The Taxonomy Song

 
Pop on over to Evolving Thoughts where John Wilkins has posted a YouTube video of kids singing The Taxonomy Song. Do you recognize the accent? I think they're Australian, no?

Problem is, they get the highest levels wrong (the rest is okay). How many people can correctly name the FIVE KINGDOMS of life? How many people can come up with a better classification scheme?

While you're over on John's blog, read Microbial Species - postlude. It's a discussion about how to identify bacteria species. Remember that the biological species concept doesn't work very well with bacteria because they don't have sex in the same that eukaryotes do. John has some important insights into this problem but it hurts my brain when I try and understand them.

Homer Jay Simpson Evolves

 
Everyone's going to be posting this but here it is anyway, ... just in case you don't see it elsewhere. As far as cartoon versions of evolution go, it's not bad. Just remember that individuals don't evolve, populations evolve. And don't forget that there's no direction to evolution and humans are not the only living mammal that evolved.

Internet Connection Speeds

 
Here are the results of a test for internet connection speed from InternetFrog.com. This is the speed I get at the university.

Now, here's some questions for all you technical experts out there. The download speed varies from a low of 2 Mbps to a high of close to 9Mbps. Why? Does anyone have faster connections on a regular basis?

The upload speed varies from a low of about 150 Kbps to a high of 1.7 Mbps. Why? And why is the upload speed so much slower than the download speed? Does that depend on the speed of my processor?



[Hat Tip: Kevin Black]

Happy 66th Birthday Richard Dawkins

 
Today is Richard Dawkins' birthday [RichardDawkins.net]. Go [here] to enter your own birthday message.

I may disagree with Dawkins on some parts of evolutionary theory but I think he's done a wonderful job of focusing attention on evolution as a scientific fact. I'm also a strong supporter of his attacks on superstition and support for rationality (e.g., The God Delusion).

Dawkins is just one of many intelligent men and women whose brains did not shut down when they turned 50 or 60. We need to point this out because there are, unfortunately, too many people who think that you can only make a contribution to science when you're under 40.

Monday's Molecule #19

 
Name this molecule. You must be specific but we don't need the full correct scientific name. (If you know it then please post it.)

As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureate. This one's easy once you know the molecule and make the connection. There'll be a few extra bonus points for guessing Wednesday's Nobel Laureate(s).

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

RNA Polymerase Genes in the Human Genome

 
The structure of yeast RNA polymerase II was solved by Roger Kornberg [Nobel Laureate: Roger Kornberg]. There are many different polypeptide subunits labelled Rpb1 to Rpb12 in the nomenclature used by yeast workers. The mammalian enzyme is very similar. Most of the same subunits are present but they have different names.

The core of RNA polymerase is composed of two very large subunits called Rpb1 and Rpb2 in yeast. In mammals they are called subunits A (220 KDa) and B (140 KDa). These subunits are homologous to the β and β′ subunits in bacterial RNA polymerases. The genes for these polypeptides in humans are called POLR2A and POLR2B. They are located on chromosomes 17p13.1 and 4q12 respectively.

The Online Mendelian Inheritance in Man database has entries for both genes but there are no genetic diseases associated with mutations in either gene [OMIM POLR2A and OMIM POLR2B]. This should not be a surprise since it is rare for genetic diseases to be associated with important essential genes.

Recall that mammals have four different RNA polymerases [Eukaryotic RNA Polymerases]. Both RNA polymerase I and RNA polymerase III have homologous large A and B subunits. The genes for these polypeptides are called POLR1A (194 KDa, chromosome 2p11.2), POLR1B (128 KDa, chromosome 2q13), POLR3A (155 KDa, chromosome 10q22-q23), and POLR3B (~120 KDa, chromosome 12q23.3). As is the case with the large subunits of RNA polymerase II, none of these genes are associated with metabolic diseases because they are essential, important housekeeping genes.

These genes make up a typical eukaryotic gene family. It's important to remember that a gene family refers to homologous genes within the same genome and not to a group of homologous genes from different species. Gene families arise from gene duplication events.

The "A" genes evolved from a common ancestral RNA polymerase β gene several billion years ago and the "B" genes evolved from an ancestral β′ gene. The β and β′ genes, in turn, evolved from a common ancestor near the time life began about 3.5 billion years ago.

The "A" and "B" genes have evolved independently by divergence. In such cases the family members are often on different chromosomes and the intron-exon organization of each member is very different in spite of the fact that the genes are still closely related in amino acid sequence.

