Saturday, April 30, 2011

Teaching Evolution: Are Geoscience Teachers Helping or Hurting?

The National Center for Science Education (NCSE) is promoting a position statement on evolution issued by the National Association of Geoscience Teachers (NAGT) [Geoscience teachers add their voice for evolution]. Apparently NCSE thinks this statement is good enough to include on their website and and publish in the next edition of Voices for Evolution. The statement can be found on the NAGT website: Position Statement - Teaching Evolution. It was published in 2006. I'm reproducing it below in order to get your opinion.

Is this statement helpful in understanding evolution and in teaching the concept correctly in high school science classes? I don't think so. I think it only adds to the confusion by conflating biological evolution with all kinds of change including geologic change. I think there's a big difference between understanding how the Hawaiian islands might have formed and why all living species have descended from a common ancestor. I think the "scientific theory of evolution" refers to biological evolution and it doesn't help when high school science teachers equate that to geologic change and cultural change.
The National Association of Geoscience Teachers (NAGT) recognizes that the scientific theory of evolution is a foundational concept of science, and therefore must also be a cornerstone of science education. Evolution in the broadest sense refers to any change over time. The study of Earth's evolution provides society with the time and space perspectives necessary to understand how Earth's physical and biological processes developed, provides insight into the natural processes active on Earth, and shapes our view of Earth's future.



In science, disagreements are subject to rules of scientific evaluation, and this includes the methodologies of teaching scientific concepts. Scientific conclusions are tested by experiment, observation, and evaluation. Sound practices of scientific education are tested and evaluated much the same way. NAGT recognizes that invoking non-naturalistic or supernatural events or beings, often guised as "creation science," "scientific creationism," or "intelligent design theory," are not scientific in character, do not conform to the scientific usage of the word theory, and should not be part of valid science curricula.


Friday, April 22, 2011

Pray for Texas








Governor of Texas
This is going to put God in a really difficult position. He's right in the middle of punishing Texas for being so stupid in the past few decades and now the Texans are pleading for relief from that punishment. It may be hopeless. After all, the Egyptians didn't get spared when they prayed to their gods to stop another god from killing all their firstborn sons.

[Office of the Governor]

Thursday, April 21, 2011

The Student-Centered Classroom

A large part of the AAAS document, Vision and Change in Undergraduate Biology Education is devoted to how to teach science. The "core concepts" take up only 2 pages out of 79 pages in the booklet.

The modern buzzword phrase for the 21st century is "The Student-Centered Classroom" and "Student-Centered Learning." The terms means lot of different things to different people but the key concept is to move away from lecturing about "facts" to a classroom format that emphasizes student participation in the learning process.
Although the definition of student-centered learning may vary from professor to professor, faculty generally agree that student-centered classrooms tend to be interactive, inquiry driven, cooperative, collaborative, and relevant. Three critical components are consistent throughout the literature, providing guidelines that faculty can apply when developing a course. Student centered courses and curricula take into account student knowledge and experiences at the start of a course and articulate clear learning outcomes in shaping instructional design. Then they provide opportunities for students to examine and discuss their understanding of the concepts presented, offering frequent and varied feedback as part of the learning process. As a result, student-centered science classrooms and assignments typically involve high levels of student–student and student–faculty interaction; connect the course subject matter to topics students find relevant; minimize didactic presentations; reflect diverse aspects of scientific inquiry, including data interpretation, argumentation, and peer review; provide ongoing feedback to both the student and professor about the student’s learning progress; and explicitly address learning how to learn.
This is a very good idea in theory but putting it into practice is much harder than it looks. I've seen some excellent examples of student-centered learning at various conferences over the past few years. One type of student-centered learning seems particularly attractive to me and I've tried it several times in my courses. Here's how it's described in the Vision and Change document (p. 26).
Typically, these strategies engage students more actively in every aspect of their learning and are interactive, inquiry driven, cooperative, and collaborative, allowing students to engage with each other and with faculty. For example, the “problem–based model of instruction,” or learning cycle (Bybee, 1997; Fuller, 2002), revolves around a series of related questions that first probe what students know about a topic and then move to unfamiliar, new ground, enabling the students to develop a more complete and accurate understanding of the topic. Faculty initiate student interactions with key guiding questions and opportunities for discussion, present a short explanation of the necessary background knowledge, and then have students work together on questions to deepen their understanding through reflection on and application of their knowledge (e.g., Ebert-May et al., 1997). This approach incorporates frequent informal assessment (e.g., Angelo and Cross, 1992) to address misconceptions and provides a balance between direct instruction and student interaction. One or two class sessions using this approach to introduce a topic such as evolution might unfold in the following way (e.g., Ebert-May et al., 2008):
  1. Engagement Question: For example, “What is evolution?” This background question probes student knowledge of the topic.
  2. Exploration: Students share their answers with other students sitting nearby and come to a consensus; volunteers from the groups share their answer with the class, allowing the instructor to listen for misconceptions and depth of understanding.
  3. Explanation: The instructor presents a short interactive lecture (15 minutes) on the topic, providing explanations to help clarify student thinking based on identified misconceptions.
  4. Extension Question: Students work together on a more advanced question that might, for example, call for them to analyze information, formulate critical questions and hypotheses, evaluate and criticize evidence, or propose alternative solutions. In the example of evolution, the extension question, tied to a learning goal, might be What mechanisms are involved in natural selection, and what role does natural selection play in antibiotic resistance in bacteria today? Again, groups are called on to explain their answers and how they came to them.
  5. Quiz Question: The final assessment (which may or may not be formally graded) allows both the student and the instructor to chart the effectiveness of teaching and learning.
The idea here is to confront misconceptions by having students come up with their own ideas about answering the "engagement question." This gives the instructor the opportunity to correct the most common misconceptions. In this example, the students will almost certainly come up with a definition of evolution that requires natural selection and excludes random genetic drift. They will frequently include mutation and recombination as part of their definition. Most of the time students will demonstrate lack of knowledge of population genetics.

