What's in Your Genome?

The total size of the human genome is estimated to be 3.2 × 10⁹ bp [How Big Is the Human Genome?]. Here are the major components.

Transposable Elements: (44% junk)

   DNA transposons:

• active (functional): <0.1%


• defective (nonfunctional): 3%

   retrotransposons:

• active (functional):<0.1%


• defective transposons
              (full-length, nonfunctional): 8%
              L1 LINES (fragments, nonfunctional): 16%
              other LINES: 4%
              SINES (small pseudogene fragments): 13%


• co-opted transposons/fragments: <0.1% ^a

  ^aCo-opted transposons and transposon fragments are those that have secondarily acquired a new function.

Viruses (9% junk)

   DNA viruses

• active (functional): <0.1%


• defective DNA viruses: ~1%

   RNA viruses

• active (functional): <0.1%


• defective (nonfunctional): 8%


• co-opted RNA viruses: <0.1% ^b

  ^bCo-opted RNA viruses are defective integrated virus genomes that have secondarily acquired a new function.

Pseudogenes (1.2% junk)

• (from protein-encoding genes): 1.2% junk
• co-opted pseudogenes: <0.1% ^c

  ^cCo-opted pseudogenes are formerly defective pseudogenes those that have secondarily acquired a new function.

Ribosomal RNA genes:

• essential 0.22%
• junk 0.19%

Other RNA encoding genes

• tRNA genes: <0.1% (essential)


• known small RNA genes: <0.1% (essential)


• putative regulatory RNAs: ~2% (essential)

Protein-encoding genes: (9.6% junk)

• transcribed region:
              essential 1.8%
              intron junk (not included above) 9.6% ^d

  ^dIntrons sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.

Regulatory sequences:

• essential 0.6%

Origins of DNA replication

• <0.1% (essential)

Scaffold attachment regions (SARS)

• <0.1% (essential)

Highly Repetitive DNA (2% junk)

• α-satellite DNA (centromeres)
• essential 1.0%
• non-essential 2.0%
• telomeres
• essential (less than 1000 kb, insignificant)

Intergenic DNA (not included above)

• conserved 2% (essential)
• non-conserved 26.3% (unknown but probably junk)

Theme Genomes & Junk DNATotal Essential/Functional (so far) = 7.7% Total Junk (so far) = 65% Unknown (probably mostly junk) = 27.3%

For references and further information click on the "Genomes & Junk DNA" link in the box

LAST UPDATES: May 10, 2011 (fixed totals, and ribosomal RNA calculations)
June 3, 2011 (added total genome size)
February 5, 2013 (reformatted)

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Junk & Jonathan: Part 3—The Preface

Here's the preface to The Myth of Junk DNA by the IDiot, Jonathan Wells. After each paragraph I've inserted a short version of the truth just so you don't get misled by all the untruths and distortions that are found in creationist books.

See:

Junk & Jonathan: Part I—Getting the History Correct

Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?

Jonathan, Moonies, and Junk DNA

The discovery in the 1970s that only a tiny percentage of our DNA codes for proteins prompted some prominent biologists at the time to suggest that most of our DNA is functionless junk. Although other biologists predicted that non-protein-coding DNA would turn out to be functional, the idea that most of our DNA is junk became the dominant view among biologists.

• It's true that in the 1970s the experts in the study of genomes proposed that most of our genome is junk.
• It's not true that they thought non-coding DNA had no function. Functions of non-coding DNA were well-established by 1970.
• The idea that most of our genome is junk was never the "dominant" view among biologists even though it's correct.

That view has turned out to be spectacularly wrong. Since 1990--and especially after completion of the Human Genome Project in 2003--many hundreds of articles have appeared in the scientific literature documenting the various functions of non-protein coding DNA, and more are being published every week.

• It's not true that the idea of a large amount of junk DNA has turned out to be "spectacularly wrong."
• It's true that there have been lots of examples of of novel functions for small pieces of the genome that were previously lumped into the junk DNA category. These dozens of functional parts of the genome may amount to as much as 1-2% of the genome (probably less).

Ironically, even after evidence for the functionality of non-protein coding DNA began flooding into the scientific literature, some leading apologists for Darwinian evolution ratcheted up claims that "junk DNA" provides evidence for their theory and evidence against intelligent design. Since 2004, biologists Richard Dawkins, Douglas Futuyma, Kenneth Miller, Jerry Coyne and John Avise have published books using this argument. So have philosopher of science Philip Kitcher and historian of science Michael Shermer. So has Francis Collins, former head of the Human Genome Project and present director of the National Institutes of Health, despite the fact that he co-authored some of the scientific articles providing evidence against "junk DNA."

