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.

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.