The lecture component will explain the reasoning behind different definitions of evolution and why one might prefer one definition over another. Part of the explanation involves creating a "minimal definition" of evolution that will allow one to distinguish between evolution and something else. (I choose human examples. Think about the increased height in Europeans over the past 500 years. Is that evolution? Why or why not? Why do some native North American populations have only O-type blood? Is that evolution?)

The "extension question" should be designed to challenge students to think about the topic in new ways. In my case, the extension question is often something like this ...
If evolution is defined as a change in the frequency of alleles in a population and if fixation of alleles can occur by several different mechanisms, then what is the most common mechanism of evolution according to the data we have?
I think the three most important criteria in science education are (1) accuracy, (2) accuracy, and (3) accuracy. Everything else is of lesser importance, including how you teach the concept. Thus, you may be an expert at student-centered learning but if you don't understand evolution then the exercise is completely ineffective no matter how much the students may enjoy it.

If we are going to fix undergraduate education in biology then we need to concentrate above all else on making sure we accurately identify the core concepts and make sure they are being taught correctly. We can move on to other things once we are convinced that the first three objectives (accuracy, accuracy, and accuracy) are being achieved. It could actually be harmful to develop a student-centered learning course based on false concepts.

Core Concepts: Pathways and Transformations of Energy and Matter

The AAAS document, Vision and Change in Undergraduate Biology Education, defines five core concepts for biological literacy. One of the core concepts is Pathways and Transformations of Energy and Matter. This is an important one for biochemistry since we are the people charged with making sure undergraduates understand the basic core concept that life obeys the laws of physics and chemistry.

Here's how the authors of Vision and Change describe the core concept.


The principles of thermodynamics govern the dynamic functions of living systems from the smallest to the largest scale, beginning at the molecular level and progressing to the level of the cell, the organism, and the ecosystem. An understanding of kinetics and the energy requirements of maintaining a dynamic steady state is needed to understand how living systems operate, how they maintain orderly structure and function, and how the laws of physics and chemistry underlie such processes as metabolic pathways, membrane dynamics, homeostasis, and nutrient cycling in ecosystems. Moreover, modeling processes such as regulation or signal transduction requires an understanding of mathematical principles.

For example, knowledge of chemical principles can help inform the production of microorganisms that can synthesize useful products or remediate chemical spills, as well as the bioengineering of plants that produce industrially important compounds in an ecologically benign manner. These are topics of intense current interest.
At first glance this seems like an adequate description of a core concept but the more you think about it the more you realize that it's just a bunch of motherhood statements without any real teeth. It sounds very nice to say that students need to understand kinetics and thermodynamics but the recommendation has no substance unless you explain exactly what it is that they are supposed to understand. We all know that both these concepts are poorly taught in undergraduate courses.

When I was teaching introductory biochemistry I always asked my students the following question to make sure they had grasped the concept of where cellular energy comes from.
There are species that are autotrophs. They grow and reproduce using only inorganic molecules as their only source of essential elements. Carbon usually comes from CO2. Some of these species are capable of photosynthesis (photoautotrophs) but others are not (chemoautotrophs). Where do chemoautotrophs get the energy to grow and reproduce if they can't carry out photosynthesis and they don't require organic molecules as food sources?
Let's look at the AAAS Project 2061 Science Assessment Website to see how they treat the topic of Matter and Energy in Living Systems. This site is for high school biology but it's the only place I know where we can assess what AAAS thinks is important in basic concepts. Students are expected to know that...
All organisms need food as a source of molecules that provide chemical energy and building materials.
  1. Food consists of carbon-containing molecules in which carbon atoms are linked to other carbon atoms.
  2. Carbon-containing molecules serve as the building materials that all organisms (including plants and animals) use for growth, repair, and replacement of body parts (such as leaves, stems, roots, bones, skin, muscles, and the cells that make up these structures) and provide the chemical energy needed to carry out life functions.
  3. If substances do not provide both chemical energy and building material, then they are not food for an organism.
  4. Chemical energy from carbon-containing molecules is the only form of energy that organisms can use for carrying out life functions.
  5. Carbohydrates (including simple sugars and starch), fats, and proteins are molecules that are food.
  6. Light is not food because it is not made of atoms and therefore cannot provide building material, and even though substances such as water, carbon dioxide, oxygen, and various minerals provide atoms for building materials for some types of organisms, they are not food because they do not contain carbon atoms that are linked to other carbon atoms and cannot be used as a source of chemical energy.
Oh dear. If this is an example of core concepts then we need to add one more item; namely "7. According to item #3, chemoautotrophs are not organisms."

I'm sure most of you recognize the problem. The focus is on plants and animals, ignoring protozoa and bacteria. This is not how to teach basic concepts in biology and it certainly isn't how to teach if evolution is supposed to be an important core concept. Complex plants and animals did not just poof into existence with specialized metabolic pathways.

