EXPELLED! - Waiting for the Creationists to repsond ...

 
By now you've all heard the news. PZ Myers was standing in line to see a screening of the propaganda movie EXPELLED when security guards asked him to leave. They didn't bother with his family or his friend, Richard Dawkins. Read PZ's account at EXPELLED!.

Now let's see how the creationists respond to this incident. Remember, the movie is about discrimination by scientists against people who are religious. It will be very interesting to see how they can justify keeping PZ Myers out of the movie when all kinds of other people were let in.

Here's one response, posted on the EXPELLED website [Richard Dawkins crashes the party at a screening of “Expelled”]. The writer is Stuart Blessman, a Christian who was given tickets to see the movie by his pastor. Blessman was present at the theater on Wednesday evening. He is responding to the charge that PZ Myers was prevented from seeing the movie because he (PZ) is an evolutionist. Here's what Stuart Blessman says ...

I just happened to be standing directly in line behind Dawkins’ academic colleague. Management of the movie theatre saw a man apparently hustling and bothering several invited attendees, apparently trying to disrupt the viewing or sneak in. Management then approached the man, asked him if he had a ticket, and when he confirmed that he didn’t, they then escorted him off the premises. Nowhere was one of the film’s producers to be found, and the man certainly didn’t identify himself. If a producer had been nearby, it’s possible that he would have been admitted, but the theatre’s management didn’t want to take any chances.

This sounds very much like a blatant, bare-faced, lie. Anyone who knows PZ Myers would know that he would bot be "hustling" and "bothering" the people waiting in line. Quite the contrary, PZ and his colleague Richard Dawkins would have been trying to keep a low profile.

In his followup posting, PZ responds by saying that Blessman's account is a complete fabrication [A late night quick one].

Now, I'm going to be looking in on creationist blogs to see how they handle this story. So far there has been deathly silence. Is that because the creationists are embarrassed? Is it because they never criticize their own kind? Or, is it because they don't see the hypocrisy? Please let me know of any creationist responses.

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Communicating Science in a Religious America

 
"Communicating Science in a Religous America" was the title of a session at the AAAS meeting in February. Here's a summary of the meeting from someone who seems to have been paying attention [Puttin Science in a Frame]. Here's a teaser ...

Framing has not been without controversy, as some have viewed it as little more than a form of empty platitude or an attempt to dumb down science. What became clear from Nisbet's talk, however, is that there can also be people left out of the ostensibly-shared values; it should be no surprise they are objecting.

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Going Public with the Scientific Process

 
Ruth Cronje is a faculty member of the Scientific and Technical Writing Program at the University of Wisconsin-Eau Claire in Eau Claire, WI (USA). She has written a letter that was published in Science last week [Going Public with the Scientific Process]. Many of you will never get to read it but you should. It is wonderful.

I'm going to take a chance here and publish her entire letter just so it gets as wide a coverage as possible.

The idea of using framing strategies to communicate science to the public has recently been taken up in scientific forums (1, 2), the mainstream media (3), and the blogosphere (4, 5). Most participants in the framing science debate limit their notion of scientific information to scientific facts. However, confining science messages to just the facts interferes with public understanding of science as a systematic, logical process of human inquiry and effaces the distinction between data and scientists' reasoning about data. To communicate successfully, we should focus on scientific process by emphasizing two important elements of scientific rationality: skepticism and dynamicism (6, 7).

Scientists deliberately integrate skepticism into their procedures by trying to refute their own hypotheses, retaining them only when confronted with compelling evidence sought through carefully controlled procedures. Scientists tend to shy away from revealing the intrinsic skepticism of science to the public, fearful that it will open the door to doubt about the validity of their conclusions. But communicating only the facts of science (framed or unframed) destabilizes public confidence in science. A fact doesn't allow science communicators to reveal, justify, and ultimately promote the skeptical reasoning process that helps make scientists more confident that their reasoning is correct.

