Six Different Kinds of Slime Moulds

 
Which one doesn't belong on the list?

1. Myxogastrea
2. Dictyostelia
3. Protostelia
4. Buddenbrockia
5. Myxococcales
6. Labyrinthulea
7. Acrasea

Check out Catalogue of Organisms, The Diversity of Slime Moulds for the correct answer.

---

The Nature of Science: Is Science the only Way of Knowing?

In my course today I described science as a way of knowing based on evidence and rational thinking. The key point is that science is a process, or a way of thinking. Science—the process—is not confined to the "natural" sciences. It can be used in any type of investigation that's designed to seek factual knowledge about the universe we inhabit (see Sokal, 2008).

Are there any other ways of knowing? Well, that depends on what kind of knowledge you seek. If you're interested in "truth", which I loosely define as factually correct information, then my answer is no. The application of evidence and rationality is the only way to go.

Lots of people disagree. For the sake of discussion, I've selected some examples from an article on The Nature of Science and Scientific Theories published by the Arkansas Science Teachers Association 2006. They propose four different ways of knowing.

People have several ways that they know about their world.  The chart below lists some of the ways of knowing.  One way of knowing is no more valid that another to most people.  However, as you read the chart please note that science is a way of knowing that requires the use of certain rules and methods that differs from the other means of knowing.  Scientific knowledge limited to the natural world. Scientific knowledge and religious knowledge do not have to be contradictory.  It is important to know these differences, so that they can be complementary.

Religious Knowledge

• Seeks answers to any question that can be posed including answers to the ultimate questions (What is my purpose? What is the meaning of life? Is there a supreme being? etc.).
• Explanations can include supernatural forces.
• Is a belief system and seeks truths.

Philosophic Knowledge

• Seeks answers to any question that can be posed including answers to the ultimate (What is my purpose? What is the meaning of life? Is there a supreme being? etc.).
• Explanations can include supernatural forces and viewpoints
• Is a point of view and seeks truths.

Cultural Knowledge

• Seeks answers to any question that can be posed including answers to the ultimate questions (What is my purpose? What is the meaning of life? etc.), but generally relates to how people treat one another.
• Explanations can include supernatural forces and other historical viewpoints.
• May be a belief system rooted in historical views and seeks truths.

Science Knowledge

• Can only seek answers about the natural world but cannot answer ultimate questions (Is there a god? What is the meaning of life?).
• Explanations cannot include supernatural forces.
• Is not a belief system nor seeks truths.

Why can't the science way of knowing address questions like "Is there any evidence of purpose in evolution?" "Does life have any meaning?" and "Is there any evidence of Gods?" Why are these questions arbitrarily ruled out of bounds? Does it mean that we can't apply evidence and rationality to questions about the possibility of purpose?

If religious, philosophical and cultural knowledge can be "beliefs" or "points of view" then what kind of knowledge is that? These may be some sort of "ways of knowing" but knowing about what? Surely not factual knowledge of the sort that would be convincing to an impartial observer?

Finally, why are the other three "ways of knowing" referred to as ways of "seeking truths" but science is the only one that does NOT "seek truth"? What does the scientific way of knowing seek ... lies?

---

Sokal, Alan (2008) What is science and why should we care?, Third Annual Sense About Science lecture February 27, 2008, University College London (UK)

Nobel Laureate: Kurt Wüthrich

 

The Nobel Prize in Chemistry 2002.

"for his development of nuclear magnetic resonance spectroscopy for determining the three-dimensional structure of biological macromolecules in solution"



Kurt Wüthrich (1938 - ) received the 2002 Nobel Prize in Chemistry for his contribution to solving complex three-dimensional structures using nuclear magnetic resonance (NMR) spectroscopy. He made significant advances in the technique of using NMR to solve the structures of proteins. Here's the description in the press release.