But not to worry. Although the six statements above seem wrong, they are soon clarified in the next section ...
Plants make their own food in the form of sugar molecules from carbon dioxide molecules and water molecules. In the process of making sugar molecules, oxygen molecules are produced as well.
  1. Unlike animals, plants do not take in food from their environment.
  2. Plants make their own food in the form of sugar molecules by means of a chemical reaction between carbon dioxide molecules and water molecules. Oxygen molecules are also a product of this reaction.
  3. The process of making sugar molecules involves linking together carbon atoms that come from molecules of carbon dioxide.
  4. The chemical reactions by which sugars are made takes place inside the plants. In most familiar land plants, the carbon dioxide molecules that are used come from the air that enters the plant primarily through its leaves, and that the water molecules that are used in the reaction enter the plant through its roots.
Here's the core concept as I teach it. I'd appreciate feedback on which way is better.
Photosynthetic organisms, such as bacteria, algae, and plants, can use light as a source of energy. They convert this energy into chemical energy in the form of ATP and other cofactors. These "high energy" molecules are used to provide energy in biosynthesis reactions that make all of the important molecules in the cell including amino acids, proteins, nucleotides, nucleic acids, fatty acids, lipids & membranes, carbohydrates, and polysaccharides.
Note that point #2 above is absolutely wrong. Oxygen is NOT produced as a result of a reaction between CO2 and H2O. That is a major misconception. The oxygen given off by some photosynthetic species is derived directly from water as part of the photosynthetic electron transfer reactions. Some photosynthetic species don't produce oxygen yet they are perfectly capable of synthesizing nucleic acids, proteins, lipids, and carbohydrates. How do they do it? You need to understand the answer to that question if you are going to understand how eukaryotic photosynthesis evolved.

My main criticism of undergraduate biology education is that the core concepts are not being taught and, when an attempt is made, they are often taught incorrectly. The Vision and Change document doesn't make a contribution toward fixing this problem. The "core concepts" it describes are not specific enough to be helpful and when they are specific they turn out to be wrong or misleading.

Vote for Omar

Here's the latest video from the Liberal Candidate in my riding. These videos are one of the many reasons why I'm going to vote for him.

Wednesday, April 20, 2011

AAAS Flunks Evolution!

As I noted yesterday, the AAAS document, Vision and Change in Undergraduate Biology Education, defines five core concepts for biological literacy [Core Concepts: Evolution]. Evolution is the first core concept and this is a very good thing. Congratulations to the committee for a wise choice.

However, the way that the core concept is described was troubling. It suggested to me that the members of the committee may not understand evolution as well as they think they do. This worry is reinforced by the AAAS Project 2061 Science Assessment Website where a series of questions and responses about evolution indicates that AAAS flunks the test.

There's no mention of the standard definition of evolution as a change in the heritable characteristics of a population over time [What Is Evolution?]. This is important because a fundamental part of the core concept is the understanding that any mechanism of change counts as evolution—not just natural selection. Another fundamental part of evolution is understanding that it is populations that evolve and not individuals. The population genetics definition of evolution was developed in the 1930s and became a key part of the Modern Synthesis in the 1940s. The definition is almost 70 years old. Why don't the authors of the report know this?

There's no mention of random genetic drift. The assessment questions are all about natural selection. In fact, the key topic concept is called "Evolution and Natural Selection." How are students supposed to understand phylogenetic trees based on sequences if they don't understand the basic stochastic process that generates these trees? How are they supposed to understand genetic variation if they've never heard of neutral mutations and how they can be fixed by random genetic drift?

There's nothing about mutation. Don't students need to understand mutation in order to understand variation? Of course they do.

There's nothing about speciation. Understanding how new species arise is an important part of evolution.

The problem with the Vision and Change document is that it identifies five core concepts but it doesn't tell us what they are beyond giving them names. If you want to reform undergraduate teaching you have to not only identify what the core concepts are but also make sure they are accurate. If you don't understand the core concepts to begin with then you aren't going to teach them properly to your students. I don't think most professors understand evolution well enough to be able to teach it effectively as a core concept. (This also applies to the other core concepts as I will explain over the next few days.)

What we really need is a committee that examines how to teach PROFESSORS the core concepts of biology. Unfortunately, ignorance of the core concept of evolution is widespread and seems to include many of the professors who created the Vision and Change document.

Tuesday, April 19, 2011

Core Concepts: Evolution







Vision & Change in Undergraduate Biology Education: Bruce Alberts

The American Association for the Advancement of Science (AAAS) has published a document called Vision and Change in Undergraduate Biology Education. Over the next few days I'm going to introduce the main recommendations and hopefully stimulate some discussion.

Today, we'll start with a video from Bruce Alberts the former head of the National Academies and currently editor-in-chief of Science magazine (published by AAAS). Pay attention to what he has to say. I agree with everything.1

Bruce Alberts understands that we (university professors) are the problem and it's up to us to fix it.
... the future of science education ... depends on what college professors do in their teaching much more than I would ever have expected ...

Dr. Bruce Alberts’ Message to Vision and Change

1. Bruce was my Ph.D. supervisor.

Monday, April 18, 2011

Are You a Canadian between the Ages of 18 and 25?

Evidence for Miracles?

A Sandwalk reader, Mike Sherlock, took some exception to my talk on Friday night and sent me this email message. He has given me permission to post it. I don't agree with his position. What do the rest of you think about miracles?
In the course of your talk you asserted that there was no evidence to support miracles, thereby implying that a belief in miracles was a superstitious belief. During the question period I suggested that it might be a good thing if we could concede that our philosophical opponents have a plausible case, notwithstanding the fact that we're bound to believe the case for our own position is stronger. Such a concession would imply that arguments and evidence require interpretation, and that the weight one gives to an argument or piece of evidence may legitimately vary according to a wide range of factors such as temperament, upbringing, what we already believe, what we would like to believe, etc., etc. Insisting, however, that the contest between naturalism and supernaturalism is nothing more than a contest between cold white truth and stark unreason, while it may simplify one's argument, immensely complicates the problem of human communication. The tendency will be to talk about the opposition rather than to the opposition--after all, what's the point of talking to self-deluding fools. Their arguments are only going to irritate.

