Nobel Laureate: Christian B. Anfinsen

 
The Nobel Prize in Chemistry 1972.

"for his work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active conformation"

Christian B. Afinson won the Nobel Prize in 1972 for his studies on the folding of ribonuclease A and the role of disulfide bonds. (See Disulfide Bridges Stabilize Folded Proteins and The Anfinsen Experiment in Protein Folding.) Anfinsen made some of the key observations demonstrating that protein folding is spontaneous. Here's part of the presentation speech by Bo Malmström,

Every living organism has its own characteristic pattern of enzymes. It can also produce a copy of itself, and this progeny has the same enzymes. An important question concerns the source of the information which has to be passed on from generation to generation for the enzyme pattern to be preserved. We know, thanks to contributions which have led to earlier Nobel Prize awards, that a specific molecule, called DNA, serves as the carrier of the traits of inheritance. These traits are expressed by DNA controlling the synthesis of enzymes. DNA accomplishes this by determining the sequence of the amino acids making up a particular protein molecule. An active enzyme does not, however, consist just of a long chain of amino acids linked together, but the chain is folded in space in a way which gives the molecule a globular form. What is the source of the information responsible for this specific folding of the peptide chain? It is this question in particular which has been the concern of Anfinsen's investigations. In a series of elegant experiments he showed that the necessary information is inherent in the linear sequence of amino acids in the peptide chain, so that no further genetic information than that found in DNA is necessary.

Snow Day

 
Today's a snow day in my town. Here's what the kids are doing in the park at the end of our street.

Now the IDiots Don't Get Evolution

 
Bill Dembski says Start the Revolution without ID. He's got his knickers in a knot over a paper that was originally published in the Jan. 25, 2007 issue of Nature. An updated version is available [here]. The original reference is,

Goldenfeld, N. and Woese, C. (2007) Biology’s Next Revolution. Nature 445:369-371.

The paper discusses Carl Woese's ideas on early evolution. The same ideas that I covered in The Three Domain Hypothesis (part 6). This isn't new, lots of people have written about it over the past dozen years or so. The idea is that rampant horizontal gene transfer obscures early phylogeny and makes it difficult to distinguish the relationship between eukaryotes and primitive prokaryotes. (It means the Three Domain Hypothesis is dead.)

Dembski probably doesn't know any of this because he's scientifically illiterate, like most IDiots. However, he can read an abstract ...

ABSTRACT: The interpretation of recent environmental genomics data exposes the far-reaching influence of horizontal gene transfer, and is changing our basic concepts of organism, species and evolution itself.

That's enough to trigger the following knee-jerk reaction from an IDiot.

So here’s the deal: When trying to derail ID in the court of public opinion, say that there is NO controversy over evolution. Say that scientists have achieved a consensus and that evolution is as well established as the earth going around the sun. But when out of the public eye, feel free to publish on how the entire field of evolutionary biology is in disarray and in need of a “next revolution.”

No, Bill, you just don't get it. Nobody is questioning the fact of evolution. We're just trying to figure out exactly how it works. You know, science and all that? I though that's what you want us to do?

What Woese and others are doing is sorting out what happened at the beginning of life on this planet, approximately 3.8 billion years ago. That's pretty amazing when you think about. A few decades ago, nobody would have thought that science could address this problem. But that's not good enough for the likes of Bill Dembski. Dembski thinks we should have all the answers before we can say with confidence that life has evolved over the past 3 billion years.

The irony here is that Dembski and his fellow IDiots refuse to tell us anything about their explanation. Dembski is even being coy about whether the Earth is that old. According to Dembski's logic, Intelligent Design Creationism must be bankrupt because they can't even give us a simple description of how humans appeared, and when.

Oh, and concerning that little quip about "out of the public eye." This was published in Nature for God's sake. If even Dembski can find it, then it's hardly out of the public eye, is it?

A Must-read From Sean Carroll

 
Sean Carroll has just posted an article on Cosmic Variance that everyone just has to read—especially the appeasers who think that Richard Dawkins is harming the "cause." Read Thank You, Richard Dawkins right now and enjoy your St. Valentine's Day.

Best and Worst of the Year Awards

 
New Mexicans for Science and Reason have just announced their Best and Worst of the Year Awards for 2006. Two of the awards in the "worst" category were no-brainers.

The "New Word: Pignorant" Award goes to Jonathan Wells, whose new book "The Politically Incorrect Guide to Darwinism and Intelligent Design" contained so many egregious falsehoods that the scientific critics decided to shorten the phrase "Pig Ignorant" to simply "PIGNORANT" in order to cope (Sept.).

The "Last Nail in The Coffin of ID" Award goes to William Dembski, who absolutely destroyed any remaining credibility Intelligent Design may have had, when he responded to Judge John E. Jones' powerful ruling of December 2005, not by defending ID in science journals, nor in courts of law, but by parodying the judge's decision with an Internet video that featured animated farting sounds. The Awards Committee had the most trouble with this award, as several members wanted to name it the "Not So Noble Gas" Award. However, all members were agreed that Dembski edged out Wells and Coulter, and did the most damage to ID this year. (Dec.)

[Hat Tip: John Pieret of Thoughts in a Haystack]

Happy Valentine's Day

Tangled Bank #73

 
Tangled Bank #73 is up at Lab Cat.

John Edwards: Short and Sweet

 
I agree with PZ Myers on this one. Edwards has just accepted the "resignation" of Amanda Marcotte after she had been pilloried by the Christian right for speaking out against Catholic stupidity on her blog. That shows a lack of courage on Edwards' part and it means I've stopped hoping that he become President (I don't have a vote).

What a shame, since Edwards looked so promising only a few weeks ago. Edwards was getting lots of praise for understanding bloggers and the internet. Clearly that praise was misguided. He doesn't get it at all.

Obama is now at the top of PZ's list. Dennis Kucinich tops mine.

Disulfide Bridges Stabilize Folded Proteins

 
Cysteine is one of the common amino acids found in all proteins. Under certain conditions two cysteine molecules can be covalently linked through their sulfur atoms creating a disulfide bridge. The figure shows how this can happen with free amino acids but disulfide bridges can also form between cysteine residues in within a single polypeptide chain. The joined molecules are called cystine.

Internal disupfide bridges are very common in proteins that are excreted from the cell or in proteins that are located on the outside surface of the cell membrane. Such proteins are often exposed to harsh conditions that are very unlike the conditions inside the cell where the protein folded into its native conformation.

Pancreatic ribonuclease A (the cow version is shown on the right) is secreted into the intestine where it aids in the digestion of RNA by cleaving it into small pieces. The acidic conditions of the small intestine would cause many proteins to unfold.