Science is also dynamic; it is a cumulative enterprise that requires scientists to situate their instrumental activities and interpretations against the evidence that has come before and to alter them in light of new evidence. Insisting that new data be interpreted within the context of past and future data will ferret out and correct error over time, but it means that a fact cannot, by definition, be anything more than the (ephemeral and fallible) consensus of scientists at a given point in time. A "just the facts" strategy can and often does backfire, ultimately fueling public alienation from science. When scientists inform the public of "facts" (like the "fact" widely disseminated in the 1970s that all dietary fats are bad for us), and then that "fact" is refined or altered (now we're told olive oil is good for us), the public is justifiably confused. Studies suggest that the public tends to regard normal scientific refinement and self-correction as equivocation or incompetence (8-10). Instead of sweeping uncertainty under the rug, science communicators should help the public understand the logical and systematic procedures by which scientists confront it.

The true majesty and promise of science lies in its systematic, logical, skeptical, and dynamic reasoning procedures. "Successful" science communication should not be regarded as any message that enlists public support for science. Rather, we should define "success" in scientific communication as achieving a public that celebrates scientific reasoning procedures.

In case Mathews and Nisbet don't get it, the new version of Science journal isn't going to let them get away with distorting science for political ends. Nisbet comments on this letter and hopes to discuss the topic with Cronje when he visits her next week [At Science, Still More Reaction to Framing]. I'd love to be there.

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Bruce Alberts on Science Education

 
Bruce Alberts, the former President of the National Academies (USA), has now taken over as Editor-in-Chief of Science.¹ Judging by his editorial in this week's issue [Considering Science Education] there could be some interesting times ahead in the Science offices.

Here's part of what Bruce has to say about science education ...

I consider science education to be critically important to both science and the world, and I shall frequently address this topic on this page. Let’s start with a big-picture view. The scientific enterprise has greatly advanced our understanding of the natural world and has thereby enabled the creation of countless medicines and useful devices. It has also led to behaviors that have improved lives. The public appreciates these practical benefits of science, and science and scientists are generally respected, even by those who are not familiar with how science works or what exactly it has discovered.

But society may less appreciate the advantage of having everyone aquire, as part of their formal education, the ways of thinking and behaving that are central to the practice of successful science: scientific habits of mind. These habits include a skeptical attitude toward dogmatic claims and a strong desire for logic and evidence. As famed astronomer Carl Sagan put it, science is our best “bunk” detector. Individuals and societies clearly need a means to logically test the onslaught of constant clever attempts to manipulate our purchasing and political decisions. They also need to challenge what is irrational, including the intolerance that fuels so many regional and global conflicts.

So how does this relate to science education? Might it be possible to encourage, across the world, scientific habits of mind, so as to create more rational societies everywhere? In principle, a vigorous expansion of science education could provide the world with such an opportunity, but only if scientists, educators, and policy-makers redefine the goals of science education, beginning with college-level teaching. Rather than only conveying what science has discovered about the natural world, as is done now in most countries, a top priority should be to empower all students with the knowledge and practice of how to think like a scientist.

Those of you who have been reading Sandwalk know that this is exactly how I think science education should be fixed. We need to teach students how to think like a scientist. The facts of science are important but they aren't nearly as important as the way in which scientific facts are determined. Science is a way of knowing—that's what students need to learn.

I think we have a long way to go. At SciBarCamp last weekend we discussed the ten things everyone needs to know about science. One of the things on my original list was that science is a way of knowing [Ten Things Everyone Should Know About Science]. Before the meeting someone had written a comment on the poster to the effect that science may not be the only way of knowing and another participate wrote in that "it kinda was."

When it came time for the discussion the moderator handed out three topics to each of the panel members. One of them got the topic "Science doesn't have all the answers" and I was given the topic "Science has all the answers." When it came time for me to present I said that science doesn't have all the answers and nobody I know claims otherwise.

I changed the topic to "science is a way of knowing" and suggested that it may be the only way of knowing. Considerable debate followed. It was clear that many participants were new to this topic since the old arguments about love and morality came up.