At the risk of irritating, I will quickly present the case for miracles as a theist might make it:

Hume famously remarked, "A miracle is a violation of the laws of Nature; and as a firm and unalterable experience has established those laws, the proof against a miracle, from the very nature of the fact, is as entire as any argument from experience can be." But we only know that the "experience" against miracles is "firm and unalterable" if we already know that all reports of miracles are false. And we only know that all reports of miracles are false if we already know that miracles never occur. Both naturalists and supernaturalists accept that it is a logical fallacy to argue in a circle, that you must not assume in your argument what your argument purports to show.

Moreover, the theist claims that so far from the case against miracles resting on "firm and unalterable experience," there is a vast amount of unimpeachable evidence in favour of miracles. The question, as John Stuart Mill rightly said, "can only be stated fairly as depending on a balance of evidence: a certain amount of positive evidence in favour of miracles, and a negative presumption from the general course of human experience against them."

Now if it were purely a question of volume of evidence, then the volume is overwhelming. Every century, every race, every culture, every kind of person has contributed to the ocean of testimony bearing witness to the possibility of interference with nature by supernatural power--in other words, we have a situation here that is very different from that of mere logical possibility, like Russell's orbiting teapot. If the explanation of this evidence be in dispute, the naturalist has to provide a series of ad hoc explanations. He explains one incident by hallucination, another by fraud, a third by faulty observation, a fourth by forged documents, a fifth by inaccurate diagnosis and so on. The supernaturalist advances one explanation which covers all the alleged facts. He claims that the supernatural exists and that supernatural beings intervene from time to time in the natural order. He cuts through a tangle of assorted explanations with the sharp edge of Occam's razor: "Explanations must not be multiplied without a reason."

Dr. Jacalyn Duffin, as you may know, is a hematologist and an atheist. Some 20 years ago she was asked to provide expert testimony--she analyzed blood samples from a leukemia patient--that was used to advance the canonization of Canada's first saint, Marie-Marguerite d'Youville. She says the Vatican's forensic work in establishing miracles is rigorous. Duffin is also a Queen's University professor and author of the 2009 book "Medical Miracles: Doctors, Saints and Healing in the Modern World." It was only after the research for her book, which chronicles her investigation into 1,400 supposed miracles, that she concluded that there are things that happen--cures, for instance--that cannot be explained scientifically. Her view differs from the Vatican's in one important area: "I disagree, because I am an atheist, that God did it." Scientists believe there must always be an explanation, she adds. "Even if we don't have an explanation, we're confident it must exist. That is a belief--it is like religion."

Dr. Duffin admits that her rejection of miracles is based on the fourth definition of faith (in my desktop dictionary): "a strongly held belief or theory." Her belief, which she says is "like religion," is that all phenomena are material in origin, and therefore any alleged miracle has a naturalistic explanation, irrespective of whether science can discover it or not. I think that position is honest and unassailable. Note, however, how her position differs from that of Hume, who tells his readers that they needn't worry their minds about any evidence for miracles because he can give them general reasons why they should reject ALL evidence in favour of miracles IN ADVANCE. Not only are there obvious philosophical objections to Hume's attitude, but it is sharply at odds with the scientific method as famously laid down by Francis Bacon. That method requires theory to emerge from the evidence, unguided by preconceived notions--especially metaphysical notions.

It seems to me that all of Hume's arguments only carry weight if you are a convinced naturalist to begin with--usually for reasons that have nothing to do with miracles, such as the conviction that no omnipotent, benevolent Being would create the sort of world that we live in. In other words, Hume's whole argument is underwritten by the sceptic's answer (solution?) to the problem of evil. Fair enough. The problem of evil has always been the main reason given by philosophers and non-philosophers alike for why they can't believe in a personal God. Though not a disproof of supernaturalism, the fact of evil (and tragedy) will always be a powerful suasion for naturalism.

Obviously, not everybody who prays for miraculous healing can expect to be healed. If everybody who prayed was healed then miracles would be accepted as one of the stranger facts of life--such as the evolution of the first cell from inanimate matter. Everybody would believe because everyone would know someone whose prayer had been answered--in many cases their own. If, on the other hand, miracles were exceedingly rare, then they would lose their evidential value even for supernaturalists. The Gospels make it clear that miracles were meant to have evidential value. Here's my favourite passage, but there are a number of others: "Now John had heard in his prison of Christ's doings, and he sent two of his disciples to him; Is it your coming that was foretold, he asked, or are we yet waiting for some other? Jesus answered them, Go and tell John what your own ears and eyes have witnessed; how the blind see, and the lame walk, how the lepers are made clean, and the deaf hear, how the dead are raised to life, and the poor have the gospel preached to them. Blessed is the man who does not lose confidence in me." (Matt 11: 2-6) There are also Gospel passages to indicate that Jesus did not claim a monopoly on healing, and that miracles could be expected in the future.

To me, the incidence of miracles seems just about right--except, of course, when one could use a miracle oneself. But the naturalist is bound to think otherwise. An interesting example is Emile Zola, self-proclaimed father of French naturalism (in literature). He wrote a novel, entitled "Lourdes", during the research for which he had a chance to meet Marie Lebranchu (Miracle #16, 1892) at the Medical Bureau of Verifications. In his novel he altered the facts. Having depicted Marie Lebranchu as a hopelessly ill person, using the name of La Grivotte, he made her die on the train home! Yet, she lived in perfect health until 1920. Zola, unable to explain the cure at Lourdes which he had investigated, stated, "I do not believe in miracles: even if all the sick in Lourdes were cured in one instant I would not believe in them." Interestingly however, after witnessing several healings he no longer dismissed the evidence: "No, I do not, or, better, I cannot believe in the Lourdes miracles. What I have seen is amazing, grandiose and moving to the utmost degree, but ultimately explainable by the natural laws."