RNase A is stabilized by formation of four disulfide bridges between cysteine residues that are only brought together once the protein folds into its proper conformation. For example, the cysteine residue at position 26 is part of an α-helix and it's a long way from the cysteine at position 84, which is part of a β-strand region of secondary structure.

Once the protein folds in the cytoplasm the Cys-26 and Cys-84 side chains are almost in contact and the disulfide bridge is easily created by an oxidation reaction that involves glutathione. This disulfide bridge is not easily reduced back to free side chains so it serves to lock in the correct folded conformation. Since there are four such bridges in riboneculease A, the folded structure is very resistant to denaturation in the harsh conditions outside the cell.

Recall that the correctly folded form of a protein is the lowest energy conformation. But this minimum free energy state only applies to the conditions inside the cell where folding takes place. If the protein has to function in a different environment, it might unfold and become inactive. Over time, there was selection for increased stability by substituting cysteine residues that could form disulfide bridges.

"Senators nail problem, flub solution"

 
I still haven't read the Senate report on Afghanistan so I'm only guessing at what it said based on yesterday's Toronto Star article. Thomas Walkom has read the report and he writes an excellent column in today's edition of the Toronto Star [Senators nail problem, flub solution]. Here are some excerpts,

There is a bizarre disjunction in the Senate defence committee's useful – and remarkably frank – analysis of Canada's military role in Afghanistan. It's as if the 11 senators on the committee, having successfully outlined the near insurmountable problems associated with the Afghan war, couldn't bring themselves to accept the logical conclusion of their own analysis.

On the one hand, their 16-page report convincingly paints a picture of a war that cannot be won. The Afghan government of President Hamid Karzai, it states bluntly, routinely shakes down its own citizens. Its army and police are, in the words of committee chair Colin Kenny, "corrupt and corrupter."

The real Afghanistan, they write, is backward, illiberal and hostile to foreign invaders. Ordinary Afghans may have found the former Taliban regime excessive in the way it enforced its brutal moral rules. But at least it had moral rules. "The word moral is probably the last word that comes to an ordinary Afghan's mind when describing the new (Karzai) government," the senators write.

They quote one former Canadian ambassador as saying that it would take five generations to make a difference in Afghanistan. They cite Lt.-Gen. Andrew Leslie, commander of Canadian land forces, as saying the Afghan military mission alone would take 20 years.

To ask these questions is to answer them. Most Canadians will not agree to a war that takes decades to prosecute yet produces no results. And if, as the senators conclude, this is the prognosis, then the last five years of Canadian involvement – and Canadian deaths – have been pointless.

Given this bleak but frank assessment, it would have been logical for the senators to recommend that Canada end its military involvement in Afghanistan. But that is not quite what they do.

Instead, they recommend more of the Band-Aids and non-solutions they've just dismissed as naive. They call for 250 more Canadian Forces instructors and 60 police trainers. They call on the Canadian government to spend more money on Afghan police uniforms and salaries even though, as Kenny acknowledged in a press conference yesterday, a good chunk of that will be skimmed off by corrupt local officials.

Senate Report Questions Canada's Mission in Afghanistan

 
The Canadian Senate Defence Committee has just issued a report on Afghanistan. I haven't seen the original but here are some comments from an article in today's Toronto Star [Senate report blasts mission].

The report, titled "Taking a Hard Look at a Hard Mission," is short – just 16 pages – but blunt and stands in stark contrast to the more rosy assessments touted by Prime Minister Stephen Harper and his cabinet ministers.

"Our troops need more than patriotic bumper stickers. They deserve thoughtful assessments," reads the report, obtained by the Toronto Star.

Canada has about 2,600 soldiers in Afghanistan, most based in the Kandahar region. Since the mission began in 2002, 44 soldiers and one diplomat have been killed in Afghanistan.

"There are all kinds of problems to be solved if the Canadian deployment to Afghanistan is to achieve what any reasonable person would define as `success,'" the report says.

For starters, it says Canada's effort to win the "hearts and minds" of the local population has been badly undermined by civilian casualties caused by NATO air strikes and a development program that has little to show for its big budget.

"The combination of too many lives being lost and too little development assistance ... contributes to making life bleak and dangerous in the Kandahar region," it reads. For that reason, it says development dollars should be given to the Canadian military – $20 million a year – to make progress quickly until aid organizations are able to function safely in the region.

"We may have something more and better to offer than the Taliban, but we don't have much time to prove it," the report says.

Sounds okay up to here. Things are going badly and we're not winning the hearts and minds of the people. I agree with that. The obvious conclusion is to get the hell out and let Afghanistan solve its own problems.

But that's not what the report says. Instead it advocates escalation. More troops and more money—that's the ticket.

The report takes aim at NATO allies for doing more "saluting" than "marching." If more troops and equipment aren't delivered – as repeatedly demanded by local commanders – Canada should rethink its promise to stay in Kandahar until February 2009, it says.

"It is ... doubtful that the mission can be accomplished given the limited resources that NATO is currently investing," it says.

Canada has placed significant political and military pressure on other NATO nations to help bolster the mission in southern Afghanistan but with little success.

The report also pokes at the Afghan government, led by President Hamid Karzai, for the systemic corruption it says runs rampant through the country's institutions. It says the Karzai government should be pressed to develop a "comprehensive, transparent and effective plan" to reduce corruption as a condition of Canada's long-term commitment.

Hmmm ... we're not succeeding and the government we support is corrupt and ineffectual. What should we do? I know, let's send in more troops and give them more money. Ridiculous.

The report is based on the testimony of dozens of witnesses to the Senate committee as well as their own visits to Afghanistan, most recently in December. The report, which was unanimously adopted by the Liberal and Conservative senators on the committee, was tabled Thursday.

The report praises soldiers for their bravery, commitment and optimism.

"Like other Canadians, we want our troops to succeed and we want them to return home safely," it says.

Oh yes, the obligatory praise for the troops. We certainly can't have anyone thinking that we don't support the troops, can we?

Look, it's time we left. The soldiers who have died already have died in vain. More of them are going to die before we realize that we're wasting our time. You don't support our troops by getting them killed in a hopeless cause.

While federal New Democrats have called for troops to be withdrawn, the Senate defence committee says there are good humanitarian and strategic reasons for Canada to remain there.

Noting that "venomous" extremists still make their base in Afghanistan, the report says "neither Canada nor its allies should acquiesce to that threat."

Most of the extremists are based in Pakistan. Should we continue to acquiesce to that threat?

But the report says the key to lasting stability in the troubled nation is the ability of the Afghan National Army and police forces taking on more of the security role for themselves.

That's why the report's key recommendations urge NATO nations to provide additional troops to help train the Afghan army. As well, Canada should send 250 more of its own troops to serve as trainers, it says.

