Monday's Molecule #12

 
Name this molecule. You must be specific. We need the correct scientific name.

This is another easy one for everyone who has ever taken biochemistry. This compound is important for understanding the real science behind epigenetics, one of the latest fads in development. As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureates. Bonus points for finding the connection. (Extra bonus points for recognizing the indirect connection to Celera and the race to sequence the human genome.)

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A Code of Ethics for Scientists

There's an article on today's ScienceDaily website about a code of ethics for scientists [Scientists Should Adopt Codes Of Ethics, Scientist-bioethicist Says]. The ScienceDaily article is based on a press release from Wake Forest University Baptist Medical Center. The press release highlights a paper by Nancy L. Jones. Jones has some experience in "ethics" according to the press release.

Jones, an adjunct associate professor at Wake Forest University School of Medicine, is an American Association for the Advancement of Science (AAAS) science and technology policy fellow at the National Institutes of Health. She is a fellow at the Center for Bioethics and Human Dignity and is a recent member of the Secretary’s Advisory Committee on Human Research Protection of the U.S. Department of Health and Human Services.

With credentials like that, you'd think she would know something about science and ethics.

Jones appears to be concerned about issues such as cloning, stem cells, and gene transfer. It's not clear to me that there are real ethical issues associated with those topics but one thing is very clear—she's focusing on the uses of science (technology) and not on pure science.

Jones wants all scientists to sign a code of ethics to regulate and control their behavior. What kind of a code is she talking about? The only example in the press release is,

“A code of ethics should provide guidance for which knowledge should be sought, define the ethical means of acquiring knowledge, emphasize thoughtful examination of potential consequences, both good and bad, and help society prescribe responsible use of the knowledge,” writes Jones.

Her prototype code compares the norms of life sciences to the Hippocratic tradition. In part, it reads, “In granting the privilege of freedom of inquiry, society implicitly assumes that scientists act with integrity on behalf of the interests of all people. Scientists and the scientific community should accept the responsibility for the consequences of their work by guiding society in the developing of safeguards necessary to judiciously anticipate and minimize harm.”

I have a problem with this. Let's unpack the mix and address each of the four parts separately.

1. Provide guidance for which knowledge should be sought.

What does this mean? What kind of "guidance" would be part of a universal code of scientific ethics? Would I have to limit my search for knowledge to that which is acceptable to a researcher at a Baptist Medical School? I'm never going to sign a "code of ethics" that restricts my ability to pursue knowledge.

2. Define the ethical means of acquiring knowledge.

This sounds okay, although I wonder how it's going to work in practice. I doubt that anyone has a scientific ethical problem with most of the work done by astronomers, physicists, geologists, chemists, and botanists. Am I correct in assuming that Jones is worried about medical researchers and is transferring her specific concerns to all scientists? Is she talking about animal research or clinical trials? Would those be the only things that require defining or is there an ethical way of using a telescope?

3. Emphasize thoughtful examination of potential consequences, both good and bad.

This is the tough one. I know it seems reasonable for scientists to consider the consequences of their quest for knowledge but, in practice, it's not that easy. In my most pessimistic moods I can imagine all kinds of evil things that might be done with the knowledge that biochemists have gained over the past few decades. What should I do about that? Should we force our colleagues to stop doing research whenever we can imagine a dire consequence? Of course not.

Does that mean we should never consider the consequences; no, it doesn't. But keep in mind that scientists have been badly burned whenever they have publicly stepped into this morass. It was scientists who raised the issue of possible consequences of genetic engineering. Even though the scientists decided that the possible risks were minimal, the lawyers soon took over and we were stuck with silly laws that impeded research for a decade. Many of us remember that fiasco.

The responsibility for the misuse of scientific knowledge lies with those who misuse it and not with those who discovered the knowledge in the first place. You can't inhibit the search for knowledge on the grounds that it might be abused by someone in the future. That's why this part of the code of ethics is naive, irresponsible, and ultimately counter-productive. It attempts to put the blame on science when it's technology that's at fault.