Interesting too is Jacalyn Duffin's response at the end of an interview on CBC's "The Current" (Oct 15/10 - Pt 1: Brother Andre; 13:50 minutes in). The interviewerconcludes by saying, "It does shake your faith as an atheist, I'm guessing?"
"Oh yes it does. And it makes me very happy."
She's not contemptuous of miraculous healings, whatever the explanation, and I'm betting that she's not contemptuous of those who believe their cause is supernatural--despite the fact she remains a naturalist.

I realize that anybody who wants to remain a naturalist must steadfastly resist the idea that "miracles" ever have a supernatural cause, however impressive the evidence. I respect that attitude, and think it can be justified by one's personal response to the problem of evil, by the fact that we don't know everything about nature, and by the fact that many strange things happen. But the conviction that miracles don't happen is not one that is rationally binding on everyone.

Sunday, April 17, 2011

Speaking of Delusions ....

I post this for entertainment purposes only.

Denyse O'Leary had a contest. She asked her readers to "predict Darwin's doom."
What do you see as the timeline for Darwinism to be replaced by a more inclusive theory of evolution? If ever. And if not, why not?
Today she announced the winning IDiot, it's someone named "Bantay at 10" (What in the world were its parent thinking when it was born?)

Here's the best prize-winning answer the IDiots could come up with. (Yes, folks, they are serious.)
5 years –
Significant scientific discoveries will enhance a relatively new scientific paradigm we know today as “ID” – As additional discoveries buttress a design framework from which new scientific discoveries can be predicted, we will see more scientists and materialists distance themselves from Darwinism (like Marulis and Fodor).

10 Years –
Significant numbers of academicians from biologists to astronomers, philosophers to office secretaries, will be talking about a design framework for the future of their scientific fields in a professional setting, without fear of legal reprisals.

20 years –
Someone will win a landmark legal case that will have a result of ID being shown to be good science, not religion. Scientists who are on the anti-ID side will be expelled from their jobs, suffer public embarrassment for their fearmongering (Barbara?) and will be regretting that they didn’t break ranks while the going was good. Also in 10 years, a movie will be made about the Dover trial and there will be renewed controversy when the credits roll “ACLU Document”

40 Years –
More than 50% of the Big Academy will be non-materialists and agnostics, with atheism showing a steady decline from it’s already lowly numbers to an even lesser significance. The beginnings of post-Darwinist history revisionism will rear its ugly head, with surviving Darwinist hold-outs fighting amongst themselves over who claimed what fossil was a precursor to man (but strangely will forget that none of them were).

60 Years – Darwinism will be relegated to a small, obscure paragraph in science text books, probably as a footnote. All of today’s living fundamentalist Darwinists will be dead, their Machiavellianism and unscientific fearmongering and back-pats a thing of the past. Meanwhile, the exciting world of science will be renewed with advances in technology that will enable scientists to reverse engineer the parts in the cell itself, helping to elucidate secrets of its design previously unknown. On the global design front, advances in technology will reveal orders of magnitude greater levels of design in the universe.

The Accommodationist Wars: Winston vs Harris

Robert Winston is a stem cell researcher with a strong interest in science education. Sam Harris is a neuroscientist who writes about the conflict between science and religion.

They recently debated whether science and religion are compatible [Is there any place for religious faith in science?].

This is part of the accommodationist wars. Winston argues that there is no conflict between one's personal religious belief and science.


one who adapts to or compromises with an opposing view

Mirriam-Webster Dictionary
This "war" is supposed to be about whether science and religion are in conflict or whether they are compatible. If they are compatible then it's perfectly reasonable for someone to support scientific reasoning as an important and valid way of knowing while, at the same time, believing the major tenets of some religion. However, as you can see in this debate, the accommodationist position is often confused. It's easy for them to forget the question and stray into other issues that upset them.

One of the things that upset accommodationists isn't the real question but whether it is polite or civil to "attack" the beliefs of legitimate scientists.

As Robert Winston puts it ...
You quote Collins in your book: "as I rounded a corner and saw a beautiful waterfall hundreds of feet high, I knew the search [for God] was over." You write, in commentary, "it is astounding that this passage was written with the intent of demonstrating the compatibility of faith and reason". But he is making his own personal judgement about his circumstances, not preaching to the world. Your writing is lovely, funny, but I don't think the denigration of a serious scientist like Collins does a lot of good. We should be very careful about criticising other scientists, except when their science is clearly at fault.
The problem for Winston is not really whether the scientific approach is consistent with evangelical Christianity but whether it is appropriate to even raise the issue because it "denigrates" compatibilists. As expected, Winston takes a few swaps at the attitude of the New Atheists.

The quotation from Winston also highlights another aspect of the accommodationist wars. Winston focuses on the ability of Francis Collins to "do science" as though that's what it's all about. ("But do his views detract from the outstanding work [Collins] has done?") This is not what the debate is about. As Sam Harris points out, there are Young Earth Creationists who do science but nobody would argue that Young Earth Creationism and science are compatible. Similarly, I have argued that there are scientists who believe in homeopathy and astrology but that does not make those subjects compatible with science.

The debate is about whether the principles of scientific reasoning are in conflict with the beliefs held by people of faith or whether the scientific way of knowing is compatible with another way of knowing that lies outside of science.

Whether one side or the other is being rude doesn't address the question. Whether a scientist can still pipette accurately while believing in silly things isn't relevant.

We need to keep the accommodationists focused on the main point and not on strawmen that have no bearing on the question. It's hard for us to do that but we need to keep trying.

[Photo Credit: David Levene:]

[Hat Tip:]

Friday, April 15, 2011

The Accommodationist Wars

Don't forget to join us tonight at the Fox & Fiddle, 27 Wellesley St., Toronto for an event sponsored by the Association for Science and Reason (ASR).