At the beginning of the 1980s, Kurt Wüthrich developed an idea about how NMR could be extended to cover biological molecules such as proteins. He invented a systematic method of pairing each NMR signal with the right hydrogen nucleus (proton) in the macromolecule (see fig. 4). The method is called sequential assignment and is today a cornerstone of all NMR structural investigations. He also showed how it was subsequently possible to determine pairwise distances between a large number of hydrogen nuclei and use this information with a mathematical method based on distance-geometry to calculate a three-dimensional structure for the molecule.

The first complete determination of a protein structure with Wüthrich's method came in 1985. At present 15-20% of all the thousands of known protein structures have been determined with NMR. The structures of the others have been determined chiefly with X-ray crystallography; a few with other methods such as electron diffraction or neutron diffraction.

Wüthrich shared the 2002 Nobel Prize with John B. Fenn and Koichi Tanaka.

THEME:
Nobel LaureatesThe presentation speech was delivered in Swedish on December 10, 2002 by Professor Astrid Gräslund of the Royal Swedish Academy of Sciences,

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

What would life be without proteins! Proteins are large molecules that do almost all the work in our cells. Every living organism, including a human being, has a large array of various kinds of proteins. Like diligent worker bees, they take care of what needs to be done. In principle, it works the same in this flower as in me or you.

To learn more about the diligent workers inside of cells, we want to know how they look, in order to understand what they do. This year's Nobel Laureates in Chemistry have developed methods that enable us to weigh and create pictures of giant molecules like proteins in new ways that we could hardly believe were possible. I am convinced that biochemistry is now standing on the threshold of a new era – we are beginning to become acquainted with the complete genetic code of many organisms. Soon we will be able to survey all the thousands of protein varieties that work simultaneously in a given cell. It is in this new era that the discoveries of the 2002 Nobel Laureates are so important.
Mass spectrometry has been part of the chemist's toolkit for identifying small molecules since the beginning of the 20th century. But for many years, being able to make accurate measurements of the molecular masses of large proteins was a dream for chemists. For this reason, it caused a minor revolution in the field when John Fenn and Koichi Tanaka, each in his own way, succeeded to making intact proteins fly through the mass spectrometer.

Fenn discovered that it was possible to spray a water solution of the protein, in the presence of an electrical field, in order to obtain hovering electrically charged drops. The water evaporates and the drops are scattered by their electrical charge, becoming smaller and smaller. Finally only pure protein molecules are left. Then their mass is determined by measuring the time it takes them to accelerate across a given distance – the principle being that the heavier the molecule is, the more slowly it moves.

Tanaka's special method was to fire a laser pulse toward the sample. With the right wavelength in the laser, he could make the proteins be released from their surroundings without falling apart, so that they hovered freely as charged particles. Their mass could then also be determined by measuring their time of flight.

This was one half of the year's Chemistry Prize – now I will move to the second half. This time it is not a matter of flying proteins, but swimming proteins. Using nuclear magnetic resonance, or NMR, a method that Kurt Wüthrich has further refined, it is now possible to determine the three-dimensional structure of protein molecules in a water solution. NMR is one of the chemist's best methods for examining molecules, and it has been used extensively for small molecules since the mid-20th century. But large molecules like proteins involve special problems. One of the fine points of NMR is that it enables us to see individual signals, for example, from each hydrogen nucleus in a molecule. But because a protein can contain thousands of hydrogen nuclei, how do you know which signal belongs to which nucleus?

Wüthrich devised a way of systematically determining how each signal fits together with its special hydrogen nucleus. In the bargain, he was also able to determine a large number of pairwise distances between hydrogen nuclei. This enabled him to calculate a three-dimensional structure for the protein molecule. It is something like drawing a picture of a house if you know a large number of distances in the house. So thanks to Wüthrich's discovery, we can now use NMR to examine and depict proteins in their natural environment, surrounded by water like in a cell.