4. Help society prescribe responsible use of the knowledge.

This is a legitimate role for scientists as long as they are explaining science. I don't have a problem with scientists describing stem cell research, for example. They can explain how it's done and explain the probabilities of success and the consequences of failure. They can describe how the new-found knowledge might help patients with various diseases and injuries. In other words, scientists can be a valuable source of knowledge.

But are scientists any better than the average citizen at "prescribing responsible use of knowledge" in the sense that Jones implies? I don't think so. Almost all American scientists would advocate funding stem cell research. Are they being ethical? What about those religious scientists who say that stem cell research is unethical? If both types of scientist signed the same code of ethics then what does it mean to say that scientists should "help society prescribe responsible use of knowledge"? What about those stem cell researchers who choose to stay out of the public limelight and get on with curing Alzheimer's? Are they unethical because they remain silent?

As you can see, science ethics is a complicated problem. Any attempt to regulate scientists based on some individual's definition of ethics is doomed to failure. I can't wait to see what Janet Stemwedel has to say about this.

Professorial Spells

 
The Little Professor has A Compendium of Professorial Magic.

Because I read student newsgroups, my favorite is,

SPEAK POP. Temporarily grants Professors knowledge of contemporary music, television, film, and video games. The Professor must perform a DC 13 Poseur check each time he or she makes an allusion; failure results in -8 Charisma rolls, plus +10 to Students' Resistance rolls.

Unfortunately, this is a level 3 spell and I just can't seem to get enough Charisma points to get beyond level 2. I also need the Magic Laser Pointer from the evil Chair monster.

(Come to think of it, once I have the Magic Laser Pointer, I won't need SPEAK POP. Or Charisma.)

I'm Not Really a Biblical Scholar

 
I didn't score as high as some but I didn't fail either. I guess this means I can criticize people who believe in God because I'm an expert on the Bible.

You know the Bible 85%!

 

Wow! You are awesome! You are a true Biblical scholar, not just a hearer but a personal reader! The books, the characters, the events, the verses - you know it all! You are fantastic!

Ultimate Bible Quiz
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Dick Cheney's Logic

I watched Wolf Blitzer interview American Vice President Dick Cheney last weekend. There were lots of things the Vice President said that really puzzled me so I've asked my friends and colleagues to explain the Cheney logic. None of them were able to come up with a satisfactory response so I thought I'd ask you to help me out.

Here's Cheney's response to questions about the failed strategy in Iraq.

Wolf, you can come up with all kinds of what-ifs. You've got to deal with the reality on the ground. The reality on the ground is, we've made major progress, we've still got a lot of work to do. There are a lot of provinces in Iraq that are relatively quiet. There's more and more authority transferred to the Iraqis all the time.

But the biggest problem we face right now is the danger that the United States will validate the terrorist strategy, that, in fact, what will happen here with all of the debate over whether or not we ought to stay in Iraq, with the pressures from some quarters to get out of Iraq, if we were to do that, we would simply validate the terrorists' strategy that says the Americans will not stay to complete the task --

Do you see my problem? Is he saying that we can't stop killing Iraqis and destroying their country because that's what the terrorists want? Is he saying that once he and Bush make a bonehead mistake they can't reverse course because they've got to show those terrorists just how pigheaded they can be?

Is there a rational argument in there that I'm missing?

Someone else seems to have a problem with Cheney Logic ....

Teach the Controversy

 
I have long advocated that the best way to defeat Creationism is to bring it into the schools and teach children what's wrong with it. We have nothing to fear from directly exposing our children to the controversy between science and religion. I'm sure that science and rationalism will win the hearts and minds of our children if we let them face off in a fair fight.