I'm going to be talking about The Accommodationist Wars.
Professor Moran will talk about the conflict between two types of atheists: those who think science and religion are not compatible, and those who think religion and science are not necessarily in conflict. The accommodationists believe it’s important to ally with moderate religious leaders to combat the intrusion of religious beliefs into our schools and political systems. An important part of this strategy is recognizing that science and religion can be compatible. The other side agrees that such alliances can be fruitful but that should not prevent atheists from speaking out against even moderate forms of religious belief. The National Center for Science Education (NCSE) in the USA is a prominent accommodationist organization and so are the science organizations such as the National Academies and the American Association for the Advancement of Science (AAAS). All of these organizations take a position on the compatibility of (some) religions. Many scientists think that these organizations should not be defending religion.

Thursday, April 14, 2011

Casey Luskin Is Confused (Again)

The IDiots have painted themselves into a corner and they don't know what to do. They have been ranting against "Darwinism" for so long that they've come to believe that their silly version of evolution is what is being taught in the schools. When scientists objected to the "Darwinist" version of evolution the IDiots assumed that this was an objection to evolution. Gradually it seems to be dawning on them that there are legitimate scientific debates over the mechanisms of evolution and the relative contributions of various processes. These controversies have nothing to do with the FACTS of evolution.

But now the IDiots are in a bind. They can't retreat by admitting that their characterization of evolution has been wrong for the past few decades. That would make them look foolish. On the other hand, they can't continue to ignore the fact that major critics of "Darwinism" (or the "Modern Synthesis" or "Neo-Darwinism") are strong supporters of evolution and opponents of creationism, including Intelligent Design Creationism. Oops!

What to do? Watch how Casey Luskin squirms as he tries to get out of the corner in Recant! Pushing Creeds as Damage Control for Darwin.
When writing in technical journals, evolutionary biologists like McPeek or Koonin admit stark problems with neo-Darwinian evolution--i.e.:


"The edifice of the modern synthesis has crumbled, apparently, beyond repair" (Koonin)

But when their criticisms are cited by a proponent of intelligent design, they quickly toe the materialist party line, designed to reassure the masses that the paradigm has everything in order. Thus, when called upon by the NCSE to publicly defend the paradigm, Koonin eagerly endorses Dobzhansky's creed. As Newton eagerly boasted:

As the geneticist Theodosius Dobzhansky famously said - and as Eugene Koonin explicitly agreed - "Nothing in biology makes sense except in the light of evolution."

Since when do creeds take precedence over the evidence?

None of this, however, changes the fact that Koonin, McPeek, and many other scientists are writing technical papers stating that the neo-Darwinian model is flawed at its very core. Koonin undoubtedly believes Dobzhansky's statement is true, but I doubt he would say "Nothing in biology makes sense except in the light of neo-Darwinism." Why, then, must this model be taught to students as unadulterated fact?
Do you see the strategy? The IDiots are going to claim that their silly misunderstanding of evolution ("Darwinism" or "neo-Darwinism") is the "fact" of evolution that's being taught in the schools. Thus, it's not their fault that their understanding of evolution is wrong—blame it on the evolutionary biologists.

Yeah, that'll work! :-)

The alternative is to admit that the IDiots are, well .... idiots. Don't hold your breath waiting for that to happen.

I suppose we should be happy that they are finally beginning to see the very problem we've been telling them about for 25 years. They simply don't understand the real scientific version of evolution.

[Image Credit: I got it from James Preller's Blog.]

Do Not Vote for the Anti-Science Green Party

There is no party platform that perfectly reflects my views on all issues. However, there is one thing I look for when deciding to support a political party and that's how they arrive at a particular policy. Is it scientific? Does the policy depend on evidence, healthy skepticism, and rational thinking?

The Green Party of Canada has outlined their platform in a document called Vision Green. Here's what they say in the introduction ...
Vision Green presents a well-researched analysis of critical environmental, economic and social challenges facing Canadians from coast to coast to coast, and presents practical solutions that can be achieved if there is the political will and leadership to take forward-looking action. It was developed by our Green Cabinet and was informed by experts, activists and citizens who participated in policy workshops held across Canada. Our vision is based on policies approved by the membership of the Green Party.
Sound promising. They don't actually say that their policies are based on sound scientific reasoning but it sounds like "well-researched" might be a synonym for "good science."

As you scan this document you encounter many positions that seem somewhat dogmatic and considerably beyond what the scientific evidence actually says. The Green Party is opposed to genetically engineered organisms, for example, and they propose to, "Phase out the use of genetically modified food products and ‘terminator’ seeds" (p. 74).

The Green Party is opposed to nuclear power and advocates a ban on new nuclear power plants and a shut-down of existing ones. The party proposes to ban uranium mining and refining. While some of their arguments are valid, the overall tone does not sound scientific.

But the real give-away comes when the document discusses health care. Here's one of the promises from page 70.
Provide funds to expand provincial health insurance to cover proven alternative therapies that are less expensive and invasive such as chiropractic, massage, acupuncture.
It is simply not true that these "alternative therapies" are proven in any scientific sense. What this tells me is that the Green Party platform is not based on scientific reasoning.

That's disappointing.

Everybody wants to promote good health. It's a motherhood issue. What's important is whether a political party has a realistic policy to achieve this goal. Most don't but the Green Party actually makes things worse ...
Health promotion is about more than health care or health education. It is about recognizing the profound health impacts of determinants of health outside the formal healthcare system and working with many stakeholders (policy-makers, NGOs, health agencies, multiple levels of government, the private sector, and most important, affected communities themselves) to reduce, eliminate, or overcome those factors that harm health or act as barriers to health enhancement, and to promote those factors that enhance the health, well-being and quality of life of all Canadians.

