Denyse Hears Lawrence Krauss

 
Denyse O'Leary is in Sudbury attending the Canadian Science Writers Conference. One of the speakers was Lawrence Krauss&mdahs;who is speaking in Toronto tomorrow evening.

Here's how Denyse reports on what she heard [Science writing: There are not - repeat, NOT - two sides to the story].

Dr. Krauss went on to say that there is an innate tension between journalism and science. The problem is, “journalists think there are two sides to every story.” According to him, this is not true: “Most times, one side is simply wrong.”

Oh well, that’s all right then. Having been informed that one side is simply wrong, the journalist can forget about getting a range of opinion and simply act as a shill for the approved view.

The beauty of that strategy is that if there are problems with the approved view, the journalist is guaranteed never to find out, so she will always be sure she and her sources are right.

Dr. Krauss later conceded that “The editors are the bad guys.” Yes, indeed, in the sense that editors often come up with additional people for us writers to interview, people who offer additional perspectives. They, like us, see most stories as having many sides, not just one, so they are guilty of multiple sins, and we are complicit (when we are doing our job, that is).

The problem with Denyse O'Leary is that she hears but doesn't listen. Krauss said that "most times, one side is simply wrong." He also said that journalists and editors don't get this, they almost always pretend that there are two sides to every story.

Denyse then proves his point.

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Brian Switek on the Darwinius Affair

 
Brian Switek is an undergraduate at Rutgers University in New Jersey (USA). He's the man behind Laelaps.

Brian knows a lot about fossils and the history of life so it's no surprise that he has an opinion about "Ida" the new fossil primate being hyped in the media. Read his article in The Times of London (UK): The dangerous link between science and hype. Brian covers all the bases from whether the science is correct to whether the media hype is justified.

Brian calls himself a science writer and that's a good choice. This is science writing at its very best.

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[Photo Credit: Laelaps]

The Perfect Gift

 
We've all had this problem. Try to choose the perfect gift for your partner without asking their opinion. Chances are, you got yourself in hot water—especially if you're a man choosing for a woman. I still remember¹ buying that cool flash attachment for her 21st birthday ....

It should come as no great surprise that sociologists have studied this phenomenon. Dave Munger at Cognitive Daily has all the details: Why my mom didn't buy me a slot car track for Christmas in 1978, even though I told her that's what I wanted.

The good news is that we aren't alone. The even better news is that women aren't any better at choosing the perfect gift for a man. (It's just that they're less likely to hear about it!)

We've solved the problem in our family. Now we just ask the gift recipient what they want. Last week I got a new GPS system for my car—it was exactly what I wanted for my birthday. How did she know?

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1. Because I'm not allowed to forget it!

[Image Credit: How to Choose the Perfect Personalized Sister Gift]

The Fallacy of the Continuum

 
I once wrote an essay called "Theistic Evolution: The Fallacy of the Middle Ground." The point I was trying to make is that Theistic Evolution does not occupy the middle ground between superstition and rationalism or between science and religion. Theistic evolution is religious, it advocates superstition over rationalism—albeit a milder form of superstition than that of Young Earth Creationists.

Joshua Rosenau supports the evolution/creationism continuum shown in the above diagram [see Creation/evolution continuum, or NCSE is too nice to theists … and to atheists!]. It's from the NCSE website [The Creation/Evolution Continuum].

Josh claims that the continuum is the proper way to illustrate the differences between those who accept evolution and those who don't.

The nice thing about the continuum graphic is that, regardless of its faults, it emphasizes an easily obscured point: one need not set evolution against belief in a deity who acts in the world, and it is possible to move toward acceptance of evolution without moving out of the realm of theistic belief. The continuum oversimplifies by making it seem like there's just one path one might take in doing so, but NCSE is not in the business of endorsing particular religious philosophies, and making an exhaustive list is beyond the scope of the continuum.

He's got one thing right. It is, indeed, possible to move toward rationalism and science without moving out of the realm of theism. What Josh doesn't understand is that there's a breakpoint not shown on the continuum. I've put it on the modified version I show here.