Mike Dunford isn't so sure. In a recent posting at The Questionable Authority (Benefits of teaching the "controversy") he addressed an article by Michael Balter in the International Herold Tribune. Mike thinks that teaching the controversy is a good idea but only if you have the right teachers. Teachers like university Professor Steven Verhey. Unfortunately, Mike concludes,

If I was confident that Balter's suggested approach would result in science being taught the way that Verhey taught it, I would be happy to support it. As things currently stand, however, I think it's a lot more likely that his approach would result in science being taught the way the Discovery Institute wants to teach it - heavy on the Jonathan Wells, light on the honesty.

This is very sad. If Mike is right it means the battle is already lost in the American schools. This means it's true that the courts are the last resort in the battle to teach science. We can't rely on the science teachers in the public schools to stand up for evolution. It's all in the hands of lawyers who must fight hard to suppress Creationism in order to save biology.

How did we ever get to this point? Is it true? Would teaching the controversy really lead to victory for the superstitious? I don't think this is true in Canada.

Lactivist & Monado Take on the US National Pork Board

 
Monado writes in support of a woman who is in trouble with the US National Pork board because she made a T-shirt promoting "the other white milk." Apparently, the Porkers want to protect their logo ("The Other White Meat").

See Big Pork threatens mother promoting breast milk at SCIENCE NOTES. The original story is at The Lactivist Breastfeeding Blog. Here's an excerpt from the lawyer for the US Porkers,

In addition, your use of this slogan also tarnishes the good reputation of the National Pork Board's mark in light of your apparent attempt to promote the use of breastmilk beyond merely for infant consumption, such as with the following slogans on your website in close proximity to the slogan "The Other White Milk." "Dairy Diva," "Nursing, Nature's Own Breast Enhancement," "Eat at Mom's, fast-fresh-from the breast," and "My Milk is the Breast.

I'm with Monado and Lactivist. Sue me too. Bloggers should register at the Lactivist Breastfeeding Blog.

• breast milk: the other white milk
• Soap flakes--the other white snow
• Latex--the other white paint
• Ivory--the other white soap
• Wiarton Willie--the other white groundhog
• Radish--the other white fruit
• Klu Klux Klan--the other white sheet

The Politics of the Minimum Wage

 
Jim Lippard (The Lippard Blog) argues against raising the minimum wage in Minimum wage increase: how to make the poor poorer. The argument is an old one. Lippard quotes approvingly from a Wall Street Journal article,

Although some workers benefit -- those who were paid the old minimum wage but are worth the new one to the employers -- others are pushed into unemployment, the underground economy or crime:

Let's think about this for a minute. Is it true that countries with higher minimum wages have higher rates of unemployment and crime than the USA? That's the first question that would occur to a scientist who wanted to test a hypothesis.

We're having a similar debate in Canada. The troglodytes want to keep the poor from rising above their station by paying them as little as possible. Raising the minimum wage will hurt small business who, by implication, profit from exploiting the poor. Since this argument doesn't sit very well in a public forum, they resort to the same argument as Jim Lippard and his friends. Raising the minimum wage will actually harm the poor, according to them.

Isn't it amazing that there are very few poor people who support that argument? You'd think they'd be fighting tooth and nail to keep the minimum wage as low as possible so they won't lose their jobs and be forced into a life of crime!

Anyway, here's an answer from the Canadian left on the effect of raising the minimum wage [The Economics of the Minimum Wage].

The cry from business and the right that decent minimum wages come at the cost of jobs flies in the face of the simple empirical reality that countries with relatively high wage floors compared to the median do not necessarily have low rates of employment or high unemployment. The proportion of full-time workers with low wage jobs (less than two thirds of the median hourly wage) is 22% in Canada, but just 7% in Sweden and 9% in Denmark. In 2005, the employment rate (the proportion of the 15-65 age groups with jobs) was actually higher in both Denmark and Sweden than in Canada. And there is no relationship between the incidence of low wage jobs and low unemployment in OECD countries. (See 2006 OECD Employment Outlook p. 175) In short, the argument of the right that countries cannot have both a decent wage floor and high employment/low unemployment is simply wrong.

Makes sense to me. The evidence from other countries suggests that a decent wage is a good thing.

