Nobel Laureates: Arber, Nathans, and Smith

The Nobel Prize in Physiology or Medicine 1978.

"for the discovery of restriction enzymes and their application to problems of molecular genetics"


Werner Arber, Daniel Nathans, and Hamilton O. Smith received the Nobel Prize in 1978 for working out the mechanism of restriction enzymes (see Restriction, Modification, and Epigenetics).

By the time the Nobel Prize was awarded it was quite clear that the discovery of restriction enzymes was transforming biology and the new era of recombinant DNA technology was upon us. Read what this meant for Hamilton Smith below the fold.

The short history of this remarkable transformation was nicely summarized in the presentation speech by Peter Reichard.

Restriction enzymes are the tools which make it possible to open the sealed book. Werner Arber discovered these enzymes in the early 1960s when he analyzed an apparently obscure phenomenon in bacteria, discovered 10 years earlier by Bertani and Weigle, called host-controlled modification. In a series of simple but elegant experiments Arber showed that this phenomenon was caused by a change in DNA and apparently served to protect the host from foreign genes. Foreign DNA is degraded, and Arber postulated that bacteria contain restriction enzymes with the capacity to recognize and bind to recurring structural elements of DNA. At these locations the DNA-helix is severed: the pages of the book are separated.

Hamilton Smith verified Arber's hypothesis. He purified one restriction enzyme and showed that it could cleave foreign DNA. He determined the chemical structure of the regions of DNA which were severed by the enzyme and discovered certain rules which later could be applied to other restriction enzymes. Today maybe 100 such enzymes are known. They all cleave DNA, each at different, defined regions. With their aid, these giant molecules can be dissected into well-defined segments which subsequently can be used for structural investigations or in genetic experiments.

'The last step in this development was taken by Dan Nathans. He pioneered the application of restriction enzymes in genetics and his work has been a source of inspiration for scientists all over the world. He constructed the first genetic map using restriction enzymes by cleaving the DNA from a monkey virus. The methodology devised by him for this purpose was later used by others to construct increasingly more complicated maps. Today we can write the complete chemical formula for the genes of the monkey virus that Nathans started to investigate.

By the early 1990's the revolution had passed Hamilton Smith by. He lost his funding in 1989 and was relegated to sitting on committees and puttering in the lab on small projects. Then he met Craig Venter.

Venter was about to fund TIGR (The Institute for Genome Research) and he needed a man like Hamilton Smith. Now only did Smith have the magic hands of a brilliant bench scientist, he also had a Nobel Prize. It's not clear which of these was more important to Ventor but the result was astounding.

Smith was responsible for making the libraries that allowed genome sequencing. He was very good at it and that's why TIGR turned out the sequence of Haemophilus influenzae in record time. (H. influenzae was the organism that Smith had worked on all his life. Later on Smith built many more bacteria libraries and in 1998 he made the Drosophila melanogaster (fruit fly) library that really put TIGR on the map and led to the creation of Celera.

Craig Venter and Celara could not have entered the race to sequence the human genome without the technical expertise of Nobel Laureate Hamilton Smith. I recommend The Genome War by James Shreeve. It's a wonderful account of Venter, Celera, and the race to sequence the human genome. Here's an excerpt,

On the morning of July 7, 1998, Hamilton Smith drove down from his farm in Howard County and pulled into the TIGR parking lot. His 1987 Mercury Grand Marquis rumbled along the rows of cherry Corollas and silver Civics like an old tug trying to dock in a marina. The car had a long piece of trim missing on the driver's side, exposing a parallel row of rusted holes, as if the car had been strafed long ago. The odometer read 244,000 miles. The radio was playing—the knob had stuck in the "on" position a couple of months before—and a sucking sound was emanating from somewhere deep in the steering column. Smith didn't mind, because he had his hearing aid turned down low. The Mercury was among his most beloved possessions. He was more ambivalent about his Nobel Prize.

Smith maneuvered the car into a spot, gathered up his briefcase, and quietly made his way through TIGR's elegant lobby. He was on his way to pop in on Craig when the receptionist called out to him, "Something came for you FedEx, Dr. Smith," she said.

Canadian Scientists Are Refusing to Sit on Grants Panels

 
The results of the September 2006 CIHR grants competition are now available. The Canadian Institutes of Health Research (CIHR) is the main funding body for biological research in Canada. The funding crisis will have a devastating effect on the careers of many of my colleagues.

A total of 310 grant renewals were submitted and 91 were funded. This represents a renewal rate of 29%. Keep in mind that most of these applications were submitted by well-established scientists with a long history of funding and publications. At this rate of renewal, 71% of functioning labs might have to shut down unless they're successful in the next competition.

When your grant is not renewed, you revert to the "new" category of applications. In the latest competition, 240 "new" applications were funded out of 1707 submissions. This is a 14% success rate. Remember, most of these "new" applications are from scientists who are in the prime of their career but who failed in their renewal last year.