The report also says Ottawa should dispatch 60 more Canadian police officers – up from the 10 now there – to boost training of Afghan police. It also suggests the federal government "significantly augment" the $10 million contribution already made to provide uniforms and in the future improve benefits and salaries.

"Most police are untrained, illiterate and don't even know what the law is," the report says in a bleak assessment of Afghan officers.

We've been "training" these police for five years now and they don't know what the law is? What does that tell us?

The report also suggests Canada, along with NATO and the Afghan government, establish a "defensible" buffer zone along the Pakistan border to stop the infiltration of Taliban fighters.

"As long as the Taliban have access to hideouts beyond the reach of our forces, our mission has little hope of success," the senators say, urging "robust action" to save the Canadian mission from being undermined.

Translation from political doublespeak: the mission is hopeless as long as the government of Pakistan refuses to cooperate against terrorists and the government of Afghanistan is too corrupt to care. However, we should continue to sacrifice Canadian soldiers because if we don't we might have to admit that we've lost. It's much better to admit defeat five years from now when things are much worse.

What is CNN up to?

 
After the firestorm of protest over their first atheist episode, the Paula Zahn show (Paula Zahn Now) gave it a second shot tonight. They scoured the entire country of 300 million for three panelists who could have an intelligent discussion about atheism.

It was a disaster of only slightly less magnitude than the first one. This time the role of ignorant bigot was played by a black pastor. If that's the best they can do then America is in a whole lot of trouble.

The Richard Dawkins interview was okay. I admire how he can keep his cool when being interviewed by people who don't have a clue (Paula Zahn).

[the video clips of the show are at onegoodmove]

Junk DNA: Scientific American Gets It Wrong (again)

In "Ask the Experts" somebody asked What is junk DNA, and what is it worth?. The question was answered by "expert" Wojciech Makalowski of Pennsylvania State University. Here's the answer ...

In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome.

This is very misleading. First, nobody today would argue that all noncoding DNA is junk and I very much doubt that Ohno made that argument in 1972 (the orignal paper is hard to get). We know tons of examples of noncoding DNA that isn't junk.

Second, the focus on repetitive DNA is inappropriate. Lots of junk DNA is non-repetitive; pseudogenes are a prime example. Makalowski has a particular bee in his bonnet over repetitive DNA but that shouldn't be allowed to warp his judgement when responding to a question in Scientific American.

Although very catchy, the term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years. After all, who would like to dig through genomic garbage?

Nonsense. Researchers have been exploring noncoding DNA intensely for the past 40 years. That's why we know so much about regulatory sequences. Regulatory sequences are noncoding DNA that control gene expression.

Furthermore, even when it comes to true junk DNA, properly defined, hundreds of papers have been published. Lots of us have been very interested in junk DNA—at least in part in order to find out whether it has a function. This work led to the indentification of hundreds of pseudogenes, the unimportance of most intron sequences, and the degeneracy of LINES and SINES. There's lots more. I don't know of any researchers that were "repelled" from studying junk DNA. Many took it as a challenge.

Thankfully, though, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. And it is because of them that in the early 1990s, the view of junk DNA, especially repetitive elements, began to change. In fact, more and more biologists now regard repetitive elements as genomic treasures. It appears that these transposable elements are not useless DNA. Instead, they interact with the surrounding genomic environment and increase the ability of the organism to evolve by serving as hot spots for genetic recombination and by providing new and important signals for regulating gene expression.

Serving as hotspots for genetic recombination is not a "function" of most junk DNA. Furthermore, it's not at all clear that increasing recombination at a particular site will have any effect on future survival. Finally, signals for regulating gene expression have been known for decades. These signals are not junk DNA.

Genomes are dynamic entities: new functional elements appear and old ones become extinct. And so, junk DNA can evolve into functional DNA. The late evolutionary biologist Stephen Jay Gould and paleontologist Elisabeth Vrba, now at Yale University, employed the term "exaptation" to explain how different genomic entities may take on new roles regardless of their original function—even if they originally served no purpose at all. With the wealth of genomic sequence information at our disposal, we are slowly uncovering the importance of non-protein-coding DNA.

The occasional piece of junk DNA may be co-opted to become part of a newly evolved function. This does not mean that all junk DNA has a function. That's a classic error in logic more common in freshmen undegraduates than in "expert" Professors.

... These and countless other examples demonstrate that repetitive elements are hardly "junk" but rather are important, integral components of eukaryotic genomes. Risking the personification of biological processes, we can say that evolution is too wise to waste this valuable information.

From time to time we will find examples of some little bit of junk DNA that acquires a function. This does not mean that all junk DNA has a function. And it certainly doesn't mean that all DNA has now been shown to be "important, integral components of eukaryotic genomes." Most of our DNA is still junk. It turns out that evolution really isn't so smart after all.

Lying for Jesus

 
Today's New York Times has an article about Marcus R. Ross [Believing Scripture but Playing by Science’s Rules]. Ross teaches earth science at Liberty University. He is a Young Earth Creationist who believes that the Earth is less than ten thousand years old.

Marcus Ross recently obtained his Ph.D. in paleontology from the University of Rhode Island and there's the rub. According to his supervisors, his thesis was very good—it analyzed the extinction of marine reptiles 65 million years ago.

How can Ross reconcile the thesis work with his belief that the Earth is less that 10,000 years old? Here's how,

For him, Dr. Ross said, the methods and theories of paleontology are one “paradigm” for studying the past, and Scripture is another. In the paleontological paradigm, he said, the dates in his dissertation are entirely appropriate. The fact that as a young earth creationist he has a different view just means, he said, “that I am separating the different paradigms.”

He likened his situation to that of a socialist studying economics in a department with a supply-side bent. “People hold all sorts of opinions different from the department in which they graduate,” he said. “What’s that to anybody else?”

Whoa! Let's unpack that statement and see where it takes us.

First, the analogy to differing points of view in an economics department is entirely specious. Capitalism and socialism are both valid positions on a controversial topic. The issue about which view is correct hasn't been settled—pehaps neither one is correct. If a socialist graduate student were to defend a thesis in front of a group of capitalist Professors, you'd expect some tough questions. The student would be expected to defend her point of view in a rational manner with evidence and facts to back up the argument.

The same thing would happen if the student was a supply-sider and the Professors were Marxists. In neither case would the student be in danger of failing just because she disagreed with her Professors. As a matter of fact, the Marxist Professors would be just as hard on a Marxist student. That's what Ph.D. orals are all about. If you can't think straight then you don't get a Ph.D., but there are many perfectly valid ways of thinking in economics.

Now, what would happen if a known Marxist student tried to deceive the Ph.D. oral committee by pretending to be a capitalist? The goal is to appease the Professors by telling them what they (presumably) want to hear, in order to get the Ph.D. That student would fail, I hope. Universities are no place for lies and deceit. You must stand up for what you believe and learn to defend it in an academic context. Otherwise, you don't deserve a Ph.D.