Bumper Stickers

 
PZ Myers found a site [StampAndShout.com] that sells bumper stickers and he posted two of his favorites (favourites). They're not bad choices but I like this one.

Those little flying fishes are so cute:

Casey Luskin Defends Academic Freedom

Some IDiot sympathizers have proposed a bill in the legislature of the State of New Mexico (USA). Here's the relevant parts of the bill

A. The department shall adopt rules that:

(1) give teachers the right and freedom, when a theory of biological origins is taught, to objectively inform students of scientific information relevant to the strengths and weaknesses of that theory and protect teachers from reassignment, termination, discipline or other discrimination for doing so; and

(2) encourage students to critically analyze scientific information, give them the right and freedom to reach their own conclusions about biological origins and provide that no student shall be penalized in any way because the student subscribes to a particular position on biological origins.

B. For purposes of this section:

(1) "biological origins" means the origin, history and diversity of life and living organisms; and

(2) "scientific information" means information derived from observation, experimentation and analyses regarding various aspects of the material world conducted to determine the nature of or principles behind the aspects being studied. "Scientific information" does not include information derived from religious or philosophical writings, beliefs or doctrines. Scientific information may have religious or philosophical implications and still be scientific in nature."

Everyone with a brain knows what this is all about. It's not about academic freedom: it's about intelligent design creationism.

If it were really about academic freedom then why does it specify "biological origins"? Why not every aspect of education; like capitalism, pre-marital sex, the rights of gays, global warming, and the periodic table of the elements?

Casey Luskin doesn't get it. His knickers are all in a knot because Darwinists Begin Their Attacks on New Mexico Academic Freedom Bill. Luskin wonders why "Darwinists" are so upset because of a bill that singles out "biological origins" and not other science topics; or history subjects; or music theory; or whatever. According to Casey Luskin, this is only about academic freedom—it has nothing to do with intelligent design creationism or attacks by the religious right on evolutionary biology. It even says so right there in Section B(2).

Yeah, right. And I suppose it's just a coincidence that Casey Luskin and the Discovery Institute are so excited about this bill. I suppose they're really strong supporters of alternative views in the classroom. I suppose they favor teaching safe sex for teenagers, for example. After all, that's a good way to encourage students to think critically and reach their own conclusions.

What a bunch of hypocrites. This bill promotes the exact opposite of academic freedom. By singling out one particular topic that's up the nose of religious fundamentalists, it will have the effect of stifling academic freedom in the biology class. Teachers will feel pressured to go out of their way to pay lip service to superstition whenever they talk about evolution. Students can refuse to learn about evolution knowing that this bill will protect their ignorance.

Our Groundhog Is Better than Your Groundhog!

 

Wiarton Willie didn't see his shadow so Spring is coming.

Professors and Unions

 
I support unions so I don't have a problem with faculty unions and I don't have a problem with strikes if things can't be settled by negotiation.

Some people do have a problem with unions. They think that workers should always take what they're offered instead of disrupting the public by going on strike. Surprisingly, this neolithic attitude is common among students on university campuses—proving, once again, how different today's students are from those in the '60's.

The California Faculty Association may soon have to go on strike because the representatives of the schools refuse to make a decent offer after 20 months of negotiations. Faced with the possible disruption of classes, a student wrote this in a school newspaper,

If the teachers care more about getting paid rather than the education of the students, I say let them walk.

See how Janet Stemwedel of San Jose State University responds [I must have missed the line in my contract that said this is volunteer work].

Kid, if I only cared about getting paid, I'd be doing something else for a living.

Bravo Janet! Part of a good university education is learning how to see both sides of an issue. I hope your students benefit from your defense of a decent wage. Maybe they'll learn something from this experience.

Americans Never Landed on the Moon!

 
Friday's Urban Legend: FALSE

See Phil Plait (Bad Astronomy) on Bullshit! and learn about the moon landing hoax. Read about his experience with Penn & Teller [Penn & Teller, the Moon Hoax, and Me (Part I)]. Wait for Part 2.