When you view it like this, it's a different sort of diagram. There is a sort of continuum as theists move farther and farther away from the most outrageous forms of anti-science belief. But there's no continuum between science and most forms of religious belief. That's a sharp line.

Is there a reason for spinning the debate in the form of a continuum? Yes, there is ... you've heard it before.

More significantly, the continuum is helpful as a way to reach out to folks who have simply never thought about the issue before, and naively assume there are two camps: one for creationism and the other for evolution. So when forced to choose (as, for instance, by a pollster) they glom onto whichever camp they think best fits them. If the question is asked in a way that frames the decision in terms of science, they'll tend to favor evolution, if framed around religion or morality, they tend to choose creationism (at least in the US). Pointing out that there is a broad and diverse middle ground, that the choice is not nearly so stark, can help people get comfortable accepting evolution before confronting religious issues.

I understand why framing the debate in this way can be helpful to your cause. What I object to is the implication that moving from theism to atheism via agnosticism is a smooth transition. That's just not true and NCSE is very much endorsing a certain philosophical position when it promotes this diagram.

The continuum is a tool, and a useful one. It helps introduce the complexities of the interplay between science and religion to audiences who may simply think that everyone has to choose one or the other. It often surprises audiences to learn that many people do not see a need to choose, do not find an inherent conflict. (Standard disclaimer/troll repellent: Those people might be wrong, and I take no position on that topic.)

No, Josh, that's not true. You are taking a position on that topic. You are saying that one does not have to choose one or the other. You are saying that the view of evolution espoused by Francis Collins differs only in subtle degrees from that espoused by atheist scientists. You must know that isn't true.

As such, the simple tactic of drawing a bridge between what people think of as two mutually exclusive beliefs is pedagogically powerful.

There is no "bridge" between the belief in supernatural being and non-belief in such beings. How can something be "pedagogically powerful" if it's wrong?

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An Ethical Question

 
Eva Amsen was reading a book in a student study lounge when she was asked to participate in a survey [Spent - Review]. The question was ....

It was a short questionnaire about what you would do if you were standing in line at the post office for more than 30 minutes, waiting to mail a package, and someone offered to take you to the front of the line in exchange for $3. Would you pay the three dollars or keep waiting?

My answer is different than Eva's so this got me thinking.

See the poll in the left sidebar. What would you answer?

Is there a "right" answer?

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Monday's Molecule #123

 
You've probably noticed already that today's "molecule" isn't exactly a molecule. That's OK, you can still try to guess what it is. I want a fairly complete description of what you see here. This is supposed to be easy in order to encourage some new readers to enter the contest. There was no winner last week!!!

There's a Nobel Prize associated with this diagram.

The first person to describe the graph and identify the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are five ineligible candidates for this week's reward: Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Adam Santoro of the University of Toronto., and Michael Clarkson of Waltham MA (USA).

The Americans have pulled ahead of the Canadians and the rest of the world is being shut out. Where are the Europeans? Are they just stupid or don't any of them stay up late? BTW, I want to thank all those smart Canadians who have been holding back in order to give the rest of the world a chance.

I still have one extra free lunch donated by a previous winner (Michael Clarkson) to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

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 Prizes 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.

Comments will be blocked for 24 hours.

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The Darwinius Affair Continues to Embarrass

 
Today's the day we get to see the global event of the century, or is it millennium?. Sometime this evening there will be a TV show on one of the cable channels. It will reveal the astonishing fossil find that proves once and for all that humans have evolved. (Or something like that.)

The Darwinius Affair continues to embarrass everyone, including the creationists.

A friend alerted me to an article in The Bapstist Press (don't ask): Experts: Fossil find exciting but lacks significance . The article quotes certain "experts" including Kurt Wise the creationist who was a graduate student of Stephen Jay Gould.

"It is always exciting to find a well-preserved fossil, especially of something as rarely preserved as a juvenile primate," Wise wrote in a statement to Baptist Press. "The Messel site has generated a large number of spectacular fossils. Although the sediments seem to have been from a lake, it is an unusual one, somehow allowing remarkable preservation of animals both of the lake and the land.