Of those grants that were funded, 26.1% of the funding awarded by the peer review committees was clawed back in order to spread the money a bit further. What this means is that some of the "renewals" were funded at lower levels than the current grants. Post-docs and research assistants will be let go even when a grant is renewed.

The average grant was $109,000 and no equipment was funded. This is not enough money to run an effective biochemistry lab.

Pierre Chartrand is the Vice President, Research Portfolio, at CIHR. He posted a wimpy message on the CIHR website [A Word on the September 2006 Operating Grants Competition]. Here's part of what he had to say.

Competition for available funding has grown increasingly intense. This trend is unlikely to change as Canada continues to expand its infrastructure for health research. For this reason, within the Research Portfolio of CIHR, we cannot afford to be consumed by disappointment. Canada owes its reputation for research excellence to an open, accountable and very rigorous peer review system for funding applications. We must re-double our efforts to ensure that the peer review processes used to guide CIHR's funding decisions are the very best that they can be. In light of the recent competition results, we have heard from a small number of active peer reviewers and others who are frustrated to the point of no longer wishing to participate in the peer review process. Such frustration, no matter how limited, leaves me gravely concerned because CIHR is at a point in time where the participation of the absolute best in its peer review processes is critical.

Let me tell you, Pierre, you damn well better be "gravely concerned." Some of my friends are sick and tired of sitting on committees where they have to reject excellent grants from their colleagues knowing that this will be a knockout blow to their future careers as scientists. Is it any wonder that they don't want to act as executioners?

Now you tell us that things aren't likely to change but you still expect Canadian scientists to volunteer to do the dirty work. Not gonna happen. About 70% of those volunteers whose grants were up for renewal have just stopped being "peers." Don't expect them to be happy. As for the rest, I urge them to boycott the process until there's a change in the CIHR leadership that got us into this mess.

God Doesn't Like Chicago

 

Here's a picture of the winning football team praying together after the big game on Sunday [New York Times]. I assume they're thanking God for the victory. I wonder what was going on in the other dressing room? Do you suppose there was a mass conversion to atheism?

Restriction, Modification, and Epigenetics

Bacteria have the ability to restrict bacteriophage (virus) infection by cutting up the 'phage DNA once it's injected into the cell. The enzyme that cuts DNA is called a restriction enzyme, or more properly, a restriction endonuclease.

Endonucleases are enzymes that cleave DNA internally by binding to the middle of a DNA strand and breaking one of the linkages that join the nucleotides. In the case of restriction endonucleases, both strands of the double helix are cut thus breaking apart the 'phage DNA before it can make new proteins and new virus particles.

The enzymes don't cut randomly. They bind to specific sequences and only cut at those sites. An example is one of the restriction endonucleases from Escherichia coli called EcoR1. It binds to the sequence GAATTC.

The top figure shows EcoR1 bound to DNA. Notice that the restriction site is palindromic—it reads the same way in opposite directions on opposite strands (see below). In order to appreciate this you need to understand that the two strands of DNA run in opposite directions and the direction of reading is important. We always read a DNA strand in the 5ʹ to 3ʹ direction. Thus, on the top strand the sequence is GAATTC while on the bottom strand the sequence is also GAATTC but read in the opposite direction.

The two identical subunits of EcoR1 (blue and purple) bind to opposite strands of the double helix and cut at exactly the same spot; in this case between the G and the A. The DNA is chopped in two.

The sequence GAATTC will occur, on average, once every 4096 base pairs (4⁶). This means there's a good chance of cutting any bacteriophage DNA that enters the cell since most bacteriophage genomes are much larger than 4096 base pairs.

This is an effective way of restricting bacteriophage infection except for one minor problem. How does the bacterium prevent it's own DNA from being cut by the restriction endonucleases?

The secret lies in blocking the restriction site in host DNA so that the restriction enzyme doesn't recognize it. One of the nucleotides is modified by an methylase enzyme (modification enzyme) that attaches a methyl group to one of the bases. The restriction enzyme doesn't bind to sites where one of the bases is modified by methylation; so all you have to do is make a methylase enzyme that recognizes the same site as the restriction enzyme.

EcorR1 methylase binds to the sequence GAATTC and methylates the first A to form N⁶-methyladenine (see Monday's Molecule #12). Like the endonuclease, the methylase has two subunits that bind symmetrically to double-stranded DNA. Both of the A's on opposite strands are methylated so neither strand can be recognized by EcoR1 and neither strand will be cut.

So far, so good, but we still have a problem. Why isn't the 'phage DNA methylated as well?

This is the cool part. Look at the figure on the left. Imagine that both strands are methylated. Following DNA replication, the sequence GAATTC will be copied but the newly synthesized strand isn't methylated. The hemimethylated DNA won't be recognized by the restriction enzyme so it's in no danger of being cut. In a very short time the methylase will bind and methylate the new strand of DNA.

The methylase binds specifically to hemimethylated DNA and not to unmethylated DNA. Thus, it will keep the host DNA fully methylated but it won't methylate the incoming 'phage DNA since the 'phage DNA is completely unmethylated.