We will promote complimentary health care – through support of chiropractic, naturopathic, homeopathic, and other non-western practices. The Green Party of Canada recognizes the value of good health as a fundamental human right, and also the key to the most vibrant, inclusive and sustainable Canadian society possible.
I will never vote for a political party that promotes naturopathy and homeopathy in such a prominent manner. Naturopathy and homeopathy are examples of anti-science quack medicine. The fact that the leaders of the party would even include this in their platform tells me that scientific thinking is not part of their worldview and it calls into question their positions on everything else.

The Green Party wants to use my tax dollars to support these quacks.
Expand healthcare coverage to include qualified complementary/alternative health professionals such as naturopaths, acupuncturists, homeopaths, licensed massage therapists, chiropractors, and dietitians.
This is very wrong.

Do not vote for the Green Party. If you want to cast a protest vote then spoil your ballot or vote for some other party that cannot be elected in your riding. Every vote for the Green Party is a vote against science.

[Hat Tips: Zak at Canadian Atheist: The Green Party Platform and Mitchell Gerskup at Skeptic North: Voting Green? Read This.]

Monday, April 11, 2011

Hunting and Gathering in Washington D.C.



Her poster will be up tomorrow ...

Friday, April 08, 2011




Guess Who I'm Voting For?

Thursday, April 07, 2011

Springtime in Washington

I'm off to Washington D.C. on Saturday to attend the American Society for Biochemistry and Molecular Biology (ASBMB) 2011 Annual Meeting [ASBMB]. It's part of a larger meeting called Experimental Biology 2011.

One of the reasons for going is to get together with the other members of the editorial board of the Biochemistry and Molecular Biology Education journal [BAMBED].Many of them are fellow textbook authors.

There's going to be a wild party on Sunday night when we all get together to talk about the citric acid cycle and free energy.

I should have recovered by Monday noon in case anyone in the Washington area wants to meet up for some more exciting discussions about biochemistry and molecular biology.

Jonathan, Moonies, and Junk DNA

This video is supposed to support the evolution side versus the Intelligent Design Creationists. There are two major flaws in this presentation.

First, it spends too much time on the background of Jonathan Wells. While it's interesting to know where he's coming from, his motives are less important that the "scientific" case he's making. His religious motivation explains WHY he gets the science wrong but the important point is that the science IS wrong.

Second, it does a poor job of explaining the actual scientific controversy over the amount of junk DNA in our genome. It almost seems to imply that scientists don't believe in junk DNA.

This is a complicated issue. I don't expect the IDiots to get it right but I do expect scientists to explain it correctly.

IDiots vs Francis Collins

Here's a video where several IDiots take on Francis Collins and his book The Language of God,. Jonathan Wells is prominently featured in this video and much of the attack is concerned with junk DNA. Wells makes his position very clear. He claims that modern scientific evidence has overthrown the "myth" of junk DNA and those of us who still believe in junk DNA are guilty of a "Darwin of the gaps" kind of argument. That's because, according to Welles, we don't have an explanation for junk DNA therefore we attribute it to Darwinian evolution (6.00 minute mark).

There is a lot of positive evidence that much of the DNA in our genome is non-functional. Wells is dead wrong about this. Furthermore, assuming that this junk DNA is non-functional and assuming that species share a common ancestor, we can explain many observations about genomes. IDiots can't do this. They have yet to provide an explanation for shared pseudogenes1 in the chimp and human genomes, for example. And I haven't heard any IDiot explain why the primate genomes are chock full of Alu sequences derived from a particular rearranged 7SL RNA sequence while rodent genomes have SINES from a different rearranged 7SL sequence and lots of others from a tRNA pseudogene [Junk in Your Genome: SINES].

Did Francis Collins use the existence of junk DNA as support for Darwin's theory of evolution? Here's what Wells says in the video (50 second mark).
If fact he relies on so-called junk DNA—sequences of DNA that apparently have no function—as evidence that Darwin's theory explains everything we see in living things.
I searched in the The Language of God for proof that Wells is correct. The best example I could find is from pages 129-130 where Collins describes the results from comparing DNA sequences of different organisms. He points out that you can compare coding regions and detect similarities between humans and other mammals and even yeast and bacteria. On the other hand, if you look at non-coding regions the similarities fall off rapidly so that there's almost no similarity between human DNA and non-mammalian genomes (e.g. chicken). This is powerful support for "Darwin's theory of evolution" according to Francis Collins. First, because you can construct phylogenetic trees based on DNA sequences and ...
Second, within the genome, Darwin's theory predicts that mutations that do not affect function (namely, those located in "junk DNA") will accumulate steadily over time. Mutations in the coding regions of genes, however, are expected to be observed less frequently, since most of these will be deleterious, and only a rare such event will provide a selective advantage and be retained during the evolutionary process. That is exactly what is observed.
I leave it as an exercise for Sandwalk readers to figure out how to explain this observation if the regions that accumulate fixed mutations aren't really junk but functional DNA. Your explanation should consist of two parts: (1) why the DNA is functional even though the sequence isn't conserved (provide evidence)2, and (2) why coding regions show fewer changes and why comparisons of different species lead to a tree-like organization.

I wasn't able to find where in Origin of Species Darwin discuss this prediction but I'm sure it must be there somewhere. Perhaps some kind reader can supply the page numbers?

1. Every knowledgeable, intelligent biologist knows that pseudogenes exist and they are junk. That's not in dispute. I haven't heard any Intelligent Design Creationists admit that there are thousands of functionless pseudogenes in our genome.

2. I can think of two or three possibilities but no evidence to support them.

Monday, April 04, 2011

Toronto Skeptics in the Pub

Join us on Friday, April 15, 2011 at the Fox & Fiddle, 27 Wellesley St., Toronto for an event sponsored by the Association for Science and Reason (ASR).

The speaker will be me and the subject is The Accommodationist Wars.