"The unusual conditions of the Messel lake were probably created by a combination of global warmth (a much warmer earth than that of the present day) and the presence of active supervolcanoes (much larger than any known today) -- both a consequence (I believe) of the earth recovering from the effects of Noah's Flood," Wise, professor of science and theology and director of the Center for Science and Theology at Southern Baptist Theological Seminary, said.

There's more than enough embarrassment to go around, however, evolutionists should take heed when Answers in Genesis (AiG) says ....

The group also said the pitch of Ida as the missing link is "full-out sensationalism by people who are bypassing the scientific community with a direct-to-the-public appeal on behalf of Darwinism."

"All of this seems a departure from the normal turn of events, where researchers study their subject and publish their findings, and let the media chips fall where they may," AiG said.

I agree with Answers in Genesis.¹ We handed this to them on a golden platter and they are right to make it into a big deal. Shame, shame on all the scientists and media types who turned this minor, but interesting, discovery into a public-relations disaster.

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1. Whew! I never thought I'd say that.

Franzen, J.L., Gingerich, P.D., Habersetzer, J., Hurum, J.H., von Koenigswald, W., et al. (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE 4(5): e5723. [doi:10.1371/journal.pone.0005723]

I'm really, really hoping this is a joke.

 

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No Democrats Allowed at Liberty University

 
Liberty University has shut down the students Democrats club. You can read all about it on Pharyngula [“Liberty” University really ought to look at the first word in their name].

The email message has been published by the Washington Post. It needs to be widely circulated to illustrate just how Liberty University is treating its students.

From: Hine, Mark (VP Student Affairs)
Sent: Friday, May 15, 2009 1:37 PM
Subject: LU College Democrats

I must inform you that the College democrats' club is no longer going to be recognized as a Liberty University club. We are unable to lend support to a club whose parent organization stands against the moral principles held by Liberty University. I expressed these concerns when we met, earlier in the spring semester.

The Liberty Way states, "It is the duty of every student to respect Liberty's Statement of Doctrine and Purpose. They may not engage in any activity on or off campus that would compromise the testimony or reputation of the University or cause disruption to Liberty's Christian learning environment."

The Liberty University School of Law had been working on a policy to govern their clubs and organizations for quite some time. They have now completed that policy and we have adopted it for Liberty University as well. Now that it has been adopted and will apply to all clubs and organizations, it is clear that this club does not comply.

Below is a copy of the policy which governs clubs and organizations at Liberty University. This policy is posted on the website.

STUDENT CLUBS AND ORGANIZATIONS POLICIES

Student clubs or organizations must request and receive permission from the Liberty University administration before they may meet on campus, advertise, distribute or post materials, or use any University facilities for their activities or events. All such clubs or organizations and their activities or events must be consistent with the University's mission, and must be and remain in compliance with the Liberty Way, the Honor Code, and any policies or procedures promulgated by the University. The University reserves the right to refuse the use of its facilities for any reason to any student club, organization, activity or event.

Consistent with the Honor Code, all students, student clubs and organizations, faculty and staff of Liberty University, have a responsibility to uphold the moral and ethical standards of this institution and personally confront those who do not.

No student club or organization shall be approved, recognized or permitted to meet on campus, advertise, distribute or post materials, or use University facilities if the statements, positions, doctrines, policies, constitutions, bylaws, platforms, activities or events of such club or organization, its parent, affiliate, chapter or similarly named group (even if the similarly named group is not the actual parent, affiliate or chapter) are inconsistent or in conflict with the distinctly Christian mission of the University, the Liberty Way, the Honor Code, or the policies and procedures promulgated by the University.

Even though this club may not support the more radical planks of the democratic party, the democratic party is still the parent organization of the club on campus. The Democratic Party Platform is contrary to the mission of LU and to Christian doctrine (supports abortion, federal funding of abortion, advocates repeal of the federal Defense of Marriage Act, promotes the "LGBT" agenda, Hate Crimes, which include sexual orientation and gender identity, socialism, etc). The candidates this club supports uphold the Platform and implement it. The candidates supported are directly contrary to the mission of LU. By using LU or Liberty University and Democrat in the name, the two are associated and the goals of both run in opposite directions.