As bacteria grow and divide they continue to inherit DNA that's methylated at the restriction site even though this inheritance isn't your typical genetic inheritance. It's called epigenetic inheritance. If something happens to the methylase, the cell will commit suicide by chopping up its own DNA. If both the methylase and restriction enzyme genes are mutated the cell survives quite nicely except that it's more susceptible to bacteriophage infection.

Epigenetic inheritance is common in mammals, including us. In this case it's not related to restriction/modification. It's a separate phenomenon where gene expression is controlled by the presence or absence of 5-methyl cytosine. The cytosine methylase works just like the modification enzymes—it binds preferentially to hemimethylated DNA. In this way, methylated regions of DNA are inherited from one generation to another.

Paula Zahn Should be Fired from CNN

 
I've just about had it with Paula Zahn. She's almost the most stupid "journalist" on TV, a fact she demonstrated in her January 31st report on atheism in America. [TRANSCRIPT]

Several bloggers have been all over this. The disgusting part is the so-called "discussion" that follows the airing of a short segment on discrimination against atheists. Paula let her invited guests get away with the most stupid and outrageous statements. She should apologize on air for inviting them on the show.

Did it never occur to CNN that having an atheist-hating Jew and two evangelical Christians discuss atheism was a bad idea? Where were the atheists on a show about atheism?

(UPDATE: Read the discussion at RichardDawkins.net.)

Here are two quotations from the ignorant atheist-hater named Debbie Schlussel. The first was in response to a question from Paula Zahn. Following a rant by the evangelical Christian Karen Hunter, Paula asked whether anyone was going to defend atheists .

No, I agree with her 100 percent. I think that the real discrimination is atheists against Americans who are religious. Listen, we are a Christian nation. I'm not a Christian. I'm Jewish, but I recognize we're a Christian country and freedom of religion doesn't mean freedom from religion. And the problem is that, you have these atheists selectively I believe attacking Christianity. You had a case in California where school children were forced to dress as Muslims and learn from the Koran. In Michigan they're saying high school (INAUDIBLE) in high school where they say Muslim prayers at the football games, public high school, (INAUDIBLE) in high school. You don't see atheists complaining about that. I really believe that they are the ones who are the intolerant ones against Christians.

Did you get that? America is a Christian country and freedom of religion doesn't mean freedom from religion! What cave did they find her in? Do you think that Debbie Schlussel might have a slight problem with Muslims as well as atheists?

Look where there are more atheists and where they've lost God, where the church is not that strong. Europe is becoming Islamist. It's fast falling and intolerance is increasing. That's the one reason our country has not become like Europe because we have strong Christians and because atheists are not strong. And I think that's a good thing.

See the complete show here.

Prince at the Superbowl

 
Apparently there was a big game last Sunday. I heard the Prince was there so I looked him up on the Uncyclopedia [Prince].

Prince Charles is one of the most widely respected individuals alive today. He is renowned for his intelligence, bravery and hard-working nature. The Prince is considered to be an expert in the fields of nuclear astro-physics, ancient Egypt, paper cutting and contemporary literature.

His recent marriage to Wallis Simpson was one of the most glamorous weddings of modern times only marred slightly by the disappointment felt among many of his female subjects.

There is not a hint of genetic inbreeding in his appearance or his demeanor. He is furthermore regarded as one of the most intelligent species of moss known by current scientists.

How to Talk to a Scientist if You're an IDiot

 
Greg Laden reminds us that Wikepedia is not the only online encyclopedia. We mustn't forget the Uncyclopedia [And when Wikipedia is just not enough…].

Good advice Greg. I checkout the entry for Intelligent Design and found an excellent article that I highly recommend to everyone who doesn't suffer from ironic deficiency [Intelligent Design]. The site is approved by the Kansas State Board of Education.

I especially liked the suggestions on how to talk to a scientist. Here are some of my favorites.

• Say things like "Well if you remember chemistry, that just disproves evolution."
• Tell them the Second Law of Thermodynamics makes evolution impossible and try to sound really serious when you say it and then point out that all scientists say this all the time and it's an indisputed fact. [6] If they show any sign of understanding the Second Law of Thermodynamics, walk away really quickly!
• Show them movies of apes doing gross, disgusting things, like the YouTube movie of a Gorilla licking his [bleep] in the zoo. Nobody wants to be related to filthy embarassing animals (even if drunk human rock-stars or intern-hungry televanglists do the same things as the apes).
• Show them studies proving that believing in evolution makes you a hippie commie liberal. If that fails, accuse them of atheism. (This isn’t so effective outside the US, because atheists don’t face resentment and persecution in other places in the civilized world. Tell them they are French instead, they’re hated the world over. If it’s a French person you’re speaking to, tell them they’re English.)

Is Scott Adams an IDiot?

 
I few days ago I asked Is Scott Adams an IDiot or does he just play one on TV?. Bill Dembski has now posted a link to Scott Adam's pathetic attempt to explain himself [Dilbert vs. P. Z. Myers.]

I guess that answers the question. Scott Adams is an IDiot.