At the end of the session, the moderator wrapped up and concluded that there was consensus on three things everyone needs to know about science. One of them was "science doesn't have all the answers." This is completely wrong, in my opinion. Of course, science doesn't have all the answers. The real question is whether it has all the questions.

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1. In the interests of full disclosure, I should reveal that he was also my graduate supervisor. (See Bruce Alberts in Toronto.)

Tangled Bank #101

 
The latest issue of Tangled Bank is #101. It's hosted at Tangled Up in Blue Guy [Tangled Bank #101].

When I first found that I would be hosting this edition of Tangled Bank, I tried to come up with a theme centered on Highway 101. It runs along the West Coast in the US and A and a stretch of it through San Francisco is also known as Van Ness Boulevard. I lived a block away from Van Ness for a year and one of my favorite pubs was an English Local, known as Highway 101. The idea for a clever theme vanished when I started receiving and reading the submissions that people sent. I decided I didn’t want to detract from the entries featured by making the show gimmicky. The Tangled Bank isn’t about me, it’s about science and the excitement of discovery as people unravel the mysteries of the natural world.

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If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

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Fun in Guelph

 
Katie Kish has a brief description of my visit to Guelph on her blog Liberal Debutante [Larry Moran At Guelph. I stole the photograph from her, I hope she doesn't mind.

The question about the evolution of the bombardier beetle was really a question about irreducible complexity in general and I tried to answer that question rather than the specific question that was asked. I was pretty sure that Dawkins had refuted the bombardier beetle "paradox" with real examples of transitional forms but I wasn't sure about this and didn't know the reference. (I said at the talk that I thought it was in The Blind Watchmaker).

Ryan Gregory, who I met for the first time on Wednesday night, has come to the rescue with a posting on Genomicron [Bombardier Beetles]. He has even found a video of Richard Dawkins "exploding" the myth of exploding bombardier beetles. Go and watch it on Ryan's blog.

There's an important lesson here. It is 2008. The evolutionary "problem" represented by the bombardier beetle was addressed—and refuted—by evolutionary biologists over 20 years ago and yet it's still being raised today by creationists as if it were a serious problem. What does that tell you about creationists?

Dealing with IDiots is very frustrating.

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Nobel Laureate: Paul Flory

 

The Nobel Prize in Chemistry 1974.

"for his fundamental achievements, both theoretical and experimental, in the physical chemistry of the macromolecules"


In 1974, Paul J. Flory (1910 - 1985) was awarded the Nobel Prize in Chemistry for his work on the physical chemistry of macromolecules in solution. His work led to an understanding of the dynamics and conformation of proteins and that's why his contributions are covered in biochemistry courses.

The presentation speech was delivered by Professor Stig Claesson of the Royal Academy of Sciences.THEME:

Nobel Laureates

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen,

This year's Nobel prize in chemistry has been awarded to Professor Paul Flory for his fundamental contributions to the physical chemistry of macromolecules.

Macromolecules include biologically important materials such as cellulose, albumins and nucleic acids, and all of our plastics and synthetic fibers.

Macromolecules are often referred to as chain molecules and can be compared to a pearl necklace. They consist of long chains of atoms which, when magnified one hundred million times, appear as a pearl necklace. The pearls represent the atoms in the chain. One should realize that this chain is much longer than the necklaces being worn here this evening. To obtain a representative model of a macromolecule all of the necklaces here in this hall should be connected together in a single long chain.

One can readily appreciate that the development of a theory for these molecules presented considerable difficulties. The forms of the chain itself, whether extended or coiled, represents a property difficult to rationalize.

A statistical description is of necessity required, and Professor Flory has made major contributions to the development of such a theory. The problem is more difficult, however. How can one compare different molecules in different solvents?

When chain molecules are dissolved in different solvents they become coiled to different degrees, depending on the interaction between repulsive and attractive forces in the solution. In a good solvent the chain molecules are extended. In a poor solvent, in contrast, the chain molecules assume a highly coiled form.