We are removing the club from the Liberty website and you will need to cease using Liberty University's name, including any logo, seal or mark of Liberty University. They are not to be used in any of your publications, electronic or internet, including but not limited to, any website, Facebook, Twitter or any other such publication.

If you have questions please do not hesitate to contact me.

Mark Hine
VP for Student Affairs
Liberty University

This is just the beginning. Mark my words. In a few weeks they're going to shut down the "Liberty University Gays and Lesbians Club" and the "Liberty University Secular Humanist Club." And it's only a matter of time before the "Liberty University Teletubbies Fan Club" is kicked off campus.

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Teaching Evolution in Natural History Museums

 
In an article published last November in Trends in Ecology & Evolution, Bruce MacFadden urges that natural history museums explore the use of new displays, such as those involving genomics and molecular biology, to educate the general public [Evolution, museums and society].

He writes ...

Public understanding of evolution has changed little over the past quarter-century [4]. The challenge therefore remains for natural history museums to improve communication about evolution, particularly the more difficult concepts.

MacFadden notes that museum visitors are more likely to accept evolution. Museums need to do a better job of taking advantage of this fact in order to enhance understanding of evolution.

Evolution represents a complex array of concepts, some of which are well understood whereas others are poorly understood by museum visitors. If an institution is committed to improving public understanding about evolution, then additional resources and effort should be directed toward more effectively communicating the more poorly understood concepts such as natural selection.

Yes, natural selection is difficult but random genetic drift is even more difficult. Unfortunately, I don't get the impression that MacFadden is counting random genetic drift as one of the basic concepts that museum visitors need to learn about.

One solution is to create displays about molecular evolution.

In this regard, there is much room to highlight research traditionally not considered to be natural history, such as genomics and molecular biology [9], although these subjects are not usually specimen based and therefore potentially less attractive to the public. In these instances, visitors are more likely to grasp difficult concepts when they have some prior understanding of a topic [10], or can place these concepts in a modern-day societal context. For example, disease vectors such as influenza and malaria mutate rapidly to become drug resistant, and therefore have negative consequences for world health.

This is a good idea. I recently visited the American Natural History Museum in New York and it had an excellent display on molecular evolution. It showed how you could compare DNA sequences and it explained that many of the mutations were just accidents that became fixed in the population by genetic drift. It even mentioned junk DNA and messy genomes.

It was a very popular display. Not only did it highlight some of the most important evidence for the history of life, it also explained the two main mechanisms of evolution. There were more people reading the material in the molecular evolution area than in the more traditional fossil areas. DNA is exciting.

Kotiaho et al. (2009) disagree. In the June issue of Trends in Ecology & Evolution they write [Evolution education in natural history museums ] ...

In his essay, MacFadden advocates the allocation of resources into novel contents, such as genomics or molecular biology, in order to increase the public understanding of evolution. We argue that museums should concentrate more on demonstrating the basic principles and outcomes of natural selection, rather than presenting fashionable novel contents such as genomics (which, it seems, even scientists often have a hard time understanding [4]).

It's clear that Kotaiho et al. see natural selection as the main (only?) mechanism of evolution. What they want is the kind of display that illustrates natural selection. They like dioramas.

If we want to educate the visitors of natural history museums about evolution by means of natural selection, we should aim at delivering the message that across species there is enormous within-species variation, that some of this variation is likely to cause differences among individuals in their lifetime reproductive success and that these differences will result in a constant change – evolution. In museums, we have a great opportunity to do this; as well as the exhibits open to the public, museums usually have extensive collections containing numerous individuals of each species. A simple illustration of the replacement of one generation by the next generation might work in making the operation of natural selection more tangible. With such an illustration, we can easily see why and how a population can undergo constant change, and thus grasp the basic principles of evolution by means of natural selection.