Science Bloggers' Vow of Chastity

 
Some 60 bloggers have vowed to write only about science for an entire week. You can see how they're doing by checking out Just Science.

The rules for The Week of Science Challenge are fairly complicated but here's the bottom line.

It boils down to this:
- One week of science blogging and only science blogging.
- At least one post a day of pure science content.
- No blogging about anti-science -- no creationism, no anti-vaccination, no global warming denialists.

Just Science from February 5 through February 11.

Those are too much for me so I'm not rising to the challenge. I'm too old for abstinence but I'm happy to see how chaste everyone else is for this week. Good luck!

Basic Concepts and the Seed Consortium

 
John Wilkins has been keeping a list of Basic Science concepts [here]. I'm on that list and so are 20 other bloggers at last count.

What disturbs me is a comment from Bora Zivkovic at Basic Terms and Concepts in Math and Science. He says,

I don't know how many of you check out the constantly growing list of links to posts that cover Basic Terms And Concepts in Science, but you should. Our Seed Overlords are cooperating and will soon set up a place where all those posts will be re-posted, commented upon, edited, etc. - a one-stop shopping for all basic stuff useful, for instance, in teaching at all levels from Kindergarden to Postdoc!

Bora, Seed is not my overlord. I don't think a private for-profit company has the right to re-post my articles and invite comment on their site. Please tell me this isn't what you meant.

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.)

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

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.

Critical Thinking in Medical Schools

 
Orac at Respectful Insolence wonders what's happening in medical schools. There's more and more of a tilt to "alternative medicine" (i.e., quackery) and this is disturbing. Read the latest at Critical thinking and the scientific method in medical education".

Another Canuck Blogger

 
There's a really good blog called Primordial Blog. As far as I can tell the author (Brian) lives in the Yukon—that's part of Canada (barely) so he must be Canadian.

Brian writes about Life at the Intersection of Science, Religion, Politics and Culture and he comes up with some really cool stuff. Check out the articles on global warming, floating windmills, and the evolution of whales.

Tangled Bank #72

 
Tangled Bank #72 has been posted at Ouroboros.

Buy a Conservative T-shirt

 
Here are three of my favorites. See the rest at ThoseShirts.com. Please tell me this is sarcasm.

Should Christians Be Armed?

 
While checking out Pat Boone's IDiotic statements about evolution [Charles Darwin's Funny Joke] I noticed this icon in the sidebar. Naturally I couldn't resist clicking on it.

I ended up at a site advertising the book Shooting Back. Here's what I read,

What would you do if armed terrorists broke into your church and starting attacking your friends with automatic weapons in the middle of a worship service?

Would you be prepared to defend yourself and other innocents?

Would you be justified in doing so?

Is it time for Americans to consider such once-unthinkable possibilities?

There is one man in the world who can address these questions with first-hand experience.

His name is Charl van Wyck – a South African who was faced with just such a shocking scenario.

In "Shooting Back: The Right and Duty of Self-Defense," van Wyk makes a biblical, Christian case for individuals arming themselves with guns, and does so more persuasively than perhaps any other author because he found himself in a church attacked by terrorists.

Wow! That's all we need. IDiots with guns. In church.

Don't you just love America?

Recognize This Guy?

 
Of course you do. That's PZ Myers of Pharyngula in a photo taken by a very talented photographer in someone's back yard in Oxford, UK.

PZ just got a nice write-up in the University of Minnesota at Morris News [PZ visits friend].

I get a mention too but no pictures of me.

Nobel Laureates: Deisenhofer, Huber, and Michel

 
The Nobel Prize in Chemistry 1988.

"for the determination of the three-dimensional structure of a photosynthetic reaction centre"

Johann Deisenhofer, Robert Huber, and Hartmut Michel received the Nobel Prize in 1988 for working out the structure of the first photosystem—the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis. We now know that this is a Photosystem II-type complex with a type II reaction center. Its chlorophyll molecules absorb a photon of light and catalyze the transfer of electrons from an electron donor (usually cytochrome c) to quinone.

The photosystem structure was one of the most complex structures ever solved by X-ray crystallography. Even today there are only a handful of solved structures that are as complicated as this one.

The complex is normally embedded in a lipid bilayer that surrounds the vertical α-helices shown in the figure. The large gray space-filling molecules in the middle are the chlorophyll molecules that absorb light. Excited electrons are released from the chlorophylls and transferred down toward the bottom of the molecule to reduce a bound quinone near the iron atom (brown dot).

The cytoplasm on the inside of the cell is at the bottom of this picture and the intermembrane space between the inner and outer bacterial membranes is at the top.

The reaction center chlorophylls need to be resupplied with electrons and these come from a type c-like cytochrome (purple) that's attached to the top of the photosystem. This particular cytochrome is unusual since it has multiple heme groups. In most other species the electron donor is cytochrome c.

As noted in the presentation speech, by solving the structure of a bacterial photosystem Deisenhofer, Huber, and Michel not only contributed to our understanding of photosynthesis but also to our understanding of all membrane proteins and of electron transfer reactions in general.