So, what would life be without proteins? Since I view the world through the eyes of a biochemist, my answer is: nothing at all! Next question: How would life be as a biochemistry researcher without the tools that this year's Nobel Laureates have given us? My answer to this question is: much more difficult, and also more dull! So I would like to conclude by saying to the 2002 Nobel Laureates in Chemistry: Thank you for your fantastic contributions, which help us to better understand the chemical miracles that constantly occur in our cells – what we call life.

Dr. Fenn, Mr. Tanaka and Dr. Wüthrich,

You have made pioneering contributions to the development of methods for identification and structure analyses of biological macromolecules. Your work to make mass spectrometry and NMR applicable for detailed studies of large molecules like proteins has given us new tools for investigations of the processes that constitute life. In recognition of your services to chemistry, the Royal Swedish Academy of Sciences has decided to confer upon you this year's Nobel Prize in Chemistry.

On behalf of the Academy, I convey to you our warmest congratulations and I now ask you to receive the Prize from the hands of His Majesty the King.

---

Monday's Molecule #87

 
This could be difficult so I'll give you a few clues. This molecule is secreted and it's function is to degrade nucleic acid. I want the name of the molecule and also a brief description of the image you see on the left. What is it showing?

There's a indirect connection between the image of today's molecule and a Nobel Prize. We are looking for the single person most responsible for the particular kind of image you see here.

The first person to correctly identify the molecule and name the Nobel Laureate, wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward. You know who you are.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: This week's winner is Dima Klenchin of the University of Wisconsin. The molecule is bovine ribonuclease and the image depicts the different conformations of the molecle in solution as solved by NMR. The Nobel Laureate is Kurt Wüthrich. Congratulations Dima!

---

Denyse O'Leary Is a "Top-flight Science Journalist"

 
Now that I've got your attention, let me explain.

Deborah Gyapong—that's her on the right—has a blog called Deborah Gyapong (of course). According to her profile ...

Deborah Waters Gyapong’s journalism career spans more than 20 years in television, print and radio, including 12 years as a producer for the Canadian Broadcasting Corporation’s television news and current affairs programming. Deborah now covers religion and politics primarily for Roman Catholic and Evangelical newspapers.

In a recent posting, Denyse O'Leary takes Rob Breakenridge to task, she comments on the op-ed article that Denyse published in the Calgary Herald (See Intelligent Design Creationism Is Just Anti-Evolutionism). Here are two quotations about Denyse O'Leary written by Deborah Gyapong.

Denyse, who is an expert on the various theories of evolution and intelligent design and a top-flight science journalist, ...

Denyse is the EZ [Ezra Levant] of intelligent design, i.e. she is well-informed, rational, and will eat you for breakfast if you don't have a logical, well-presented, well-researched factual argument.

No comment is necessary except to note that science journalism is in even worse shape that I imagined.

---

[Hat Tip: Eamon Knight in the comments section of The Big Tent Springs a Leak.]

Teaching Both Sides of the Controversy

 
I found this on Sneer Review [Teach Both Sides Of The Controversy - part 2]. It's an accurate portrayal of the weight of evidence for evolution and for Intelligent Design Creationism. So, what are we afraid of?


What we're afraid of is that the controversy won't be taught properly. I think we need to make this clear. Scientists aren't the least bit afraid of going head-to-head with any form of creationism. Teaching critical thinking and analyzing controversies is a valid part of science education and, if done properly, it can be a wonderful way to learn.

But that's not what's going to happen when creationist teachers cover evolution. They are not going to teach the controversy. They are going to teach lies about science. Teaching the controversy only applies to qualified teachers who are knowledgeable about their subject.

Let's not get trapped into opposing critical thinking and controversy. Let's focus on making sure that teachers are qualified to teach the curriculum.

---

The Big Tent Springs a Leak

 
It doesn't happen very often but every now and then some of the Intelligent Design Creationists slip up by not keeping on message. Here's an example of Denyse O'Leary revealing that there's a wee bit of difference between "Evolutionary Creation" and "Intelligent Design Creation" [ Evolutionary Creationism? I am supposed to promote THAT?].