What Is Intelligent Design Creationism? - Is It Science?

One of the common claims of Intelligent Design Creationists is that their creationist worldview is actually real science. What they do, according to this claim, is investigate nature looking for solid evidence of design. This usually involves some form of specified complexity or irreducible complexity. The "scientific" evidence of design, according to the creationists, means that God must have played a role in the creation of intelligent god-fearing humans.

In fairness, they often try to avoid stating the obvious implication of their "findings" in order to avoid criticism. They pretend that just proving the existence of intelligent design is as far as they go and the rest ("God did it") isn't really part of their movement. Nobody is fooled by this silliness.

Any objective view of the IDiot literature reveals that attacks on evolution constitute >99% of their activity. It's rare to find an article or book that presents a positive case for a creator design. Whenever you poke an IDiot with this fact they will almost always deny it, saying that Intelligent Design Creationism really is scientific—it's the scientific demonstration of design.

Denyse O'Leary knows better. She wonders, Are ID researchers making progress?. She's troubled by the fact that much of the literature is just attacks on evolution and positive contributions to intelligent design are few and far between. She has an explanation for this focus on attacking evolution. I repeat it here because it's one of the few honest appraisals of the goals of the movement.
I have thought about that one for a while, and now usually reply:

Because, just as bad money drives out good, bad ideas drive out good. Let us say your country’s carefully regulated money supply is assaulted by counterfeiters. Does it make more sense to start by exposing them or to just virtuously ignore them and continue to print good money – while they continue to print bad money?

Remember, they have no obligation to balance the money supply with available goods, but you do.


I too look forward to the day that ID researchers are free to do positive work, but right now we are swamped in a Darwinism whose fraudulence is often unrecognized because it is so often ridiculous. So, as with counterfeit money, the first goal is to demonstrate that much intellectual currency is bogus. Don’t accept it and don’t pass it on. And don’t imagine that everyone will want to know this. Quite the opposite.

So can good money ever drive out bad? Yes, but it is tough slogging.
I assume that the new book by Jonathan Wells will be mostly evolution-bashing. I'm not expecting to see any evidence of intelligent design.1

1. Yes, I know this can be taken two ways.

[Photo Credit: Canadian Writers Who Are Christian]

Saturday, April 02, 2011

Cat Bowling

Jerry Coyne posted this [Caturday felids: Lasers!] but I just have to put it on Sandwalk for others to see. You need a cat and a laser pointer ...

Carnival of Evolution #34

This month's Carnival of Evolution is hosted by Stephen Matheson at Quintessence of Dust [Carnival of Evolution: #34].

It's the April 1, 2011 version but don't be fooled. Some of the postings are serious!

Friday, April 01, 2011



Denyse O'Leary asks, "Interestingly, in the “nail dump is Ming vase” story, no one insists that nobody ever thought it was just another piece of junk. They almost always say, “Yes, we thought so but had no idea …” So what’s behind the failure to admit an error in this case?" It's hard to figure out what she means but I think she's wondering why biologists don't just admit they were wrong about junk DNA. Jonathan Wells interprets the question differently.
Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.”

This claim is easily disproved: Francis Crick and Leslie Orgel published an article in Nature in 1980 (284: 604-607) arguing that such DNA “is little better than junk,” and “it would be folly in such cases to hunt obsessively” for functions in it. Since then, Brown University biologist Kenneth R. Miller, Oxford University biologist Richard Dawkins, University of Chicago biologist Jerry A. Coyne, and University of California–Irvine biologist John C. Avise have all argued that most of our DNA is junk, and that this provides evidence for Darwinian evolution and against intelligent design. National Institutes of Health director Francis Collins argued similarly in his widely read 2006 book The Language of God.

It is true that some biologists (such as Thomas Cavalier-Smith and Gabriel Dover) have long been skeptical of “junk DNA” claims, but probably a majority of biologists since 1980 have gone along with the myth. The revisionists are misinformed (or misinforming).
It's in the best interests of the IDiots to promote the idea that all "Darwinists" believed in the "myth" of junk DNA and that it wasn't until the predictions of the IDiots were confirmed (not) that the biologists changed their minds.

The truth is somewhat different. Wells says, "Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.”" The truth is that the mainstream biologist community never, ever claimed that all non-coding DNA was junk. Most of them didn't even believe that a majority of our genome was junk.

The issue has come up many times over the past few years on blogs and newsgroups. The last time I took a poll was a few years ago and here are the results.

As you can see, there's a wide range of opinion among people who read Sandwalk. I think this is a pretty good reflection of the opinions of most biologists.

In responding to the question, Wells makes one serious error when he claims that biologists promoted junk DNA because it "provides evidence for Darwinian evolution." It does nothing of the sort. In fact, it goes against any prediction of Darwinian evolution by natural selection. The reason why the concept of (huge amounts of) junk DNA was resisted by so many biologists was because of this conflict.

Wells also says that junk DNA was promoted by some biologists because it "provides evidence ... against intelligent design." This is partly true, especially when the arguments center on conserved pseudogenes. That part of junk DNA (pseudogenes) is accepted by almost all biologists but it's only a tiny part of our genome. There is no evidence to suggest that pseudogenes are anything but junk and all the evidence indicates that we have thousands of them in our genome. (If they have a function then they aren't pseudogenes.)

Many mainstream biologists have supported the idea that a majority of our genome is junk. There's no denying that. I agree with them. None of them are changing their minds in spite of what Jonathan Wells is telling you. What Wells is doing is picking sides in a genuine scientific dispute. He could have done this 30 years ago and the result would have been the same. The genuine scientific controversy is not about to be resolved and there's no new evidence that seals the case one way or the other.

In my opinion, our genome is almost 90% junk DNA and that's the view that's going to win in the end.