Professor Flory showed that if one takes a solution of extended chain molecules in a good solvent, and slowly cools the solution, then the molecules become progressively more coiled until they are no longer soluble.

Thus, there must be an intermediate temperature where the attractive and repulsive forces are balanced. At this temperature the molecules assume a kind of standard condition that can be used, generally, to characterize their properties.

This temperature Professor Flory named the theta temperature. A corresponding temperature exists for real gases at which they follow the ideal gas law. This temperature is called the Boyle temperature after Robert Boyle who discovered the gas laws. By analogy, the theta temperature for macromolecules is often referred to as the Flory temperature.

Profssor Flory showed also that it was possible to define a constant for chain molecules, now called Flory's universal constant, which can be compared in significance to the gas constant.

When one, in retrospect, reads about an important scientific discovery, one often feels that the work was remarkably simple. This actually indicates, however, that it was brilliant insight in a new and until then unexplored research area. This is highly characteristic of Professor Flory's scientific discoveries, not only those concerned with the Flory temperature and Flory's universal constant but also many of his other important research studies. Further examples are found in his investigation of the relationship between the reaction mechanism and the length of the chains formed when chain molecules are prepared synthetically, as well as his important contribution to the theory of crystallization and rubber elasticity. These achievements have been of major importance for technological developments in the plastics industry.

In recent years Professor Flory has investigated, both theoretically and experimentally, the relation between rotational characteristics of the chain links and the form of the chain molecules. This is of fundamental significance for the understanding of both biological macromolecules and synthetic chain molecules.

During the time Professor Flory has been active as a scientist, macromolecular chemistry has been transformed from primitive semi-empirical observations into a highly developed science. This evolution has come about through major contributions by research groups from both universities and many of the world's largest industrial laboratories. Professor Flory has remained a leading researcher in the area during this entire period, giving further evidence of his unique position as a scientist.

Professor Flory,

I have tried to describe briefly the fundamental importance of your many contributions to macromolecular chemistry and in particular those concepts introduced by you and now referred to as the Flory-temperature and the Flory universal constant.

On behalf of the Royal Academy of Sciences I wish to convey to you our warmest congratulations and I now ask you to receive your prize from the hands of His Majesty the King.

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Gene Genie #27

 
The 27th edition of Gene Genie has been posted at DNA Direct Talk [The Gene Genie: Yes, But What About Me?].

Welcome to another edition of Gene Genie, the blog carnival about genes, genomics and gene-related diseases. With Craig Venter and 23andMe and decodeME all over the news, I thought this edition might be appropriately focused on genes and “me.” What does the gene genie have to say about us?

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

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Dawn of Man

 
In his tribute to Arthur C. Clarke, John Dennehy mentions the opening scene from 2001: A Space Odyssey [Goodbye Arthur C. Clarke]. That was a scene that made a big impression on me as well, although I was a good deal older than John when I first saw it. Here it is.

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Arthur C. Clarke (1917 - 2008)

 

Science can destroy religion by ignoring it as well as by disproving its tenets. No one ever demonstrated, so far as I am aware, the non-existence of Zeus or Thor - but they have few followers now.

                                                      Arthur C. Clarke

It may be that our role on this planet is not to worship God-but to create him.

                                                      Arthur C. Clarke

I don't believe in God but I'm very interested in her.

                                                      Arthur C. Clarke

The greatest tragedy in mankind's entire history may be the hijacking of morality by religion.

                                                      Arthur C. Clarke

Information is not knowledge¹, knowledge is not wisdom, and wisdom is not foresight. Each grows out of the other, and we need them all.

                                                      Arthur C. Clarke

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1. This simple statement of fact is much more important in today's world than most people realize. Information should not be confused with knowledge.

[Photo Credit: ABCNews - Arthur C Clarke turns 90]

Billboard Censorship

 
According to the Grand Rapids Press, the Freedom From Religion Foundation is having trouble renting billboard space to advertise its message "Beware of Dogma" [Atheists claim censorship by billboard company].