The structural determination awarded has led to a giant leap in our understanding of fundamental reactions in photosynthesis, the most important chemical reaction in the biosphere of our earth. But it has also consequences far outside the field of photosynthesis research. Not only photosynthesis and respiration are associated with membrane-bound proteins but also many other central biological functions, e. g. the transport of nutrients into cells, hormone action or nerve impulses. Proteins participating in these processes must span biological membranes, and the structure of the reaction center has delineated the structural principles for such proteins. Michel's methodological contribution has, in addition, the consequence that there is now hope that we can determine detailed structures also for many other membrane proteins. Not least important is the fact that the reaction center structure has given theoretical chemists an indispensable tool in their efforts to understand how biologic electron transfer over very large distances on a molecular scale can occur as rapidly as in one billionth (American English, trillionth) of a second. In a longer perspective it is possible that such research can lead to important energy technology in the form of artificial photosynthesis.

Poor IDiots, Wrong Again

 
GilDodgen over at Uncommon Descent has put his foot in it once again. This time the IDiots have jumped all over the book Chance & Necessity by Jacques Monod. The book was written 36 years ago but that doesn't seem to faze the IDiots. Anything that conflicts with their worldview is a target. See [Classic Darwinian Texts — (soon to be, if not already) On the Ash Heap of History].

Here's what GilDodgen has to say,

Read Monod’s book — a foundational Darwinian text. Nowhere in it does he ever address probabilistic resources; he just assumes on faith that random mutation and natural selection can produce everything.

Now I've seen some pretty stupid things over at the Dembski headquarters but calling Monod's book "a foundational Darwinian text" just about takes the cake. This is not classic Darwinism. Classic Darwinism tries to deny the role of chance as much as possible. What Monod does is emphasize the importance of chance and contingency.

The entire book is devoted to addressing the probability of evolution—something that seems to have escaped the notice of IDiots like GilDodgen. Here's a short excerpt from pages 43-44 where Monod explains his view of probability and the inability of natural selection to make predictions.

The thesis I shall present in this book is that the biosphere does not contain a predictable class of objects or of events but constitutes a particular occurrence, compatible indeed with first principles, but not deducible from those principles and therefore essentially unpredictable.

Let there be no misunderstanding here. In saying that as a class living beings are not predictable on the basis of first principles, I by no means intend to suggest that they are not explicable through these principles—that they transcend them in some way, and that other principles, applicable to living systems alone, must be invoked. .... All religions, nearly all philosophies, and even a part of science testify to the unwearying, heroic effort of mankind desperately denying its own contingency.

That ain't Darwinian, baby. Can you imagine Richard Dawkins ever saying that we are here by chance? And it sure as heck ain't intelligent design either—that's the part that annoys the IDiots.
The classic quote from Monod's book can be found on page 112. He discusses the various kinds of mutations that had been discovered by 1971. Then he concludes,

We call these events accidental; we say that they are random occurrences. And since they constitute the only possible source of modifications in the genetic text, itself the sole repository of the organism's hereditary structure, it necessarily follows that chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact. And nothing warrants the supposition—or the hope—that on this score our position is ever likely to be revised.

You know what surprise me the most about the IDiots? It's not that they are ignorant about evolution, after all there are many scientists who cling to the old-fashioned Darwinian worldview as well. No, the thing that surprises me is that the IDiots are completely incapable of recognizing the different points of view within evolutionary biology. Here we have an example of an IDiot who has read Chance & Necessity but still calls it "a foundational Darwinian text." The mind boggles at such stupidity.

Memo to IDiots: there's more to evolution than Darwinism.

Of course GilDodgen can't resist taking a few other potshots at Monod. After all, Monod is French, an atheist, and (gasp!) a socialist to boot. Those evil socialist evolutionists, where do they get off caring for the downtrodden and the oppressed?

Footnote: GilDodgen begins his rant with,

I just pulled out my 1972 edition of Jacques Monod’s “classic” work, Chance and Necessity, subtitled A Philosophy for a Universe without Causality.

He can't even get the subtitle right. What he's quoting is a blurb on the cover that says "A philosophy for a universe without causality—by the Nobel Prize-winning French biologist." The actual subtitle is "An Essay on the Natural Philosophy of Modern Biology."

What Is a Valid Argument?

 
As part of the basic concept series, Janet Stemwedel explains arguments [Basic concepts: arguments]. For example, she says,

Here's an example of a valid argument:
1. Britney Spears is from Mars. (premise)
2. Martians have astounding vocal range and are great dancers. (premise)
3. Hence, Britney Spears has astounding vocal range and is a great dancer. (conclusion)

Are you convinced that this is a valid argument?

DNA Packaging and DNA Replication

 
The first part of this video shows how long strands of DNA are packaged in eukaryotic cells. It's pretty good. The second part is a demonstrating of how the replisome works. The replisome is a little molecular machine that copies DNA. The animation doesn't do a very good job of conveying the idea that the various components of the replisome interact with each other to form a compact blob at the replication fork.