Natural history museums are our collective memory of the past. Their collections can, and have been, used to study evolution (e.g. [7]). Perhaps even more importantly, however, they could also be used to illustrate to the general public the evolutionary changes that have taken place. We challenge the exhibit designers of natural history museums to emphasize variation within species, and to demonstrate change due to natural selection, rather than stasis in nature.

Here's the problem. It might be fine to mount a display showing variation within a population. It might be possible to construct a display where the next generation has a different degree of variation. But it would be wrong to attribute that to natural selection unless you could present evidence that there were fitness differences associated with those variants.

I fear that these authors are not distinguishing between evolution and natural selection. They think that evidence of evolution is evidence of natural selection.

I don't understand why Kotaiho et al. would want to ignore molecular evolution and genomics. There's no better way to illustrate random genetic drift and there's no excuse for eliminating one of the most important fields in modern evolutionary biology.

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The Darwinius Affair

 
The Darwinius Affair is getting messier. Not only did some scientists commit a serious breach of scientific ethics by exaggerating their claims about the fossil, but they also prevented legitimate science journalists from doing their job.

As most of you know, I think that science journalists should examine the claims of scientists in order to ensure they are accurate. They should not just take the word of the scientist, no matter how famous he or she is.¹

In order to do their job, the science journalists need access to the scientific paper before it is released to the public. This is standard practice. Journalists are used to, and respect, news embargos.

In this particular case, it appears that scientists and the editors of PLoS ONE prevented journalists from seeing the paper until the press conference and all the associated hoopla was under way. Carl Zimmer has the story at Science Held Hostage.

Shame on PloS ONE, on the scientists who wrote the paper, and on everyone else who is associated with this media event. This is not how science is supposed to work. This is not how we should be communicating with the general public.

Franzen, J.L., Gingerich, P.D., Habersetzer, J., Hurum, J.H., von Koenigswald, W., et al. (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE 4(5): e5723. [doi:10.1371/journal.pone.0005723]

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1. Most professional science journalists don't do this, but that's another issue.

It's that time of year, again.

The course is over, the exam has been written, the marking is done, and the grades have been submitted. There's a short lag while the marks are checked and then they're posted so that students can learn how they've done in the course.

At my university we submit grades as percentages. They are converted to grade points (out of 4) in order to calculate a grade point average. The percent score is reported on the transcript and so is the grade point average. A mark of 76% is a 3.0, a mark of 77% is a 3.5 and a mark of 80% is a 3.7. A mark of 76% is a 3.0, a mark of 77%-84% is a 3.7, and a mark of 85% or above is a 4.0. There is no 3.5—shows you how much attention I pay to those sorts of things.

The email messages start as soon as the marks are posted. Every year there are students who want more marks. Usually it's just a few more marks to raise their grade points from 3.3 to 3.7 or something similar. That's by far the most common request. Sometimes the student wants lots more marks because they worked really hard in the course and deserve a much higher grade.

The most common reasons for asking for more marks are ...

• losing a scholarship
• not going to get into medical school/graduate school
• grade doesn't reflect effort
• parents will be disappointed
• the final exam was unfair
• student wasn't feeling well during the test that gave the lowest score
• this is the lowest grade ever received

Some of the letters just ask me to give them more marks because I feel sorry for them. But many contain the suggestion that they are willing to pay for a higher grade. Fortunately, I can handle all these requests by just referring students to the standard appeal process. Once the grades are submitted to the Faculty I can't change them. It's one of the few times that I like the rules and regulations.

Every Professor in the Department gets these requests at this time of the year.

Here's the important part—it's not fair to put the entire blame on the students. There's something about the way we run the university that makes it seem acceptable to beg for higher marks. What are we doing wrong? How can we fix it?

I have a trivial solution that will deal with many of the problems.