She refuses to promote a book called Evolutionary Creation: A Christian Approach to Evolution by Denis Lamoureux because he had the audacity to criticize Michael Behe.

I have had several conversations with Lamoureux, and he has struck me as a typical fatuous sellout of the decaying “evangelical Christian” culture that currently helps to deform Canada.

Earth to Lamoureux: Darwin is not the answer to any problem we now have. There is NO need to figure out how to incorporate him into our life together.

Just forget him and start figuring out what really happened in the history of life. Stop attacking people who know that Darwinism - and all its works - is false.

Hmmm ... many the wedge strategy is working after all.

---

Science Writers Need Science History

 
Carl Zimmer does it again! This time he shows why he's the best science writer by getting three things right in the same article: (1) junk DNA, (2) the existence of regulatory sequences isn't news, and (3) history is important [Science Writers Need Science History].

I bet he reads the blogs [What's Wrong wiht Modern Science?] [Junk in Your Genome: Protein-Encoding Genes] [Stop the Press!!! ... Genes Have Regulatory Sequences!].

---

Into the Textbooks It Goes

 
This week's issue of Science contains an important paper.

Maier, T,, Leibundgut, M. and B. Nenad (2008) The Crystal Structure of a Mammalian Fatty Acid Synthase. Science 321:1315-1322.

We've known for a long time that this is a very important enzyme and that it's a classic example of a little protein machine combining the activities of may different enzymes in order to carry out the complex reactions of fatty acid synthesis. Here's how I described it in the last edition of my book ...

In bacteria, each reaction in fatty acid synthesis is catalyzed by a discrete monofunctional enzyme. This type of pathway is known as a type II fatty acid synthesis system (FAS II). In animals, the various enzymatic activities are localized to individual domains in a large multifunctional enzyme and the complex is described as a type I fatty acid synthesis system (FAS I). The large animal polypeptide contains the activities of malonyl/acetyl transferase, 3-ketoacyl-ACP synthase, 3-ketoacyl–ACP reductase, 3-hydroxyacyl–ACP dehydratase, enoyl–ACP reductase, and thioesterase. It also contains a phosphopantetheine prosthetic group (ACP) to which the fatty acid chain is attached. Note that the malonyl CoA:ACP transacylase enzyme shown in Figure 16.3 is replaced by a transferase activity in the FAS I complex. This transferase catalyzes a substrate loading reaction where malonyl CoA is covalently attached to the ACP-like domain on the multienzyme polypeptide chain. The eukaryotic enzyme is called fatty acid synthase.

The structure (shown below) will be going right into the textbooks.

---

Citation Classic: Recombinant DNA

 
Read John Dennehy's citation classic for this week at This Week's Citation Classic: Genetic Engineering. The paper is one of the first examples of genetic engineering and recombinant DNA technology. Before you go, try and guess when the paper was published. Was it before you were born or after?

---

[Photo Credit: Protesters at the National Academy of Sciences Forum on Recombinant DNA from The Maxine Singer Papers]

Sue Blackmore on Teaching Critical Thinking

 
Susan Blackmore is an interesting person. According to her Website ...

Sue Blackmore is a freelance writer, lecturer and broadcaster, and a Visiting Lecturer at the University of the West of England, Bristol. She has a degree in psychology and physiology from Oxford University (1973) and a PhD in parapsychology from the University of Surrey (1980). Her research interests include memes, evolutionary theory, consciousness, and meditation. She practices Zen and campaigns for drug legalization.

Sue Blackmore no longer works on the paranormal.

Yesterday she published an article in The Guardian (UK) [Opening Minds].

Should science teachers in Britain challenge their students' religious beliefs? Is it their right? Is it even their duty?