Marcus Ross thinks it's okay to write a thesis about 65 million year old reptiles when, in fact, he doesn't believe a word of it. He justifies this by referring to "different paradigms." Apparently, there's one kind of "paradigm" when you are trying to get your Professors to give you a Ph.D. and another kind of "paradigm" at all other times. This is just a euphemism for "lying." In this case, it's lying for Jesus.

If I had been on the Ph.D. oral exam, I would have honed in on the discrepancy between the dates in the thesis and the known beliefs of Marcus Ross. It is not intellectually honest to write something in a thesis that you "know" to be incorrect. I would want to know what Ross means when he writes that his marine reptiles went extinct 65 million years ago and I would expect an answer that's not intended to deceive me. If I'm not convinced, he doesn't get a "yes" vote from me no matter what the thesis says.

[Hat Tip: RichardDawkins.net]

Thinking Blogger Award

 
I won an award! It's called the Thinking Blogger Award. Thanks to Greg Laden for electing me.

I'd like to thank my agent, my loving wife, my wonderful children, and my mother. Most of all I'd like to thank God, without Him this blogger just wouldn't be the same.

The rules of the Thinking Bloggere Awards are [here]. According to the rules I have to nominate five other thinking bloggers—presumably ones that haven't already won. (This could get difficult very quickly.)

In alphabetical order, here are the five nominees for Thinking Blogger ...

Brian at Primordial Blog one of the newest thinkers in blogdom.

Carl Zimmer of The Loom who doesn't think enough. More blogging, Carl.

Jim Lippard of The Lippard Blog who thinks most of the time except when we disagree.

John Wilkins of Evolving Thoughts who perhaps thinks too much. But that's what philosophers do.

Monado a fellow Torontonian thinker at Science Notes who deserves more recognition.

Happy Birthday Charles Darwin

 
Today is the birthday of the greatest scientist who ever lived. When you visit Darwin's home (Down House) you get a sense of what he must have been like. One of the things that's obvious is the number of bedrooms for the children. The house must have been alive with the activities of young children. It's no wonder that Darwin needed some peace and quiet from time to time.

Gwen Raverat was Darwin's granddaughter (daughter of George Darwin). She described Down House as she knew it in the years shortly after Darwin died.

Of all places at Down, the Sandwalk seemed most to belong to my grandfather. It was a path running round a little wood which he had planted himself; and it always seemed to be a very long way from the house. You went right to the furthest end of the kitchen garden, and then through a wooden door in the high hedge, which quite cut you off from human society. Here a fenced path ran along between two great lonely meadows, till you came to the wood. The path ran straight down the outside of the wood--the Light Side--till it came to a summer-house at the far end; it was very lonely there; to this day you cannot see a single building anywhere, only woods and valleys.

I became interested in Darwin's children about fifteen years ago when I first began to appreciate the influence they had on his life. We all know the story of Annie's death when she was ten years old and how this led to Darwin's rejection of religion. There were other tragedies but Charles and Emma turned out to be very good parents.

Here's a short biography of each of Darwin's children from AboutDarwin.com

William Erasmus Darwin
The first of Darwin's children was born on December 27, 1839. He was a graduate of Christ’s College at Cambridge University, and was a banker in Southampton. He married Sara Ashburner from New York, but they had no children. William died in 1914.

Anne Elizabeth Darwin
Born on March 2 1841, and died at the age of ten of tuberculosis on April 22, 1851. It was the death of Annie that radically altered Darwin’s belief in Christianity.

Mary Eleanor Darwin
Born on September 23, 1842 but died a few weeks later on October 16th.

Henrietta Emma Darwin ("Etty")
Born on September 25, 1843 and married Richard Buckley Litchfield in August of 1871. She lived 86 years and edited Emma's (her mother) personal letters and had them published in 1904. She had no children.

George Howard Darwin
Born on July 9, 1845. He was an astronomer and mathematician, and became a Fellow of the Royal Society ... in 1879. In 1883 he became the Plumian Professor of Astronomy and Experimental Philosophy at Cambridge University, and was a Barrister-at-Law. He studied the evolution and origins of the solar system. George married Martha (Maud) du Puy from Philadelphia. They had two sons, and two daughters. He died in 1912.

Elizabeth Darwin
Born on July 8, 1847 and died in 1926. She never married and had no children.

Francis Darwin
Born on August 16, 1848. He became a botanist specializing in plant physiology. He helped his father with his experiments on plants and was of great influence in Darwin's writing of "The Power of Movement in Plants" (1880). He was made a Fellow of the Royal Society in 1879, and taught at Cambridge University from 1884, as a Professor of Botany, until 1904. He edited many of Darwin's correspondence and published "Life and Letters of Charles Darwin" in 1887, and "More Letters of Charles Darwin" in 1903. He also edited and published Darwin’s Autobiography. He married Amy Ruck but she died when their first child, Bernard, was born in September of 1876. He then married Ellen Crofts in September of 1883, and they had one daughter, Frances in 1886. Francis was knighted in 1913, and died in 1925.

Leonard Darwin
Born on January 15, 1850. He became a soldier in the Royal Engineers in 1871, and was a Major from 1890 onwards. He taught at the School of Military Engineering at Chatham from 1877 to 1882, and served in the Ministry of War, Intelligence Division, from 1885-90. He later became a liberal-unionist MP for the town of Lichfield in Staffordshire 1892-95, and was president of the Royal Geological Society 1908-11. Leonard married Elizabeth Fraser in July of 1882. He married a second time, but had no children and died in 1943.

Horace Darwin
Born on May 13, 1851. He was a graduate of Trinity College, Cambridge, and became an engineer and a builder of scientific instruments. In 1885 he founded the Cambridge Scientific Instrument Company. He was the Mayor of Cambridge from 1896-97, and was made a Fellow of the Royal Society in 1903. Horace married Emma Farrer in January of 1880 and they had three children. He died in 1928.

Charles Waring Darwin
Born on December 6, 1856 but died on June 28 1858.

Monday's Molecule #13

 
Name this molecule. You must be specific. We need the correct scientific name. This one's a bit difficult.

As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureate. Bonus points for finding the connection.

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

Not Ready to Make Nice

 
I'm not usually a fan of country music and I'm not usually fond of people from Texas, but I'll make an exception for the Dixie Chicks. I just watched them sing Not Ready to Make Nice on the Grammy Awards show. Introduced by Joan Baez, no less (see below).

Joan Baez and Friend

 

Joan Baez: The Night They Drove Old Dixie Down

 
I think you have to be over 50 to remember her and what she stood for.

Gene Genie Carnival

 
There's a new Carnival in town. It's called gene genie and the description is,

A blog carnival on genes, gene-related diseases. We plan to cover the whole genome before 2082.