• It's true that well-established bits of junk DNA—like known pseudogenes—have been effectively used to challenge the idea that our genome appears designed. Those examples remain powerful, and true, examples of evolution that cannot be explained by Intelligent Design Creationism. They have not been refuted and they have not been explained by the IDiots.

These authors claim to speak for "science," but they have actually been promoting an anti-scientific myth that ignores the evidence and relies on theological speculations instead. For the sake of science, it's time to expose the myth for what it is.

• The truth is that those authors still speak for science and truth and their evidence is sound.
• Wells, on the other hand, speaks for the other side.

Theme

Genomes
& Junk DNA

Far from consisting mainly of junk that provides evidence against intelligent design, our genome is increasingly revealing itself to be a multidimensional, integrated system in which non-protein-coding DNA performs a wide variety of functions. If anything, it provides evidence for intelligent design. Even apart from possible implications for intelligent design, however, the demise of the myth of junk DNA promises to stimulate more research into the mysteries of the genome. These are exciting times for scientists willing to follow the evidence wherever it leads.

• It's certainly true that non-coding DNA performs a wide variety of functions. Some of them are listed in various postings under Genomes & Junk DNA
• It's certainly not true that the organization of our genome—the majority of which is junk—provides evidence of intelligent design.
• It's certainly not true that the idea of junk DNA is a myth.
• It's true that these are exciting times and that smart people must follow the evidence wherever it leads even if it refutes cherished religious beliefs.

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[Hat Tip: Preface to The Myth of Junk DNA by Jonathan Wells]

Carnival of Evolution #35

This month's Carnival of Evolution (35th version) is hosted by Lab Rat at Lab Rat [The Carnival is here!]. ("Lab Rat" isn't really a rat. She's a biochemistry undergraduate who works on bacteria.)

Here are the subtitles ...

• The Ecologists


• The Plant Scientists


• The Computer Scientists


• The Microbiologists


• The Medical Scientists


• The Archaeologists and Anthropologists


• The Social and Political Scientists

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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.

Evolutionary studies apply to most branches of science, including organic evolution, cosmic evolution, geologic evolution, planetary evolution, and cultural evolution. Each of these subdisciplines of science provides evidence that evolution is pervasive: galaxies have changed, stars and planets have changed, Earth has changed, life forms on Earth have changed, and human culture has changed. Evolution is therefore factual and is a unifying concept of the natural sciences. For this reason, the National Science Education Standards (NRC), Benchmarks for Science Literacy (AAAS), numerous national education policy documents, and individual states, through their published science education frameworks, all recognize that evolution is a unifying concept for science disciplines and provides students with the foundation to help them understand the natural world. NAGT fully agrees with and supports the scientific validity of evolution as reflected in the position statements of the numerous scientific societies that unanimously support evolution on scientific grounds. NAGT further maintains that the scientific theory of evolution should be taught to students of all grade levels as a unifying concept without distraction of non-scientific or anti-scientific influence.

Published and reaffirmed position statements on the scientific validity of evolution by all of the scientific societies clearly demonstrate that the modern scientific community no longer debates whether evolution has occurred. Scientific investigation of the mechanisms of evolution and the interconnected "details" of mechanism, process, history, and outcome remain at the current scientific forefront of evolutionary studies. This is the nature of scientific inquiry itself: to continually evaluate scientific theories with an eye towards improving our scientific models and adding more details to our understanding of the natural world. Scientists often disagree about explanations of how evolution works, the importance of specific evolutionary processes, or the patterns that are observed, but all agree that evolution has occurred and is occurring now. Global change will be the future projection of past and ongoing evolutionary processes. While evolution is factual, evolution is also a "scientific theory", which is an explanation for the observed changes. This usage of theory should not be confused with the non-scientific usage of theory as an ad-hoc idea unsupported by testing or evidence.

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.

As stated in NAGT's Constitution, the purpose of the NAGT is to foster improvements in the teaching of the earth sciences at all levels of formal and informal instruction, to emphasize the relevance and cultural significance of the earth sciences, and to disseminate knowledge in this field to educators and the general public. The NAGT fully accepts its role in the evaluation and betterment of the teaching of scientific evolution in formal and informal educational settings, with the explicit goal of helping everyone to understand the scientific merit this fundamental concept has in modern science. The Journal of Geoscience Education publishes papers related to research concerning the pedagogy, assessment, history, philosophy and culture of teaching and learning about the geosciences, especially of fundamental concepts like geologic time and faunal and stratigraphic succession, all aspects of evolution.