ABOLISH GRADE POINTS AND GRADE POINT AVERAGES

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Nobel Laureate: Charles Robert Richet

 

The Nobel Prize in Physiology or Medicine 1913

"in recognition of his work on anaphylaxis"

Charles Robert Richet (1850 - 1935) won the Noble Prize in 1913 for discovering the phenomenon known as anaphylaxis. This is a condition where the administration of an antigen causes severe symptoms, even death. Richet found that anaphylactic shock occurs only after an animal had been previously immunized and even then only after some days had passed.

It appeared as though the first immunization took several days to develop but when the process was complete a second attempt at boosting immunization causes a severe reaction. Anaphylactic shock was rare, it only happens in a small percentage of cases. We are familiar with the risk when people are known to be allergic to peanuts or insect stings.

Today we know what causes the symptoms of anaphylaxis; it's due to massive release of histamines, prostaglandins, and leukotrienes from mast cells. The release of these chemicals produces rapid heartbeat, sweating, and constriction of the airways. The symptoms can be relieved, and death prevented, by rapid treatment with epinephrine.

The primary cause of most anaphyaxis is overproduction of antigen-specific immunoglobulin E (IgE) molecules on the mast cells.¹ It's the IgE molecules that interact with the antigen to cause release of histamines etc. It's not known why some antigens lead to overproduction of IgE such that subsequent exposure to the same antigen cause a massive allergic reaction. (Normal antibodies are immunoglobulin G or IgG.²)

Immunology is complicated. That's why we can't cure asthma and other allergic reactions even though the phenomena have been intensely studied for more than 100 years.

Here's an excerpt from the 1913 Presentation Speech.
THEME:
Nobel Laureates

In an age in which the leading members of the medical profession tend to concentrate on innumerable experiments demonstrating the growing immunity of the organism towards poisons already resisted successfully once, you, Sir, have found that in certain cases a completely opposite result is produced. You did not restrict yourself to this isolated observation: studied in depth by you, it has become the foundation on which you have based the evidence of a reaction that is sometimes just as regular as the phenomenon of immunity. We are not concerned solely with specific prophylaxis; thanks to you, we are now aware of a specific anaphylaxis.

We do not discount the work of those who, following your lead, have observed similar phenomena, but to you goes the honour of having established the basis of a new biological reaction, anaphylaxis, and of having been the first to demonstrate it clearly. Thereby you have opened up to medical science an enormous field of study as yet unexplored. The Staff of Professors of the Caroline Institute wishes to reward you for this achievement by conferring on you the prize instituted by our compatriot Alfred Nobel for those «who have made the most important discovery in the field of physiology or medicine».

Please accept the warm congratulations of the Institute and myself, together with the wish of us all that success will continue to crown your devoted work.

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1. I do not mean to imply that IgE molecules are produced by mast cells. They are not.

2. There are several different classes (isotypes) of antibodies; IgG, IgD, IgM, IgA, and IgE. The most abundance class is IgG—that's the one most often depicted in the textbooks. It's probably the type most people think about when they think about antibodies. I did not mean to imply that the other classes are not "normal."

[Photo Credit: Wikipedia]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Science Journalism at its Worst

 
This video is an embarrassment. At a time when we are trying to convince the public that science is credible, along comes a trashy exploitation that sets science back several decades.

This is not how science works. It is not accurate science and it is not an accurate depiction of how scientists will react to the discovery of Darwinius masillae.

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Cafe Inquiry: Freedom of Speech and the Atheist Bus Campaign

 
Join us on Friday night for a discussion about Freedom of Speech and the Atheist Bus Campaign.

Modeled on the highly popular Cafe Scientifique, Centre for Inquiry presents Cafe Inquiry. Join us for a series of interactive forums exploring contemporary issues in science, reason, philosophy and politics. We bring you 2 or 3 guest experts that open by addressing the issue from a variety of perspectives and responding to moderator questions. Then we open it to the floor for your questions and comments to the panel and each other. This is your chance to interact with a diverse group of people on CFI's broad topics.

I've met some of the people who were involved in the atheist bus campaign. This promises to be a fun evening. If you've never been to an event at the Centre for Inquiry you can get in touch with me. I'll be happy to meet up with you and take you to the location.

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