I'm going to assume that they're talking about the human genome. Dibs on the chaperone genes.

The plan is to publish a collection of articles every two weeks. That's 26 per year. In order to get done by 2085 we'll have to post articles on eleven different genes every two weeks. Better get busy.

Heat Shock and Molecular Chaperones

 
Protein folding takes place inside cells at their normal temperature. This temperature is 37°C in the case of mammals. If cells encounter higher temperatures, their proteins become unfolded since the minimal energy conformation at one temperature isn't the same minimum at a another temperature.

The difference in temperature isn't large. Many mammalian proteins become unstable at 42°C. This is a temperature encountered with high fever but it's also common in skin cells that have been exposed to the sun or the water in a hot tub. Temperature differences are even more common in species that do not regulate their temperature (e.g., plants, fungi, bacteria, invertebrates).

All living cells have defense mechanisms that protect against exposure to high temperature. They produce special proteins called heat shock proteins in order to recover damaged proteins that have unfolded at the high temperature. Many of the heat shock proteins are molecular chaperones. These are proteins that guide proper refolding of damaged proteins.

Shortly after the discovery of heat shock proteins we learned that these proteins are always present even in cells that haven't been stressed. In other words, molecular chaperones play a role in normal protein folding as well as helping to recover from damage. This role is illustrated in the energy diagram (top left).

One of the pathways to the energy minimum follows the line labeled "B." This traverses a local energy well and proteins can get trapped in this pit. What happens is that they adopt a less-than-optimal conformation but they can't easily unfold and refold to fall down into the deeper well because that would require an increase in energy. It will happen eventually, but it could take a long time. Chaperones help direct folding along the proper pathway and his speeds up the folding process.

Recall from the earlier discussion of How Proteins Fold that folding is an entropy-driven process where the end result is to bury hydrophobic residues in the central core of the protein. Another thing that can happen during folding is that exposed hydrophobic surfaces of one protein can interact with similar surfaces in another protein leading to aggregation. Chaperones can bind to these hydrophobic surfaces and prevent aggregation. This is another way of speeding up folding.

There are many different chaperones. My personal favorite is HSP70 (Heat Shock Protein of relative molecular mass 70,000). This is a protein that's found in every type of living species. It is the most highly conserved protein in all of biology so it's an excellent protein for looking at deep phylogeny. The role of HSP70 as a molecular chaperone is to bind to proteins as they are being synthesized in order to prevent improper folding. It also prevents aggregation.

Another famous chaperone used to be called HSP60 since it was a heat shock protein of M_r= 60,000. It was also known as GroE since it allowed for the growth of bacteriophage λ gene E mutants. Now it's known as chaperonin. Note that the term "chaperonin" refers to a specific molecular chaperone.

Chaperonin is a barrel-shaped molecule consisting of two rings of seven subunits surrounding a central cavity (one subunit is colored green in the image) . The top of the cavity is sealed by cap of seven smaller subunits. The chaperone works by capturing small unfolded proteins in the cavity where the hydrophobic environment encourages rapid folding to the correct conformation. Aggregation is also prevented by keeping the folding protein away from other proteins.

The inside of the cavity is referred to as an Anfinsen cage after Christian Anfinsen, a Nobel Laureate who worked on protein folding (see next Wednesday's Nobel Laureate). The release of unfolded protein is coupled to the hydrolysis of ATP. This is a common feature of most molecular chaperones.

Daniel vs the Christians

Let me make it clear that I'm not a fan of Daniel Dennett. I think his version of evolution is sophomoric and wrong. His book "Darwins' Dangerous Idea" was one of the worst books on evolutionary theory that has ever been published.

Nevertheless, from time to time Dennett gets things right. One of those times was in the New York Review of Books last month where he took on Allen Orr [letter from Daniel Dennett].

You might recall the kerfuffle over Orr's review of The God Delusion. Orr claimed that Dawkins had ignored all the more sophisticated arguments for the existence of God. Here's part of Dennett's reply,

H. Allen Orr, in "A Mission to Convert" [NYR, January 11], his review of Richard Dawkins's The God Delusion and other recent books on science and religion, says that Dawkins is an amateur, not professional, atheist, and has failed to come to grips with "religious thought" with its "meticulous reasoning" in any serious way. He notes that the book is "defiantly middlebrow," and I wonder just which highbrow thinkers about religion Orr believes Dawkins should have grappled with. I myself have looked over large piles of recent religious thought in the last few years in the course of researching my own book on these topics, and I have found almost all of it to be so dreadful that ignoring it entirely seemed both the most charitable and most constructive policy. (I devote a scant six pages of Breaking the Spell to the arguments for and against the existence of God, while Dawkins devotes roughly a hundred, laying out the standard arguments with admirable clarity and fairness, and skewering them efficiently.) There are indeed recherché versions of these traditional arguments that perhaps have not yet been exhaustively eviscerated by scholars, but Dawkins ignores them (as do I) and says why: his book is a consciousness-raiser aimed at the general religious public, not an attempt to contribute to the academic microdiscipline of philosophical theology. The arguments Dawkins exposes and rebuts are the arguments that waft from thousands of pulpits every week and reach millions of television viewers every day, and neither the televangelists nor the authors of best-selling spiritual books pay the slightest heed to the subtleties of the theologians either.

Who does Orr favor? Polkinghorne, Peacocke, Plantinga, or some more recondite thinkers? Orr brandishes the names of two philosophers, William James and Ludwig Wittgenstein, and cites C.S. Lewis's Mere Christianity, a fairly nauseating example of middle-brow homiletic in roughly the same league on the undergraduate hit parade as Lee Strobel's The Case for Christ (1998) and transparently evasive when it comes to "meticulous reasoning." If it were a book in biology—Orr's discipline—I daresay he'd pounce on it like a pit bull, but like many others he adopts a double standard when the topic is religion....

[Hat Tip: [RichardDawkins.net]

Sylvia Browne Is a Fraud

 
The so-called psychic Sylvia Browne is a fraud. There's a website called stopsylviabrowne devoted to exposing her. Recently Sylvia Browne's lawyers tried to shut down the website but the owner wasn't cowed. He got his own lawyers to fight back. You should see the letter they sent to Sylvia Browne's lawyers. Read it [here].

Delicious.

[Hat Tip: The Bad Astronomer]

The Separation of Church and State

John Pieret and I have often argued about religion and science. He is a classic appeaser even though he doesn't support any of the established religions. John notes that this is the anniversary of a famous court decision in America [Madison's Avenue].

John list ten "rules" concerning the separation of church and state. I thought I might respond to those rules in the context of a non-American. It will be interesting to see if there's a difference in how Americans perceive "separation of church and state" and how it's perceived in other countries.