The concept of a "molecular machine" was promoted by Bruce Alberts who worked on DNA replication. It gets the IDiots all in a tizzy whenever we talk about molecular machines. They think we're advocating intelligent design!



[Hat Tip: Living the Scientific Life]

A Typical Graduate Course in Biochemistry

 
Vince LiCata was kind enough to publish a generic course syllabus that applies to most graduate courses—and many senior undergraduate courses. Read it at MY NEW GRADUATE COURSE OFFERING.

[Hat Tip: The World's Fair]

Student Evaluations Don't Mean Much

Inside Higher Ed has just commented on a new study of student evaluations [New Questions on Student Evaluations]. The results are not surprising. They confirm all previous studies showing that student evaluations aren't what everyone thinks they are.

Previous studies suggested that students are rating generosity and personality and not quality of teaching. For example, a study of ratings on RateMyProfessor [‘Hotness’ and Quality] showed that,

... the hotter and easier professors are, the more likely they’ll get rated as a good teacher. As far as students — or whoever is rating professors on the open Rate My Professor site — are concerned, nothing predicts a quality instructor like hotness.

The new study from Ohio State University finds "... a strong correlation between grades in a course and reviews of professors, such that it is clear that students are rewarding those who reward them." Duh!

Now a cynic might say that this simply means that good teachers are doing such a good job that their students get higher grades. Thus, the evaluations truly represent the quality of the teacher and not how easy they mark. Well, that's not what the study suggests,

The Ohio State study, however, provides evidence for the more cynical/realistic interpretation — namely that professors who are easy (and aren’t necessarily the best teachers) earn good ratings. The way the Ohio State team did this was to look at grades in subsequent classes that would have relied on the learning in the class in which the students’ evaluations were studied. Their finding: no correlation between professor evaluations and the learning that is actually taking place.

The authors of the report show that student evaluations are practically worthless but in the interest of appeasing students they close with a mealy-mouthed sop as reported on the Inside Higher Ed site,

The authors stress that there are many ways — such as adjusting for student bias for easy graders or bias against certain groups of instructors — to continue to use student evaluations as one tool for measuring professors’ performance. But they write that, used alone and unadjusted, they appear highly questionable.

Let's see if I understand this logic .... student evaluations are biased and useless but instead of abolishing them we continue to use them to measure Professor's performance as long as we use other criteria as well.

Why? Why not get rid of student evaluations? We've known for decades that they don't work. Let's try and find another way for students and Professors to work together to improve university education. Student evaluations are ignored by all responsible Professors and they give students the false impression that their opinion is valued.

There has to be a better way. I believe that university students can provide useful and constructive criticism but only if they give up on the popularity contest and stop pretending that it has anything to do with quality of learning.

(As I write this, I'm supposed to be making up exam questions. I think I'll make some of them a bit easier .... )

[Hat Tip: Uncertain Principles]

Engineers Learn Workplace Skills

 
From the University of Toronto website comes this press release about how engineers learn workplace skills that will help them in their careers. The first two paragraphs are,

Gathered in the main dining room of the Faculty Club on the evening of Jan. 17, more than 100 engineering students sat down for an important professional lesson: dining etiquette. Led by Faculty Club manager Leanne Pepper, students were taken through the dos and don’ts of a five-course meal.

Organized by the Leaders of Tomorrow (LoT) program in chemical engineering and applied chemistry, the dining etiquette session was one of a series of talks and workshops that aim to develop the broader skills needed for engineers in the workplace.

Leanne is a friend of mine so I'll resist commenting.

Guernica

 
Remember Guernica? Thanks to the team of senior public health scientists and practitioners at Effect Measure for finding this video.

Is Nutritional Science Really a Science?

 
I have my doubts, and so does Jonah Lehrer [Why is Nutritional Science So Bad?].

John Kasich Interviews Atheist Brian Flemming about the Blasphemy Challenge

 
We don't get FOX News up here so I've never seen this John Kasich dude in action. Watch him interview Brian Flemming, the originator of the Blasphemy Challenge, at [onegood move]. With people like John Kasich around we have a long way to go before the majority gives up their supersitutions and becomes rational.

Kasich just doesn't get it. One is left with the distinct impression that Kasich has never, ever, questioned his religious beliefs. In other words, he has been so thoroughly brainwashed that alternative viewpoints just don't exist for him. Disgusting.

[Hat Tip: RichardDawkins.NET]

Monday's Molecular #11

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

This is another easy one for everyone who has ever taken biochemistry. This compound is one of the most important energy molecules in living cells. We will discuss the very important reactions that result in synthesis of this molecule after you've been given a chance to identify it.

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

What Is a Gene?

(Other definitions are at Discovering Biology in a Digital World, Pharyngula, and Greg Laden.)

The concept of a gene is a fundamental part of the fields of genetics, molecular biology, evolution and all the rest of biology. Gene concepts can be divided into two main categories: abstract and physical. Abstract genes are the kind we refer to when we talk about genes “for” a certain trait, including many genetic diseases. Most geneticists and many evolutionary biologists use an abstract gene concept.