The group that asked Hudsonville to remove God from the city's mission statement says it is having a hard time placing a billboard espousing its position.

"This is new, that a billboard company is censoring us," said Annie Laurie Gaylor, co-president of the Freedom From Religion Foundation. The Madison, Wis.-based group, dedicated to the separation of church and state, bills itself as North America's largest group of atheists and agnostics with 12,000 supporters.

The billboard with the words "Beware of Dogma" and the group's Web address has been used around the country, she said.

Gaylor said CBS Outdoor Advertising in Grand Rapids declined to rent a billboard to Freeedom From Religion, telling her it had been through controversy in the past and community reaction would force the billboard down within a day. She is working with other area firms, she said, but their locations are not her first choice.

We discussed this issue before when I declared that this was a "freedom of speech" issue [What Freedom of Speech Really Means]. Many readers disagreed , stating that a private company had the right to discriminate on the basis of religious beliefs (or lack of them).

This time there's a very interesting discussion going on at RichardDawkins.net [ Atheists claim censorship by billboard company]. Read the comments on that site.

This is clearly a gray area but, personally, I'd like to live in a society where a private billboard company wasn't afraid to rent space to all kinds of groups—including those groups whose opinions aren't shared by the management of the company. I'd like to live in a society where everyone understood that this was ethical behavior on the part of the billboard company and they didn't hold the company responsible for the message on the billboard. Even better would be to live in a society where the average person celebrated diversity of opinion and looked forward to seeing and hearing about contrary views. They would also look forward to debating and discussing those views.¹

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1. In case anyone is wondering whether this can be construed as support for teaching the controversy, the answer is yes. I think Christian private schools should be teaching about evolution and the scientific views on the age of the Earth. I think public school students should be discussing the conflict between evolution and creationism (and science vs. religion).

[Photo Credit: More Billboards in Chambersburg PA]

Are You as Smart as a Third Year University Student? Q7

 
Question 1
Question 2
Question 3
Question 4
Question 5
Question 6Choose the INCORRECT statement about protein folding.

a) protein folding is a cooperative phenomenon
b) the energy of the final folded protein is at the bottom of a free energy well
c) most proteins fold extremely rapidly
d) folding is an enthalpy-driven reaction (ΔH)
e) protein folding can be assisted by molecular chaperones

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Are You as Smart as a Third Year University Student? Q6

 
Question 1
Question 2
Question 3
Question 4
Question 5
Here are the names and structures of the aldohexoses. The common ones in biology are shown in blue.


Identify the monosaccharide shown below in three different views.



               a) D-allose
               b) D-altrose
               c) D-galactose
               d) D-glucose
               e) D-mannose

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THEME: Protein Structure

 
Jan. 28, 2007
Free Love, the '60's, and Protein Synthesis

Feb. 8, 2007
How Proteins Fold

Feb, 11, 2007
Heat Shock and Molecular Chaperones

Feb. 13, 2007
Disulfide Bridges Stabilize Folded Proteins

THEME:

More posts on
Protein Structure
Feb. 14, 2007
The Anfinsen Experiment in Protein Folding

Feb. 15, 2007
Gene HSPA5 Encodes BiP-a Molecular Chaperone

Feb. 20, 2007
Glycoproteins

Feb. 27, 2007
Collagen

March 12, 2007
How Cells Make Tryptophan, Phenyalanine, and Tyrosine

June 5, 2007
Protein Turnover

July 10, 2007
Fixing Carbon: the Structure of Rubisco

Aug. 1, 2007
Hemoglobin

Aug. 1, 2007
Myoglobin

Aug. 1, 2007
Heme Groups


Oct.13, 2007
HSP90 Structure

March 2, 2008
The α Helix

March 10, 2008
β Strands and β Sheets

March 13, 2008
Loops and Turns

March 13, 2008
Levels of Protein Structure

March 13, 2008
Examples of Protein Structure

March 14, 2008
Evolution and Variation in Folded Proteins


April 3, 2008
The Peptide Bond

April 3, 2008
Ramachandran Plots

April 4, 2008
Levinthal's Paradox

April 6, 2008
One Protein - Two Folds

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A Challenge to Jonathan Wells

 
On February 29th Jonathan Wells published a short review of a scientific paper by Maurice et al. (2008). You can read the original Wells posting at: The Irrelevance of Darwinian Evolution to Antibiotic Resistance.