John's rules are in boldface and my response are in italics.

10 Commandments of the Separation of Church and State:

1. Neither a state nor the Federal Government can set up a church.

I disagree in the sense that many countries with a state church don't seem to have as the same problems as the USA. So, I would not advocate a hard and fast rule that forbids state religions. I don't think a modern country should set up a new state religion but neither do I think that existing ones need to be abolished. I would definitely support disestablishment, myself, but antidisestabishmentarianism shouldn't be illegal.

2. Neither a state nor the Federal Government can pass laws which aid one religion, aid all religions, or prefer one religion over another.

I disagree with this as well. There's nothing seriously wrong with tax breaks for religious charities, for example and there's nothing wrong with laws that proclaim national holidays on days with special religious significance for one group. (e.g., Good Friday) I prefer to live in a society that chooses not to favor religions but it shouldn't be illegal.

3. Neither a state nor the Federal Government can force nor influence a person to go to or to remain away from church against his will.

Nobody disagrees with the "force" part but the "influence" part is a different story. I favor a government that influences people to stay away from churches that preach hatred and bigotry.

4. Neither a state nor the Federal Government can force a person to profess a belief or disbelief in any religion.

Everyone agrees with this one.

5. No person can be punished for entertaining or professing religious beliefs.

I agree in principle. There might be some extreme cases of religions that merit banning but these are exceptions. In a case where one's religious beliefs might case harm (e.g., refusing blood transfusions for children) the state is justified in stepping in even though this can easily be seen as punishment.

6. No person can be punished for entertaining or professing religious disbeliefs.

This one seems pretty straightforward. It's the one that's most difficult to enforce, however. Right now atheists would have a very hard time getting elected in many parts of the USA.

7. No person can be punished for church attendance or non-attendance.

Same as #5.

8. No tax in any amount, large or small, can be levied to support any religious activities or institutions, whatever they may be called, or whatever form they may adopt to teach or practice religion.

I disagree. Tax money is used to support religious schools in Canada and many European countries. While I would argue strongly against such a practice, I see no reason to make it against the law. It's a matter for society to decide, not the courts.

9. Neither a state nor the Federal Government can, openly or secretly, participate in the affairs of any religious organizations or groups.

Lots of countries have state religions. In modern civilized countries, they're pretty harmless for the most part. I don't see any reason to have a constitutional amendment in Great Britain.

10. No religious organizations or groups can, openly or secretly, participate in the affairs of a state or the Federal Government.

Same response as #9.

What a Surprise!

 

You are 100% atheist!

 

Hooray you are an atheist with respect to most or all gods. Good work. Hope you aren't disbelieving in the wrong one...

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All Seven Continents

 
I was just checking to see where you all were coming from when I realized that in the past few hours I've had visitors from all seven continents!!!

Isn't that amazing? (I'm pretty sure there are Sandwalk readers in Antarctica—you just can't see the white dots against the snow.)

Uncommon Descent Supports Bigots

 
Considering the mess that Paula Zhan has created, you'd think the Intelligent Design Creationists wouldn't touch it with a ten foot pole. After all, they don't want to be seen defending bigots, do they?

Yep, they do. Bashing atheists and Muslims is just too much for DaveScot to resist [Karen Hunter and Debbie Schlussel - YOU GO, GIRLS!].

(I think I've figured it out. The best way to predict how the IDiots are going to behave is to assume they'll do the stupidist thing you can imagine.)

Here's the original show—the one that impressed DaveScot. Watch the followup tonight when Paula Zhan interviews Richard Dawkins. Given Paula's track record I'm predicting that she will look very stupid foolish. I'm betting the IDiots are gonna love it.

The IDiots Don't Under stand Irreducible Compexity

 
Evolution News & Views, the Intellgent Design website, has just posted a quotation from a Professor of Design and Nature(?) at Bristol University in the UK.

I've been designing systems like spacecraft for more than 20 years. One of the lessons I've learnt is that complex systems require an immense amount of intelligence to design. I've seen a lot of irreducible complexity in engineering. I have also seen organs in nature that are apparently irreducible. An irreducibly complex organ is one where several parts are required simultaneously for the system to function usefully, so it cannot have evolved, bit by bit, over time.

I thought that by now even the IDiots would know that irreducibly complex systems can arise by evolution. Apparently I was wrong. The IDiots haven't been paying attention to anything that scientists have been saying over the past 15 years.

I guess that's why they're IDiots.

American Museum of Natural History

 
The American Museum of Natural History has just opened its new exhibit on human origins (see The New York Times). PZ Myers notes a paragraph in the article about balancing religion and science,

One issue cannot be entirely sidestepped in any public presentation of human evolution: that many people in this country doubt and vocally oppose the very concept. In a corner of the hall, several scientists are shown in video interviews professing the compatibility of their evolution research with their religious beliefs.

Fine, I understand why this might be considered necessary in a science museum but shouldn't the other side be presented as well? After all, most scientists are non-believers.

Why not have a video presentation of atheist scientists who point out the conflicts between science and religion? Why not present the reasons why evolutionary biology is incompatible with many religious beliefs?

I wonder which "scientists" are featured in the presentation? Do you suppose it's the usual suspects like Ken Miller and Francis Collins or are there some Hindus, Muslims, Jews, and Buddhists as well?

Toronto City Council

 
Last Tuesday the Toronto City Council met for their annual photo. Several of the more senior—and more conservative—councillors were upset because they couldn't sit in the first row, which was reserved for the Mayor and the Executive Committee.

The squabbling persisted for so long that the photo shoot had to be canceled. I love the cartoon in today's Toronto Star and I just can't resist posting a copy. It captures the mood exactly. (It also reminds me of the Discovery Institute.)

Tuition

 
Hundreds of students turned out yesterday for a rally at Queen's Park (Ontario Parliament Buildings). Many of the students marched from the University of Toronto campus and they waited in the freezing cold for more than an hour before the contingent from Ryerson marched along College St. and up University Ave. to join them.

Like most Professors, I want tuition to be as low as possible because education is a right. The government of Ontario should at the very least hold the current tuition at its present level for the foreseeable future. It should increase direct funding to the universities to maintain quality and allow for expansion.

The long-term goal should be to provide free education to all qualified students.

How Proteins Fold

The protein shown here is pyruvate kinase, one of the key enzymes in metabolism. This particular example comes from the common domestic cat (Felix domesticus).

Cartoons such as this one are intended to show how the backbone chain of amino acids is folded to produce the final three-dimensional structure of a protein. In this case the polypeptide chain is represented by a blue ribbon. There are spiral sections representing regions of secondary structure called α-helices and flattened sections called β-strands. The β-strand regions are often twisted.

