lined up for this show broadcast on Feb. 6, 2015.

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Evidence for the existence of god(s)

I am always on the lookout for evidence that some sort of god actually exists. The reason I'm an atheist is because I've never seen any evidence that's the least bit convincing. I keep asking for evidence but nobody ever supplies any. Somebody suggested to Barry Arrington that there was no evidence for god(s) and that really set him off [Astonishingly Stupid Things Atheists Say].

He responded with a list of all the evidence for god(s). Here's the list. I don't find it very convincing but some of you may want to head off to the the nearest church after reading the list.

• The fine tuning of the universe.
• The moral sense.
• The fact that a natural universe cannot logically have a natural cause.
• The fact that there is something instead of nothing.
• The overwhelming odds against the Darwinian story being true (estimated at 10^-1018 by atheist Eugen Koonin).
• The irreducible complexity of biological systems.
• The vast amounts of complex computer-like code stored in DNA.
• The miracles that have been reported throughout history.
• My subjective self-awareness.
• The fact that we do not even have plausible speculations to account for the origin of life.

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Does the Discovery Institute want Intelligent Design Creationism presented to public school students?

There are legal issues about teaching anything that smacks of religion in American public schools. This is why the leading Intelligent Design Creationists are very careful to avoid saying that they want to mandate teaching of Intelligent Design Creationism in the public schools.

Recently, a reporter for the Sioux Falls (South Dakota, USA) Argus Leader wrote an article about teaching IDC. He implied that the Discovery Institute lied to him when they said they weren't pushing Intelligent Design Creationism in public schools. The Discovery Institute didn't like that at all [Journalistic Malpractice in South Dakota: Argus Leader Won't Correct Misleading Story.

Here's their policy as outlined on their website [Darwinian Evolution, Intelligent Design and Education Policy].

Don’t Require The Teaching of Intelligent Design
All of the major pro-intelligent design organizations oppose any efforts to require the teaching of intelligent design by school districts or state boards of education. The mainstream ID movement agrees that attempts to mandate teaching about intelligent design only politicize the theory and will hinder fair and open discussion of the merits of the theory among scientists and within the scientific community.

Teach More About Evolution
Instead of mandating intelligent design, the major pro-ID organizations seek to increase the coverage of evolution in textbooks by teaching students about both scientific strengths and weaknesses of evolution. Most school districts today teach only a one-sided version of evolution which presents only the facts which supposedly support the theory. But most pro-ID organizations think evolution should be taught as a scientific theory that is open to critical scrutiny, not as a sacred dogma that can't be questioned.

Protect Academic Freedom
Although pro-ID organizations do not advocate requiring the teaching of intelligent design in public schools, they also believe there is nothing unconstitutional about voluntarily discussing the scientific theory of design in the classroom. Pro-ID organizations oppose efforts to persecute individual teachers who may wish to discuss the scientific debate over design in an objective and pedagogically appropriate manner.

Get it? The policy clearly states that the Discovery Institute doesn't want to require, or mandate, teaching Intelligent Design Creationism. Instead, it greatly favors a policy where evolution will be "correctly" taught. That includes "voluntary" coverage of design theory in the classroom.

They include a link to The Theory of Intelligent Design: A Briefing Packet
FOR EDUCATORS where they explain the correct way to teach Intelligent Design Creationism, if educators choose to do so voluntarily.

They also link to an article about the (American) law [Teaching About Evolution in the Public Schools: A Short Summary of the Law]. They say,

... school boards and administrators need to bear in mind that any presentation of a science curriculum dealing with evolutionary theory should focus on scientific evidence and theories reasonably inferable from that evidence, rather than upon claims that rest upon religious beliefs. Resources discussing scientific criticisms of aspects of neo-Darwinian and chemical evolutionary theories include the Icons of Evolution Study Guide and the Icons of Evolution Curriculum Modules.

In other words, if you voluntarily choose to teach the controversy then the Icons of Evolution book by Jonathan Wells would be a good choice.

Now you know. The Discovery Institute wants very much to get Intelligent Design Creationism into the public schools but they'll sneak it in the back door by pretending that it's part of legitimate scientific criticism of neo-Darwinism.

Note: I think it would be a great idea to get students to read Icons in high school biology classes in my home province of Ontario, Canada. I'd be happy to visit any schools who want to try this and explain why the book is a load of crap. It would be a good exercise for students to engage in critical thinking and examine the evidence. I like the idea ot teaching the controversy. It usually ends up by revealing that one side is wrong.

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Why I don't like English literature

There's an article on the PBS website that's making the rounds. It's by Wendy Thomas Russell and the bottom line is admirable. She's proud of the fact that her husband is getting their daughter interested in science by telling stories [Skip the fairy tales, and tell your daughter science bedtime stories].

That's not the part that's attracting the attention of science bloggers. What bothers us is the opening part of the article where Wendy Thomas Russell explains why she never liked science.

I decided to re-write those opening paragraphs with a slight twist. Hopefully you will see what's wrong.

I was never very good at English. Mostly because it was taught to me the same way history was taught to me: It wasn’t. I mean it was, technically. But not in a way that inspired me or held my interest for very long.

