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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.


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.

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.

Wednesday, February 18, 2015

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?

Tuesday, February 17, 2015

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.

Sunday, February 15, 2015

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.

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.

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?

Friday, February 13, 2015

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.

Thursday, February 12, 2015

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.

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..

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)...

Wednesday, February 11, 2015

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."

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

Tuesday, February 10, 2015

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.

Monday, February 09, 2015

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.

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.

Sunday, February 08, 2015

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
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.

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.

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.

Friday, February 06, 2015

John F. Kennedy, Carnival cruises, blood plasma, sea water, and evolution

Here's a video of a commercial by Carnival Cruises. Apparently it aired during some recent football game in the USA. (They play football in January?)

The voice is that of US President John F. Kennedy. He says ...
I really don’t know why it is that all of us are so committed to the sea, except I think it is because in addition to the fact that the sea changes and the light changes and ships change, it’s because we all came from the sea. And it is an interesting biological fact that all of us have, in our veins the exact same percentage of salt in our blood that exists in the ocean, and, therefore, we have salt in our blood, in our sweat, in our tears. We are tied to the ocean. And when we go back to the sea, whether it is to sail or to watch it we are going back from whence we came.
Here are the facts as I explain them in the latest edition of my textbook (p. 33).

There was a time when people believed that the ionic composition of blood plasma resembled that of seawater. This was supposed to be evidence that primitive organisms lived in the ocean and land animals evolved a system of retaining the ocean-like composition of salts.

Careful studies of salt concentrations in the early 20th century revealed that the concentration of salts in the ocean were much higher than in blood plasma. Some biochemists tried to explain this discrepancy by postulating that the composition of blood plasma didn’t resemble the seawater of today but it did resemble the composition of ancient seawater from several hundred million years ago when multicellular animals arose.

We now know that the saltiness of the ocean hasn’t changed very much from the time it first formed over three billion years ago. There is no direct connection between the saltiness of blood plasma and seawater. Not only are the overall concentrations of the major ions (Na+, K+, and Cl-) very different but the relative concentrations of various other ionic species are even more different.

The ionic composition of blood plasma is closely mimicked by Ringer’s solution, which also contains lactate as a carbon source. Ringer’s solution can be used as a temporary substitute for blood plasma when a patient has suffered blood loss or dehydration.
Here's a copy of something I posted on on Oct. 5, 1998.
It turns out that one of the most important researchers who investigated this problem was A.B. Macallum who was chair of my department from 1907-1917. [See Archibald Byron Macallum (1858 - 1934)] Macallum wrote a major review in 1926 (1) in which he debunked the idea that the ionic composition of blood plasma was nearly the same as that of sea water. Here's what he said seventy years ago,
"Quinton, in 1897 (2), advanced the view that in the great majority of multicellular animals organisms the internal medium, the circulatory fluid, or hemolymph, is, as regards its organic composition, but sea water.... Analysis of the salts of the blood plasma, Quinton holds, indicates that they are the same as those which obtain in sea water and the elements of both appear in the same order of importance; Chlorine, sodium, potassium, calcium, magnesium, chuphur, silicon, carbon, phosphorus, fluorin, iron, nitrogen, etc. ...

This indicates how uncritical he is in the examination of his data in his aim to demonstrate that the internal medium is but sea water. The elements do not appear in the same order of importance as stated. In sea water they rank thus: chlorine, sodium, magnesium, potassium, sulphur, calcium, etc., whereas in the blood plasma they rank: chlorine, sodium, potassium, calcium, sulphur, magnesium etc. In sea water the sodium is to the magnesium in amount as 100:12, whereas in the blood plasma of the higher vertebrates the ratio is as 100:0.7, which reveals a wide discrepancy. As regards the sulphur, which occurs almost wholly in sea water as sulphates, it is in amount in proportion to the sodium as 8.4:100, whereas in mammalian blood plasma if all the sulphur therein is reckoned as present in the form of sulphate, the proportion is 1.4:100."
p. 320-321
Macallum reviews his own extensive data on ionic composition and points out that not only the proportions but also the concentrations do not agree. The salt concentration of plasma is "less than one-fourth that of sea water".