Philosophers have coined the term “Gene-P” for the abstract gene concept. The “P” stands for “phenotype” indicating that this gene concept defines a gene by it’s phenotypic effects and not its physical structure.

Physical genes consist of stretches of DNA with a beginning and an end. These are molecular genes that can be cloned and sequenced. Philosophers call them “Gene-D” where “D” stands for “development”—a very unfortunate choice.

This essay describes various modern definitions of physical genes (Gene-D). I like to define a gene as “a DNA sequence that’s transcribed” but that’s a bit too brief for a formal definition. We need to include something that restricts the definition of gene to those entities that are biologically significant. Hence,

A gene is a DNA sequence that is transcribed to produce a functional product.

This eliminates those parts of the chromosome that are transcribed by accident or error. These regions are significant in large genomes; in fact, the confusion between accidental transcripts and real transcripts is responsible for the overestimates of gene number in many genome projects. (In technical parlance, most ESTs are artifacts and the sequences they come from are not genes.)

We could refine the definition by including RNA genes but that’s such a insignificant percentage of all genes that the refinement is hardly worth it. As we shall see, there are more significant limitations to the definition.

This "DNA sequence that's transcribed" definition describes a physical entity. Let’s examine a simple molecular gene to see how the definition applies.

This is a simple bacterial protein-encoding gene. The horizontal line represents a stretch of double-stranded DNA with the rectangular part being the gene. The gene is copied into RNA as shown by the arrow below the gene. This process is called transcription. Transcription begins when the transcription enzyme (RNA polymerase) binds to a promoter region (P) and starts copying the DNA beginning at the initiation site (i). The DNA is copied until a termination site (t) is reached at the end of the gene. According to my preferred definition of a gene, it starts at “i” and ends at “t.”

The part of the gene that’s transcribed includes the coding region, shown in black. This is the part of the gene that contains sequential codons specifying the amino acid sequence of the protein. At the beginning of the gene, called the 5ʹ (5-prime) end, there’s a short stretch of sequence that will be transcribed but not translated into protein. This 5ʹ untranslated region (5ʹ UTR) will contain various signals for starting protein synthesis.

The other end of the gene is called the 3ʹ (3-prime) end and there’s almost always a stretch that’s transcribed but not translated (3ʹ UTR). The 3ʹ UTR contains signals that cause transcription termination and also signals that regulate translation.

There are regions upstream of the promoter that control whether or not the gene is transcribed. These regions are called regulatory regions. They may contain binding sites for various proteins that will attach there in order to enhance the binding of RNA polymerase to the promoter. One of the differences between my preferred definition of a gene and others is that some other definitions include the promoter and the regulatory region.

There are two problems with such definitions. First, they’re not consistent with standard usage when we talk about the regulation of gene expression. We don’t say that only “part” of a gene is transcribed, which would be correct if we included the regulatory region in our definition of a gene. How often have we heard anyone say that regulatory sequences control the expression of part of the gene? That doesn’t make sense.

Second, by including regulatory sequences in the definition of a gene the actual extent of the gene becomes ill-defined. For most genes, we don’t know where all the regulatory sequences are located so we don’t know for sure where the gene begins or ends. Furthermore, there are some regulatory sequences, especially in eukaryotes, that are not contiguous with the gene and this leads to “genes” that are split into various pieces. It’s much easier to use a definition like “a DNA sequence that’s transcribed” because it defines a start and an end.

The organization of a typical eukaryote gene is shown below.

The main difference between this type of gene and a typical bacterial gene is the presence of introns and exons. These genes are transcribed from an initiation site to a termination site just like bacterial genes. When the RNA transcript is finished it undergoes an additional step called RNA processing. In that step, parts of the original transcript are spliced out and discarded. These parts correspond to the introns in the gene—shown as thinner rectangular region within the genes.

Note that the coding region (black) can be interrupted by these introns so the final messenger RNA (mRNA) cannot be translated until RNA processing is completed. The important point for our purposes is that the introns are part of the gene since they are transcribed.

My preferred definition has been used by molecular biologists for many decades but there are several other definitions that have been popular over the years. All of them have good points and bad points. I’ve already dealt with the definition that includes regulatory regions.

Some people still prefer a gene definition that corresponds to one used over half a century ago; namely, a gene is a sequence that encodes a polypeptide. This is the so-called one gene:one protein definition. It’s very old-fashioned. We’ve known for years that there are genes that do not encode proteins in spite of the fact that we commonly show protein-encoding genes whenever we describe typical genes. (As I did above.) There are genes for transfer RNA (tRNA), genes for ribosomal RNA, and genes for a large heterogeneous class of small RNAs. None of them have coding regions. The transcript is the functional product, often after RNA processing.

Because this old-fashioned definition is rarely used, the examples of alternative splicing producing different proteins pose no problem for modern definitions. These modern definitions refer to the transcript as the important product and not a protein.

There are exceptions to every generality in biology. Here’s a short list of gene examples that do not conform to my preferred definition.