Wells was trying to make a point. Concerning the work from Dardel's lab (Maurice et al, 2008), Wells claimed ...

Yet Darwinian evolution had nothing to do with it.

First, some bacteria happen to have a very complex enzyme (acetyltransferase), the origin of which Darwinism hasn’t really explained. Come to think of it, most cases of antibiotic resistance (including resistance to penicillin) involve complex enzymes, and the only “explanations” for them put forward by Darwinists are untestable just-so stories about imaginary mutations over unimaginable time scales.

Second, the acetyltransferase story is about minor changes in an existing species of bacteria. But Darwin’s theory isn’t really about how existing species change over time. People had been observing those long before 1859, and most of the new insights we’ve gained since then have come from genetics, not Darwinism. Yet Mendel’s theory of genetics contradicted Darwin’s, and Darwinists rejected Mendelian genetics for half a century. And although an understanding of genetics is important when dealing with antibiotic resistance, Darwin’s theory of the origin of species by natural selection is not.

Third, Dardel and his colleagues made their discovery using protein crystallography. They were not guided by Darwinian evolutionary theory; in fact, they had no need of that hypothesis.

We all know how creationists use the word "Darwinism." Most of the time, it's a synonym for evolution. All of the time, it's an attempt to obfuscate and confuse their audience. What Wells is saying is that evolution had nothing to do with the paper. All that happened was a bit of genetics. According to Wells, "Darwin's theory of the origin of species by natural selection" was not involved.

The senior author of the paper posted a comment on Pharyngula saying, "Actually, we did indeed use darwinian evolution within this work (something unusual in structural biology)." [see Why the Right People Hate IDiots, and links within that posting].

Michael Egnor gallops to the defense of his hero. Today he posted a rebuttal to my criticism of him and Wells [Dr. Larry Moran, Darwinism, and Vicious Personal Invective]. Here's what Egnor says,

Dr. Wells pointed out that research on antibiotic resistance wasn’t guided by Darwinian evolutionary theory. That evolution occurred — that is, that the population of bacteria changed over time — is obviously true, and obviously was relevant to the antibiotic resistance research. Dr. Wells made the observation that the research owed little to Darwin’s theory that all biological complexity arose by natural selection without teleology.

This is an incredible admission from a creationist. Egnor admits that the bacteria evolved. He then goes on to define some bizarre version of "Darwin's theory."¹ But the cat is out of the bag. What we see here folks, is the recognition that there is a distinction between Darwinism and evolution by natural selection. We're still not clear about the difference but it seems that bacteria can evolve resistance to antibiotics.

Egnor admits that the paper used evolution but it just wasn't Darwinism.

Now let's see if Jonathan Wells agrees. I'll apologize to Wells if he will post a comment here, or on Evolution News & Views, agreeing to the following ..

I, Jonathan Wells, agree that Maurice et al. (2006) employed evolution by natural selection in their methodology. My position is that evolution by natural selection is not what I mean when I use the word Darwinian.

Note that I'm not asking him to agree that "Darwinism" was involved in the paper. All he has to do is admit that evolution by natural selection is not what he means when he uses the word "Darwinian."

Michael Egnor has indicated that this is what Wells actually means. Now let's see if Wells himself will admit it.

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1. The standard version of Darwin's Theory of Evolution by Natural Selection is that populations evolve due to the differential survival of individuals with a fitter genotype.

Maurice, F., Broutin, I., Podglajen, I., Benas, P., Collatz, E. and Dardel, F. (2008) Enzyme structural plasticity and the emergence of broad-spectrum antibiotic resistance. EMBO Rep. 2008 Feb 22 [Epub ahead of print] [PubMed]