I say yes. This is (amongst much else) what education is for; to teach children how to think for themselves. And thinking for yourself is challenging, especially if your previous beliefs were based on dogma and ancient books.

This may illustrate one of the ways that education in the UK differs from that in the USA.

I don't mean that science teachers should belittle religious beliefs, or scoff at them, or even tell students they are wrong. They need not even mention religion or creationism. What they must do is explain so clearly how natural selection works that those students, like one or two in Dawkins' series, begin to feel the terrifying impact of what Darwin saw. This realisation will change them. It will challenge what mummy and daddy told them, it will cry out against what they heard in chapel or synagogue or mosque. It will help immeasurably in their ponderings on human nature, the origins of life and the meaning of existence. This is growing up. This is learning. This is the process that skilful science teachers need to initiate, encourage, and help sensitively to guide.

They should never shy away from challenging their students' religious beliefs and opening their minds, because understanding the world through science inevitably does just that.

I'm all for challenging students to think. Problem is, you'd better make sure you know what you're talking about. I'd like to challenge Sue Blackmore to stop thinking about Darwin, Dawkins and natural selection and start thinking about the 21st century version of evolution.

Next question is, how do we evaluate students in such a course? Can they still pass if they reject evolution and critical thinking?

---

[Hat Tip: RichardDawkins.net]

The Earth's Axis Has Shifted by 26°!

 
Friday's Urban Legend: FALSE

Today's dose of non-critical thinking comes from the August 9th issue of New Scientist [Tilting Earth Cover up].

WORRIED by hurricanes, earthquakes and volcanoes? Wondering what to blame? Would you believe that these have all been linked to the Earth's axis shifting by 26 degrees in two stages, one in late 2004 and one in early 2005?

How is it, you may well ask, that you didn't notice? It's because the US government covered it up, as you will learn at http://axischange.wordpress.com. Apparently the Global Positioning System broke down at these times and it was kept secret.

Even bigger laughs can be had at Divulgence.net.

Apparently Phil Plait of Bad Astronomy dealt with this issue some time ago.

Bad Astronomy points out that if the Earth's axis had shifted that much, we would have been in sunlight at midnight, whereas in fact it was quite definitely dark. What's more, even if we didn't look out of the window, we would surely have spotted the satellite TV blinking off as the satellite dishes ceased to point to where the satellites are.

I'd like to link to Phil's posting on this issue—does anyone have a URL? Here's the link to Bad Astronomy [Tilt!]

---

Knowing How to Learn

The August 9, 2008 issue of New Scientist contains an important commentary by A.C. Graying on The importance of knowing how.

The key point is in the third paragraph ...

So although everyone coming out of an educational system should at least know the periodic table, the salient dates of world history, the fundamentals of geography, and other kinds of basic information, they are much more in need of knowing how to find things out, how to evaluate the information they discover, and how to apply it fruitfully. These are skills; they consist in knowledge of how to become knowledgeable.

I agree with this statement. The most important goal of a university education is, in my opinion, to teach students how to think. An important part of that goal is teaching students how to acquire reliable information.

Knowing how to evaluate information, therefore, is arguably the most important kind of knowledge that education has to teach. Some schools offer courses in it, and there are a number of books about it on the market. But only the International Baccalaureate makes critical thinking ("theory of knowledge") a standard requirement, and in this as in so many ways it leads the field, because critical thinking and evaluation of claims to knowledge should always be right at the centre of the educational enterprise.

I'm not so sure that the IB program is the only one that teaches critical thinking but I agree with the general idea here. I think every university should require that students take certain courses on logic and knowledge. These courses should be taught by philosophers.

I wonder whether the need for critical thinking lessons is more urgent in the humanities than the sciences because the latter, by their nature, already have it built in. The science lab at school with its whiffs, sparks and bangs is a theatre of evaluation; the idea of testing and proving is the natural order there, and the habits of mind thus acquired can be generalised to all enquiry.