This particular protein adopts a structure with three distinct parts called domains. As a general rule, each domain has a well-defined shape with a characteristic pattern of strands and helices. The pattern is called a fold and it it thought that there are only 1000 or so different folds in the protein universe. Different folds can be combined to make up all known proteins.

(For those who might be interested, the three domain folds in this protein are TIM beta/alpha barrel, PK beta-barrel, and the PK C-terminal domain.)

When proteins are first synthesized you can think of them as a long extended chain of amino acids with no particular secondary or tertiary structure. We refer to such unordered macromolecules as random coils. Within seconds, this random coil spontaneously folds itself into a highly ordered three-dimensional structure such that every single molecule of a given protein has the exact same shape. For example, every molecule of pyruvate kinase looks exactly like the one shown here.

The rapidity of this folding reaction tells us something about the mechanism of protein folding. We know that folding is rapid and spontaneous because proteins can be purified then unfolded by treating them with certain chemicals that cause them to become denatured or unfolded. These denatured proteins can then be allowed to re-fold when the chemicals are removed.

Cyrus Levinthal did some back-of-the-envelope calculations on the rate of protein folding. He assumed that a protein could randomly try all possible three-dimensional conformations until it found the correct one. Under those conditions it would take 10⁸⁷ seconds to fold a protein of 100 amino acid residues. This is quite a bit longer than the age of the universe (6 x 10¹⁷ seconds).

Obviously, there's something wrong with the assumptions behind what came to be known as the Levinthal Paradox. As a matter of fact, the paradox was never really a paradox since the whole point of the calculation was to shown that proteins did not fold by randomly searching though the conceptual universe of all possible shapes.

The final structure of a protein minimizes the energy of the random coil by burying hydrophobic amino acids in the interior of the molecule. Hydrophobic (water fearing) amino acids are those that don't like to be exposed to water. Just as scattered oil droplets in your salad dressing will eventually coalesce to form a layer of oil over a layer of vinegar and water, so too will hydrophobic amino acids come together to form an "oily" globule in the middle of the protein. Water is excluded from this "molten globule" and this makes folding an entropically driven spontaneous reaction.

You can visualize the process by picturing a field of all possible energy levels of the random coil. The one representing the properly folded protein is the deepest well on the energy surface. The bottom of the well is the lowest energy level for the protein and this represents the stable three-dimensional structure. Protein folding, then, is like finding the well and falling down into it.

As mentioned above, the search for the lowest energy well is not a random search of all possible shapes. That would take far too long. Instead, folding proceeds in a cooperative stepwise manner with small regions of secondary structure forming first.

The most striking regions of secondary structure are the short α-helices. Certain stretches of amino acid residues will rapidly form α-helical regions involving local bonding between amino acids. These form extremely rapidly since the amino acids are already in close contact. Furthermore, the formation of these local secondary structures takes place simultaneously in many different parts of the random coil.

The helix and strand regions represent the minimal energy conformations of the local parts of the protein. Subsequent folding proceeds by forming the helices and strands into the appropriate three-dimensional folds that are characteristic of each domain. The possibilities here are much fewer than the total of all possible conformations because you are now combining blocks of amino acids that have already adopted some structure.

The figure below shows some hypothetical examples of folding pathways. Very few folding pathways have been worked out in detail but the basic principles are well understood. The biggest unsolved problem is predicting the three-dimensional structure of a protein from its amino acid sequence. This involves finding the predicted lowest energy level and that's turning out to be a tough problem indeed.

IDiot "Irony"

 
GilDodgen is one of the IDiots who post regularly to Uncommon Descent. Recently he put up a comment on a photo of Darwin's tomb that I posted one month ago. GilDodgen thought he was being so clever that he re-posted his comment in an article on Uncommon Descent [Darwin’s Final “Resting” Place]. Here's what he said,

Over at Larry Moran’s blog, where I am identified as one of the ID movement’s stellar idiots, there is a picture of Darwin’s tombstone with the caption: “Here’s a photo of Darwin’s final resting place in Westminster Abbey.”

I posted the following comment:

Darwin doesn’t have a resting place. When he died he entered eternal oblivion. Nothing he did, and nothing that any of us do, has any lasting significance or meaning.

One day our sun will turn into a red giant. When that happens its corona will expand beyond the orbit of the earth. The earth’s atmosphere will be stripped away, the seas will boil away, the sands will fuse into glass, and all life will be exterminated. There will be no record of anything anyone has ever done, created, or thought.

For those familiar with me at UD, the irony should be self-evident.

Guess what? The "irony" isn't self-evident to me. I'm not really sure what the fuss is about. Are they objecting to the phrase "final resting place" on the grounds that Darwin's soul will survive? Is he thinking that Darwin will never rest because he has to suffer forever for his heretic views? Or is it something else that I'm missing?

I dunno, so I did the normal thing and posted a question on Uncommon Descent—forgetting that I am persona non grata over there. Naturally my comment never made it past the IDiot censors. Can someone help me out? What's the problem?

As you might expect, the readers at UD are falling all over themselves in support of the clever, ironic comment by GilDodgen. For example, scordova posted the following comment at Uncommon Descent.

Gil, I noticed you pointed out your professional credentials to Moran. Actually, imho, when people like Moran are knocked off of their elistist horse by a lowly peasant, it’s a more satisfying victory. It’s more fun when people like Moran get taken out by people they view as their inferior….

"Taken out"? I was? Hmmm ... I must have missed the take out.

Incidently, I'm unaware of the "professional credentials" of GiDodgen. All I know is that he doesn't understand science and that makes him look pretty stupid. I suppose that's a form of "professional credential."

GilDodgen replied,

Good point. However, in the case of Moran, he thinks that anyone who doubts Darwin is a rube and a simpleton who should be flunked out of college for no other reason. He should be made aware that it is possible to doubt Darwin and still be capable of rational, logical thought.

Oh dear. The IDiots reveal once again that they are incapable of distinguishng between Darwinism and evolution. I have lots of doubts about the validity of Darwinism as a complete explanation of evolution and I haven't been the least bit shy about expressing those doubts.

People who doubt the exclusive role of natural selection are not rubes or simpletons. People who don't understand the real meaning of Darwinism are rubes and simpletons. There are tons of them over at Uncommon Descent.

"IDiots" is my special scientific term for those people who are anti-evoluton and anti-science. GilDodgen and scordova are IDiots. The fact that they are also rubes and simpletons is simply a nice bonus.

Flock of Dodos and Haeckel's Embryos

 
Randy Olson made a movie called Flock of Dodos where he pokes fun at the IDiots. Unfortunately, Olson made a mistake when he said that the old faked images of Haeckel's embryos were not in modern textbooks.

The Discovery Institute pounced on this error and made a clever video that discredits Olson. The DI video may have some errors of its own; for example, I'm not sure if the embryo picture in the Raven & Johnson biology textbook is actually based on a Haeckel drwaing as they say. Also, the picture of the Haeckel woodcut in the Alberts texbook isn't as significant as they imply.