Operons: In some cases adjacent “genes” are transcribed together to produce a large initial transcript containing several coding regions. In other cases the primary transcript is subsequently cleaved to produce multiple functional RNAs. In these cases it doesn’t make sense to refer to the co-transcribed genes as a single “gene.” Instead, we identify the stretches of DNA that correspond to a single functional unit as the “gene.” Thus, the lac operon contains three “genes” and the ribosomal RNA operons contain two, three, or four genes.

Trans-splicing: There are examples of “genes” that are split into pieces. The transcript from one piece is joined to the transcript from another to produce a functional RNA.

Overlapping Genes: Some “genes” overlap. This means that a single stretch of DNA can be part of two, and in at least one case, three genes.

RNA Editing: In some cases the primary transcript is extensively edited before it becomes functional. In the most extreme cases nucleotides are inserted and deleted. What this means is that the information content of the “gene” is insufficient to ensure a functional product and the assistance of other “genes” is required.

The Richard Dawkins Definition of a Gene Is Seriously Flawed

(This is an updated version of an article that I originally posted to talk.origins on Sept. 6, 1999)

We are interested in the correct definition of a "gene" (see ...). Part of the confusion is due to popular science writers who don't get it right. For example, Richard Dawkins does some serious handwaving in The Selfish Gene and he compounds it in The Extended Phenotype.

Dawkins knows that his defintion of "gene" in the Selfish Gene is unusual so he returns to the subject in The Extended Phenotype in his discussion of the selfish replicator. Dawkins is forced to concede that his use of the word "gene" is incorrect. That's why he says,

I am happy to replace 'gene' with 'genetic replicator where there is any doubt.

Nevertheless, he tries very hard to defend his point of view by claiming that geneticists and molecular biologists can't come up with a good definition of gene either. This leads him to make some very silly statements about genes and cistrons. He defines his genetic replicators in terms of alleles which means that they don't exist unless there is variation in the genome. He then goes on to restrict his discussion of changes in frequency to the results of natural selection, which means that his "genes" are effectively defined by the mechanism he prefers. This is why he quotes George Williams,

This is the rationale behind Williams's definition: 'In evolutionary theory, a gene could be defined as any hereditary information for which there is a favorable or unfavorable selection bias equal to several or many times its rate of endogenous change.'
                ....The Extended Phenotype p.89

The hand-waving in The Selfish Gene is even more obvious,

In the title of this book the word gene means not a single cistron but something more subtle. My definition will not be to everyone's taste, but there is no universally agreed definition of a gene. Even if there were, there is nothing sacred about definitions. We can define a word how we like for our own purposes, provided we do so clearly and unambiguously. The definition I want to use comes from G.C. Williams. A gene is defined as any portion of chromosomal material that potentially lasts for enough generations to serve as a unit of natural selection.
                ....The Selfish Gene p.28

In the new version of The Selfish Gene (1989) Dawkins adds a footnote where he again addresses his critics, especially Sewall Wright. Dawkins defends his definition of a gene as a unit of selection.

More handwaving,

I am using the word gene to mean a genetic unit that is small enough to last for a number of generations and to be distributed around in many copies. ... The more likely a length of chromosome is to be split by crossing-over, or altered by mutations of various kinds, the less it qualifies to be called a gene in the sense I am using the term.
                ....The Selfish Gene (1989) p.32

I said that I preferred to think of the gene as the fundamental unit of natural selection, and therefore the fundamental unit of self-interest. What I have now done is to *define* [Dawkins' emphasis] the gene in such a way that I cannot really help being right!
                ....The Selfish Gene (1989) p.32

The fact that Dawkins uses the word "gene" in such a non-standard way is not an issue as long as one recognizes that the Dawkins "gene" has nothing to do with the genes that molecular biologists and geneticists talk about. It's not an issue as long as one doesn't try and pretend that Dawkins has avoided handwaving and "clearly" refuted the problems raised by his critics.

The most reasonable definition of gene is that it is a piece of DNA that is transcribed but there are exceptions to everything in biology. Some genes are made of RNA, for example, and sometimes it's better to define a gene in terms of the protein it encodes. In no case is it reasonable to define a gene in terms of its ability to be selected or whether recombination can occur within it.

Jane Fonda Is Back

 
It's about time. Jane Fonda spoke at the Washington rally for peace yesterday. She said "I haven't spoken at an anti-war rally for 34 years. But silence is no longer an option." Jane is right. Silence is no longer an option. We need to get out of Iraq and Afghanistan.

Many of us will remember when "Hanoi Jane" visited North Vietnam in 1972. Is it time for her to visit Iraq?

[Photo Credit: According to Wikipedia "This photograph was shot by a public affairs officer of the Peoples Republic of Vietnam, and released worldwide for distribution."]

Psychic Sylvia Browne Is Nothing but a Con Artist and a Fake

 
Anderson Cooper on CNN does something right. He exposes Sylvia Browne as a con artist. She told the parents of a missing boy that their son was dead but he turned up alive after four years. James Randi takes part in the debunking.

Now, if only we could get Larry King to admit that psychics are frauds ....