A Simple Version of Photosynthesis

The 1988 Nobel Prize went to Johann Deisenhofer, Robert Huber, and Hartmut Michel for solving the structure of the first photosystem [see Nobel Laureates]. The photosystem was isolated from a purple bacterium and those bacteria have a relatively simple form of photosynthesis compared to cyanobacteria and chloroplasts.

It's worth looking at this simple version because it illustrates the main principles of photosynthesis without getting bogged down in excessive detail.

The type of photosystem is called photosystem II or PSII. Photons of light are absorbed by the chlorophyll molecules (P870) in this complex. Excited electrons are ejected from the chlorophyll molecules and they pass down a short path where they are picked up by quinone (Q). When Q acquires a pair of electrons, it brings in two protons from the cytoplasm (below) to form QH₂.


QH₂ diffuses in the membrane to another protein complex called the cytochrome bc₁ complex. This is the same complex that works in membrane associated electron transport, or respiration (as in mitochondria and non-photosynthetic bacteria: see Ubiquinone and the Proton Pump). The cytochrome bc₁ complex catalyzes the oxidation of QH₂ causing the release of protons on the outside of the membrane. The reaction—one of the most important reactions in biochemistry—is called the Q-cycle.

The net effect of these reactions is a light-driven proton pump that creates a gradient across the membrane. This is exactly what happens in respiration as well. The proton gradient, or protonmotive force, drives the synthesis of ATP by ATP synthase, another membrane protein.

The electrons that were ejected from the chlorophylls need to be replaced. The original electrons are passed on to cytochrome c by the cytochrome bc₁ complex during the Q-cycle reactions. Cytochrome c then diffuses back to the photosystem were it resupplies electrons to the chlorophylls in a cyclic pathway.

This is how light drives the synthesis of ATP.

Is Scot Adams an IDiot or does he just play one on TV?

 
Scot Adams, the creator of Dilbert, published an insane, unintelligible comment about the Big Bang and intelligent design. It looks for all the world like he's a tyical IDiot and PZ Myers shot him down [Will Scott Adams Never Learn?].

The Dilbert fans are up in arms. Some of them claim that we shouldn't take Scott Adams seriously—he was only joking. I don't think so. PZ was right. PZ has a history with this dingbat and he knows Adams isn't smart enough to be pulling our leg.

In any case, the question is now settled since Scott addresses it on his blog [Am I Serious?]. Here's his response,

I can’t rule out theory 1, that I am very, very, stupid and uninformed. That’s exactly the sort of thing that a person can’t know about himself. You really need to rely on other people for that diagnosis. Frankly, I’m rooting for that theory to be true; it would be comforting to be a member of the majority.

Then there’s the question of whether I believe what I say. This is a tricky question because people have wildly different opinions of what I’m actually saying. For example, do I believe in psychic powers, or did I simply write a story about a fascinating encounter with a self-described psychic in my book, The Dilbert Future? Interpretations vary.

I can only guess at my own motives for writing on these God-related topics. My understanding of the human mind is that our reasons are just rationalizations for our urges. I try to resist writing on these topics until the urge to do it pushes out all the other urges. I can’t explain the “why” of it. But I can tell you what I enjoy about it.

The part I like the most is the comments. I like the smart comments because they make me think. I like the dumb ones because they fascinate me and make me feel smart at the same time. I like the funny comments because they make me laugh. And the whole process makes me feel connected to something larger than myself.

Unlike most pundit-types, I don’t have a heavy investment in being right. I like to propose a line of reasoning and see what people think. If it exposes my ignorance – or more commonly, the reader misunderstands it and assumes ignorance, also known as the SHAAH method – that doesn’t bother me much.

Well, that does it for me. Scot Adams is an IDiot. What's more he seems to be the worst kind of IDiot, the kind that weaves and dodges in order to avoid being pinned down. Does he reject science in favor of GodDidIt? You bet he does, he's just too cowardly to come right out and admit it.