Macallum was a confirmed evolutionist and he went on to argue that the salt concentration of mammalian plasma may reflect that of the ancient ocean where our ancestors lived. He was under the impression that the salinity and composition of the oceans has changed over the past several hundred million years. (We now know that this is not correct.) Furthermore, the ionic composition of cells is quite different from that of the plasma and Macallum suggests that this is a reflection of an even more ancient origin of cells in a Archaen ocean.

The point is that our blood is NOT like sea water. The sea is much more salty and the relative concentrations of the various ions is different.

1. Macallum, A.B. (1926) The Paleochemistry of the Body Fluids and
Tissues. Physiol. Rev. 6, 316-357.

2. Quinton, R. (1898) Hypothese de l'eau de mer, milieu vital des
organisimes eleves. Compt. rend. de la Soc. de Biol. 935
I added more information on May 30, 2005.
The concentration of salts in seawater is more than three times higher than the concentration in most organisms. For example, the ionic concentration of seawater is 600 millequivalents and that of human blood plasma is only 150 milliequivalents. The same difference holds true for most species, including many single-cell organisms. Many bacteria can live quite happily in the sea or in fresh water because they are not dependent on the ionic composition of the surrounding medium. Many organisms are not isotonic with their surrounding if by "isotonic" one means within a few percent.

Perhaps modern salt concentration in human plasma reflects that of the ancient ocean? This idea has been around for a long time. The original chair (1907) of my department was A.B. Macallum and he was a leading proponent of this concept. The most widely cited paper was a review published near the end of three decades of work on this subject.

Macallum, A.B. (1926) The Paleochemistry of the Body Fluids and Tissues.
Physiol. Rev. 6: 316-357.

(Finding this paper was quite an adventure - I've told the story before on

Macallum published estimates of the salt concentration of the Cambrian sea and these estimates agree closely with the salt concentrations in modern human plasma. Unfortunately the salt concentrations in sharks and lobsters are twice as high as in humans so this meant that sharks and lobsters originally had salt concentrations that were higher that seawater. No problem. The salt in sharks and lobsters has increased over time as the ocean got more salty but the human values reflect the time when their ancestors emerged from the sea.

It's a nice idea but it was spoiled by a nasty little fact. The salt concentration of the oceans has not changed very much since they reached equilibrium about three billion years ago. Gould has a nice little essay about this in "On Rereading Edmund Halley" (EIGHT LITTLE PIGGIES p.168). In addition to discovering comets, Halley proposed a method for calculating the maximum age of the Earth based on the increase of salt in the ocean.

He was wrong for the same reason that Macallum was wrong.
It's interesting that the myth of blood plasma resembling sea water persisted for over a century in spite of the fact that leading biochemists knew the truth 75 years earlier. Part of the problem was textbook writers who perpetuated the idea because it seemed so sensible in light of evolution. (In fact, it's not sensible at all if you really understand evolution.) Those textbook writers didn't bother to check the scientific literature. Neither did the typical lecturer in a biochemistry course.

That's still a problem today. Here's the former President of the American Society of Hematology repeating the myth in 2008 [The Wonders of Blood].
Our blood is the foundation of our very existence as multicellular animals, said Andrew Schafer, a professor at Weill Cornell Medical College and the outgoing president of the American Society of Hematology. Blood is the one tissue that comes into contact with every other tissue of the body, and it is through blood that our disparate parts communicate, through blood that our organs cooperate. Without a circulatory system, there would be no internal civilization, no means of ensuring orderly devotion to the common cause that is us.

“It’s an enormous communications network,” Dr. Schafer said — the original cellphone system, if you will, 100 trillion users strong.

Blood can also be thought of as a private ocean, a recapitulation of what life was like for all the years we spent drifting as microscopic, single-celled organisms, “taking up nutrients from sea water and then eliminating waste products back into sea water,” Dr. Schafer said. Not only is blood mostly water, but the watery portion of blood, the plasma, has a concentration of salt and other ions that is remarkably similar to sea water.

Note: PZ Myers didn't like the commercial either ["]. One of his reasons was that the facts are wrong.