In spite of the possible mistakes in the video (below) the DI has been quite clever. The IDiots have cast doubt on all the claims in Flock of Dodos because of one little slip-up.

Debbie Schlussel

 
UPDATE: PZ Myers tells us that CNN will rebroadcast the segment tonight at 8PM EST with a new panel, including Richard Dawkins (CNN must have felt the heat).

Do you remember Debbie Schlussel? She was the atheist-hating Jewish idiot who appeared on the Paul Zahn show last week (see Paula Zhan Should be Fired from CNN). Readers might recall that I was wondering whether Schlussel might have a slight bias against Muslims as well as atheists.

Well, it turns out Debbie Schlussel has been receiving emails about her remarks on CNN (Duh!). She has a blog where she has just confirmed our worst fears.

Here's part of what she says at "When Atheists a/k/a Future Muslims Attack."

I don't mind receiving the atheist hate mail, since I know that in a few years, many of these same people will either be Muslim extremists (redundant) or helping the country fall further in its fight against the creep of Islamic imposition on America . . . or both.

Look at famous atheists and what happened to them. Adam Gadahn a/k/a Azzam Al-Amriki--now a top Al-Qaeda video "personality"--was raised by his hippie Jewish father and equally bizarre gentile mother as an atheist. And look how he turned out. Ditto for hippie-spawn John Walker Lindh.

Those two people are enemies of America, and many of those who think like them are of equally weak mind. If you don't believe in anything, you'll easily fall for virtual nothings. That's why Europe is so quickly turning Islamist--because atheism dominates and Christianity is rapidly dying there. Over there, the number one cause for which atheists are suddenly finding "god" is Islam.

No, your eyes aren't deceiving you. She actually said that on her blog. Go check it out if you don't believe me. She's a genuine loony nutcase.

All the more reason why Paula Zhan should stop pretending to be a journalist.

On her blog Schussel attacks those critics who claim they just saw the Paula Zhan show.

It's hard to believe their letters because they were all attacking me for my appearance on CNN's "Paula Zahn Now," a week ago, but coincidentally each letter claims the sender just watched me on CNN. First of all, the video of that segment appears nowhere on the net. Believe me, if it did, I'd link to it.

I linked to the videos on the net and so have dozens of other bloggers who are astonished at the stupidity of CNN. It looks like Schlussel is incompetent at many different things in addition to thinking logically. Her list of failings includes searching the internet.

Read the posting on Dr. Joan Bushwell's Chimpanzee Refuge [Debbie Schlussel: A case study in 15 minutes too many] for a calmer attack on Debbie Schussel. Schlussel is a journalist who's greatest achievement to date was winning the title of "Outstanding Teen Age Republican in the Nation" in 1987 (Wikipedia). Why is it that so many kooks seem to be Republicans?

[Hat Tip: Friendly Atheist]

The Real Genetic Code

 
This is the genetic code. It shows the relationship between a sequence of nucleotides in messenger RNA (mRNA), or DNA, and the amino acids that are inserted into a growing polypeptide chain.

Each codon consists of three nucleotides and you read them from 5ʹ ("five prime") to 3ʹ ("three prime"). The first one is one the left of the box, the second one is at the top, and the third one is along the right-hand edge. The genetic code tells you that codon CUU encodes leucine (Leu), and so do codons CUC, CUA, and CUG. (The Genetic Code is redundant.)

The three STOP codons tell the protein synthesis machine to stop making protein. The methionine (Met) codon (AUG) is usually the start codon that tells the machinery to start making a protein. There are a few unusual variants of the genetic code that aren't shown in the figure.

The Genetic Code was cracked in the early 1960's when the meaning of each codon was worked out. Since then it has become routine to decode any message in the coding regions of DNA and RNA by simply referring to the genetic code shown above. For example, you can decode the following sequence of RNA if you know that it starts on the left at the initiation codon AUG.


This is the same procedure that we use to translate a string of dots and dashes sent over a telegraph line. The string of dots and dashes is the message, the Morse Code is the lookup table that we use to decode the mesage. We do not say that the string of dots and dashes is the Morse Code. We say that it's a message encrypted using the Morse Code. Similarly, we do not say that a string of nucleotides is the genetic code. It's the message that's translated using the Genetic Code.

The Wrong Version of the Genetic Code

 
Hsien Hsien Lei over at Genetics & Health has posted a recommendation for winter reading [Freakenetics: The Freakonomics of Genetics]. She suggests that Survival of the Sickest by Dr. Sharon Maolem and Jonathan Prince might be a good read.

Here's a quotation from the book,

…DNA isn’t destiny–it’s history. Your genetic code doesn’t determine your life. Sure, it shapes it–but exactly how it shapes it will be dramatically different depending on your parents, your environment, and your choices. Your genes are the evolutionary legacy of every organism that came before you, beginning with your parents and winding all the way back to the very beginning. Somewhere in your genetic code is the tale of every plague, every predator, every parasite, and every planetary upheaval your ancestors managed to survive. And every mutation, every change, that helped them better adapt to their circumstances is written there.

Now, this may or may not be a good book but I'd like to use the quotation as a way of introducing one of my pet peeves. In doing so I don't mean to impugn the sense of what's said in the quotation.

The sequence of DNA in your genome is not the "genetic code." The Genetic Code is the lookup table shown in the accompanying posting [The Real Genetic Code]. The sequence of nucleotides in your genome is the message that may be interpreted using the genetic code in the same sense that the message received over a telegraph may be interpreted using the Morse Code.

It's appropriate to say that somewhere in this message is the record of your survival but it's inappropriate to say the genetic code is altered by evolution. (At least in this context.)

I realize that when science writers use the term "genetic code" they are writing for the general public. Those writers may know the difference between the real Genetic Code and what they say in a popular article. They may know the difference, but somehow I doubt it. Most people who know the difference wouldn't make the common mistake of confusing the code with the message.

In any case, the book would be no less accurate if it talked about the message in your genome instead of the genetic code. So why not use the correct term?

Similarly, I'm getting tired of hearing about the latest sequencing project that "cracked" the genetic code. The real Genetic Code was cracked forty years ago in an astounding display of technology that earned the decoders a Nobel Prize. What sequencing projects do is determine the sequence of a genome, not its genetic code. The standard Genetic Code is (almost) universal. All species use the same Genetic Code.

Dilbert Parody

 
This is priceless. I know every one of my blogger friends is going to post this parody of Dilbert by The Bronze Blog but I can't resist. For those of you who haven't been following the saga of Scott Adams and his IDiocy, see "Is Scott Adams an IDiot?."

Click on the cartoon to enlarge.