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Pray for Texas

TO ALL TO WHOM THESE PRESENTS SHALL COME:

WHEREAS, the state of Texas is in the midst of an exceptional drought, with some parts of the state receiving no significant rainfall for almost three months, matching rainfall deficit records dating back to the 1930s; and

WHEREAS, a combination of higher than normal temperatures, low precipitation and low relative humidity has caused an extreme fire danger over most of the State, sparking more than 8,000 wildfires which have cost several lives, engulfed more than 1.8 million acres of land and destroyed almost 400 homes, causing me to issue an ongoing disaster declaration since December of last year; and

WHEREAS, these dire conditions have caused agricultural crops to fail, lake and reservoir levels to fall and cattle and livestock to struggle under intense stress, imposing a tremendous financial and emotional toll on our land and our people; and

WHEREAS, throughout our history, both as a state and as individuals, Texans have been strengthened, assured and lifted up through prayer; it seems right and fitting that the people of Texas should join together in prayer to humbly seek an end to this devastating drought and these dangerous wildfires;

NOW, THEREFORE, I, RICK PERRY, Governor of Texas, under the authority vested in me by the Constitution and Statutes of the State of Texas, do hereby proclaim the three-day period from Friday, April 22, 2011, to Sunday, April 24, 2011, as Days of Prayer for Rain in the State of Texas. I urge Texans of all faiths and traditions to offer prayers on that day for the healing of our land, the rebuilding of our communities and the restoration of our normal way of life.

IN TESTIMONY WHEREOF, I have hereunto signed my name and have officially caused the Seal of State to be affixed at my Office in the City of Austin, Texas, this the 21st day of April, 2011.

RICK PERRY
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.

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[Office of the Governor]

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.

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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.

4. PATHWAYS AND TRANSFORMATIONS OF ENERGY AND MATTER:

Biological systems grow and change by processes based upon chemical transformation pathways and are governed by the laws of thermodynamics.

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.

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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.

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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.

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Core Concepts: Evolution

The AAAS document, Vision and Change in Undergraduate Biology Education, defines five core concepts for biological literacy. Evolution is at the top of the list, right where it belongs.

1. EVOLUTION:

The diversity of life evolved over time by processes of mutation, selection, and genetic change. Darwin’s theory of evolution by natural selection was transformational in scientists’ understanding of the patterns, processes, and relationships that characterize the diversity of life. Because the theory is the fundamental organizing principle over the entire range of biological phenomena, it is difficult to imagine teaching biology of any kind without introducing Darwin’s profound ideas. Inheritance, change, and adaptation are recurring themes supported by evidence drawn from molecular genetics, developmental biology, biochemistry, zoology, agronomy, botany, systematics, ecology, and paleontology. A strong preparation in the theory of evolution remains essential to understanding biological systems at all levels.

Themes of adaptation and genetic variation provide rich opportunities for students to work with relevant data and practice quantitative analysis and dynamic modeling. Principles of evolution help promote an understanding of natural selection and genetic drift and their contribution to the diversity and history of life on Earth. These principles enable students to understand such processes as a microbial population’s ability to develop drug resistance and the relevance of artificial selection in generating the diversity of domesticated animals and food plants.

I would have written a different description—one that placed emphasis on Darwin's contribution but did not imply that his views represent modern evolutionary theory. I would also have mentioned genetics, especially population genetics, as the key to understanding modern evolution.

Nevertheless, one can't argue that evolution is the number one core concept in the biological sciences. Are we teaching it correctly in undergraduate courses. No, we are not. Are we teaching it enough in our undergraduate courses? No, again.

I think the main problem was completely ignored by the committee that drew up this document. The problem is that most professors don't understand evolution well enough to integrate this core concept into their courses. It's not enough for everyone to agree that evolution is a core concept. You also have to understand the core concept in order to teach it properly.

I see evidence in the description above suggesting that even the committee members were fuzzy on the core concept. What, for example, is "the theory of evolution"?

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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

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1. Bruce was my Ph.D. supervisor.

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

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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.

http://www.cbc.ca/thecurrent/2010/10/oct-1510---pt-1-brother-andre.html

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.

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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.

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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.

accommodationist

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.

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[Photo Credit: David Levene: guardian.co.uk]

[Hat Tip: RichardDawkins.net]