In elementary school, English literature was something contained in a much-too-heavy textbook adorned with things I didn’t care about: sonnets, Shakespeare in a funny collar, grammar, the elements of style, pathetic fallacy. (I hated pathetic!) Not even the occasional picture of Jane Austen could save English literature for me. As much as I would have loved to meet James Joyce, learning in school about his drinking habits or various abodes just made him seem more distant from me.

In high school, most of my English teachers were middle-aged women who seemed to aim their instruction right over my head. Everything struck me as dry and unemotional. I always felt I was missing something — some basic brain function. I learned things as though they were random pieces of information to be memorized and quickly forgotten, rather than stacks of wisdom neatly piled on a solid foundation of understanding.

Later, at the University of Nebraska, I was able to avoid English and the humanities for the most part (the biology department was kind to me). I did take one history class — and was pretty excited about it! — until I realized that the teacher was a very old Japanese man whose heavy accent destroyed any chance I had at making sense of the universe.

He pronounced “war” like this: “wah-waaaah.” I barely scraped by with a C-.

Most people would react negatively to something like that. They would quickly recognize that the problem was me, and not my teachers. After all, what kind of person can't manage to learn English literature? I must be very stupid.

Why is it socially acceptable for a woman to write those things about her inability to appreciate science?

Note: I really don't hate English literature.

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Barry Arrington blows it by assuming he knows the mind of an atheist

I think it's ridiculous for atheists to get dragged into the argument from evil. As soon as you start down that path you are conceding that you are willing to debate "sophisticated theology" and not whether god(s) actually exist. The atheist must then be prepared to read a massive amount of literature beginning with St. Augustine of Hippo through Thomas Aquinas and including the most famous "sophisticated" theologians of the 20th century like Alvin Plantinga and Richard Swinburne. If you don't engage the arguments made by those people, and many others, then you are not being honest.

The "problem of evil" is not simple and atheists do not do themselves any favors by pretending that it is. That's exactly the criticism we level at theists who don't even try to understand nonbelievers.

Let's look at an example of a stupid argument used by a Christian. Barry Arrington thinks that atheists are "simpering cowards" [The New Atheists Are Simpering Cowards]. Why in the world would he think that?

Because he's using the argument of angst to promote the idea that atheist logic is flawed. What is the argument from angst? It's a favorite of naive Christians like Barry Arrington and it goes like this. Friedrich Nietzsche was a troubled man and part of his problem was that he couldn't cope with the moral freedom that came from abandoning god. It drove him crazy. (Syphilis may have helped, but he was certainly manic-depressive.)

Christians would have you believe that this is what should happen to all intelligent people who don't believe in any gods. Here's how Barry Arrington explains it ...

Nietzsche was wrong and tragic and, in the end, insane. But at least he was brave and honest. Brave enough to stare into the abyss and honest enough to report back what he saw there. He would be disgusted by the puerile, simpering cowardice that characterizes atheism in the 21st century.

Apparently, the people of Denmark are just not experiencing enough angst and that's because they are "simpering cowards." They have built a secular society that avoids facing up to the extremely troubling aspects of not believing in god(s). This pretty much applies to most of the people in my neighborhood as well. We seem to be getting along just fine without any gods to guide us but, according to Barry Arrington, we aren't suffering enough.

I feel like my ears are going to bleed at the bleating of the new atheists who write in these pages. They go on and on and on and on about how morality is rooted in empathy and the avoidance of suffering. Nietzsche would have spit his contempt on them, for they are espousing the “herd animal” Christian slave-morality he disdained and which, ironically, they claim to have risen above. How many times have the atheists insisted, “we are just as ‘good’ as you”? Why have they failed to learn from Nietzsche that “good” means nothing. Why do they insist that they conform to a standard that they also insist does not exist?

The answer to these questions is the same: They refuse to acknowledge the conclusions that are logically compelled by their premises. And why do they refuse? Because they are simpering cowards.

I can respect while disagreeing with a man like Nietzsche, a man who follows his premises where they lead, even if they lead to asking questions such as “Is there still any up or down? Are we not straying, as through an infinite nothing? Do we not feel the breath of empty space? Has it not become colder? Is not night continually closing in on us?” I have nothing but contempt for smiley-faced, weak-kneed, milquetoast atheism that insists that God is dead and all is well because we are just as nice as you.

For the record, I do not insist that gods are dead. They never existed in the first place. Being good was an important value for all societies long before they invented the Christian god.

In addition to their ridiculous "problem of evil," it looks like Christians also have a "problem of good." They don't understand how you can be good without god. It's probably better if they keep believing in their gods because, otherwise, the streets would be full of ex-Christian mass murderers. Here's what Barry Arrington thinks ...

When Nietzsche urges us to go beyond good and evil, he is urging us to recognize the implications of God’s death for morality. God is the only possible source of transcendent objective moral norms. If God does not exist then neither do transcendent objective moral norms. And if transcendent objective moral norms do not exist, neither do “good” and “evil” in the traditional senses of those words. There is only a perpetual battle of all against all, and “good” is a synonym for prevailing in that battle, and “evil” is a synonym for losing.

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