When we talk of scientific literacy, one thing we should mean is acquisition of just this mindset; without it, too much rubbish gets through.

Hmm ... I don't think I would have had the gumption to claim that science students may be better at critical thinking than humanities students. I may think it, but writing it is a different story.

If true, the problem may be related to what passes for "postmodernism" in the humanities. Believe it or not, there are humanities Professors whose ideas about critical thinking are quite bizarre. I've met some of them. They think it's wrong to pick a side in an intellectual dispute because all sides are equally valid. They think that we can't really "know" anything. For them, I guess "knowing how to learn" is an oxymoron.

---

[Photo Credit: Professor A.C. Grayling, Professor of Philosophy, Birkbeck, University of London UK.]

Is Your Name Steve or Stephanie?

 
If you answered "yes" to that question then you are one third of the way toward winning a huge prize. All you have to do is answer "yes" to two more questions: (1) do you have a Ph.D., (2) do you agree with the following statement ...

Evolution is a vital, well-supported, unifying principle of the biological sciences, and the scientific evidence is overwhelmingly in favor of the idea that all living things share a common ancestry. Although there are legitimate debates about the patterns and processes of evolution, there is no serious scientific doubt that evolution occurred or that natural selection is a major mechanism in its occurrence. It is scientifically inappropriate and pedagogically irresponsible for creationist pseudoscience, including but not limited to “intelligent design,” to be introduced into the science curricula of our nation’s public schools.

Check out Panda's Thumb for more details about Project Steve [Looking for Dr. 900].¹

---

1. You don't have to be American (I think).

Critical Thinking Skills in Science

 
I start teaching a course next week on misconceptions and controversies in science. One of the goals is to teach critical thinking skills. I think we'll start out by discussing the objectives of the recently passed law in Louisiana. It looks like a good description of what we should be trying to do in university and it has the added advantage that we can segue right into creationist lies, cynicism, and hypocrisy.

AN ACT

To enact R.S. 17:285.1, relative to curriculum and instruction; to provide relative to the teaching of scientific subjects in public elementary and secondary schools; to promote students' critical thinking skills and open discussion of scientific theories; to provide relative to support and guidance for teachers; to provide relative to textbooks and instructional materials; to provide for rules and regulations; to provide for effectiveness; and to provide for related matters.

Be it enacted by the Legislature of Louisiana:

Section 1 R.S. 17:285.1 is hereby enacted to read as follows:

285.1 Science education; development of critical thinking skills

A. This Section shall be known and may be cited as the "Louisiana Science Education Act."

B. (1) The State Board of Elementary and Secondary Education, upon request of a city, parish, or other local public school board, shall allow and assist teachers, principals, and other school administrators to create and foster an environment within public elementary and secondary schools that promotes critical thinking skills, logical analysis, and open and objective discussion of scientific theories being studied including evolution, but not limited to evolution, the origins of life, global warming, and human cloning.

     (2) Such assistance shall include support and guidance for teachers regarding effective ways to help students understand, analyze, critique, and objectively review scientific theories being studied, including those enumerated in Paragraph (1) of this Subsection.

C. A teacher shall teach the material presented in the standard textbook supplied by the school system and thereafter may use supplemental textbooks and other instructional materials to help students understand, analyse, critique and review scientific theories in an objective manner, as permitted by the city, parish, or other local public school board.

D. This Section shall not be construed to promote any religious doctrine,promote discrimination for or against a particular set of religious beliefs, or promote discrimination for or against religion or nonreligion.

E. The State Board of Elementary and Secondary Education and each city, parish, or other local public school board shall adopt and promulgate the rules and regulations necessary to implement the provisions of this Section prior to the beginning of the 2008/2009 school year.

I ain't no lawyer but to me it looks like this is going to be a hard law to challenge in court. We all know its purpose—to promote religion—but its authors may have done a good job of phrasing it in a way that avoids a challenge.

Any lawyers out there?

---