In addition to the "A" and "B" genes for each RNA polymerase, there are genes for three different subunits of RNA polymerase I (POL1C, POL1D, POL1E), 12 different subunits of RNA polymerase II (SURB7 and POL2C - POL2L), and 9 different subunits of RNA polymerase III. There are also dozens of genes for the general transcription factors required for initiation, elongation, and termination. Altogether, there are at least 80 different genes required for transcription and that's not counting any gene-specific regulatory genes.

The fourth RNA polymerase in humans is the mitochondrial version. Its gene is POLRMT located on chromosome 19p13.3. The large subunit of the mitochondrial RNA polymerase is only distantly related to the others. There are no metabolic defects associated with mutations in POLRMT [OMIM POLRMT].

Happy Birthday Elton John!

 
Elton John is 6o years old today.

The Salem Conjecture

 
The Salem Conjecture was popularized by Bruce Salem on the newsgroup talk.origins. It dates to before my time on that newsgroup (1990) and I haven't been able to find archives to research the exact origin. The conjecture was explained by Bruce on numerous occasions, here's a statement from Sept, 5, 1996.

My position is not that most creationists are engineers or even that engineering predisposes one to Creationism. In fact, most engineers are not Creationists and more well-educated people are less predisposed to Creationism, the points the statistics in the study bear out. My position was that of those Creationists who presented themselves with professional credentials, or with training that they wished to represent as giving them competence to be critics of Evolution while offering Creationism as the alternative, a significant number turned out to be engineers.

This is the so-called "soft" version of the conjecture. The "hard" version is that there is something about being an engineer that leads one to become a creationist. That's not what Bruce said,

For a long the so-called "soft" hypothesis is the one I have been putting forth, not the one earlier attributed to me. I have also further qualified it by saying numerous times that religious belief was the most significant factor. The reason I prefer to call my idea a "conjecture" is that I have had only anecdotal data to support it.

The Salem Hypothesis has its own entry on Wikipedia [Salem Hypothesis]. Both versions of the Salem Conjecture are listed there. The talk.origins Jargon File is incorrect because it only lists the hard version and attributes it to Bruce Salem.

We all know that scientists overwhelmingly reject creationism so it doesn't come as a surprise that there are so few scientists in the creationists movement. Ironically, the creationists long for scientific validity while, at the same time, they attack all the basic principles of science. The few so-called scientists who subscribe to superstition get very prominent play among the creationists.

Engineers are not scientists and they did not have much scientific training in school. They are technologists (i.e., engineers) and that's not the same thing. I don't think engineers spend much time studying evolutionary theory in university. (It's probably too difficult for them.)

Among the general public the distinction between scientists and technologists is lost so whenever an engineer comes out in favor of superstition (s)he is counted as a scientist. This is what the Salem Conjecture says. Whenever you see a common run-of-the-mill creationist who claims to have scientific knowledge, chances are they're an engineer and not a scientist.

Here's how Bruce explained it on talk.origins on May 10, 1996 in response to an engineer who was objecting to the conjecture.

By your own admission you are running the risk of becoming yet another data point for something called the "Salem Hypothesis" or "Salem Conjecture" in which I noticed some time ago the number of people publically supporting Creationism whether in Creationist publications or this group claiming to be "scientists" were mostly engineers. Most of them had little knowledge of the scientific disciplines that relate to the scientific acceptance of evolution and an old earth. Many people have noticed subsequently that while engineers as a group seem more inclined as a majority to believe Darwin, those with a background in certain religions and those concerned with intelligent design seemed predisposed to accept
Creationism or the arguments that support it.

This morning Larry Faraman, the author of the blog I'm From Missouri, posted this message [The Salem Hypothesis].

I have been aware for a long time that engineers have an especially strong tendency to be skeptical of Darwinism, but I just now learned that this tendency has a name: the "Salem hypothesis." I am especially interested in this tendency because I am an engineer myself ....

I feel that the reason why we engineers tend to be skeptical of Darwinism is that we are a logical, practical, no bullshit, cut the malarkey, "I'm from Missouri," "show me" kind of people.

The irony is palpable. Mr. Faraman, an engineer, is skeptical of evolutionary biology and, by implication, most of the rest of science. On the other hand, he's not the least bit skeptical of creationism. Another solid data point for the Salem Conjecture. In this case, it's the "hard" version that Mr. Faraman is supporting. He claims that training in technology predisposes one to believe in superstitious nonsense. Maybe he's right. I look forward to hearing from other engineers on this point.

BTW, Missouri must be a very strange state. These days when someone begins a conversation with "I'm from Missouri" it's usually following by something irrational.

Dennis Kucinich on Universal Health Care

 
This is why I would vote for Dennis Kucinich ... if only I could vote. Why don't you vote for him?



[Hat Tip: Corpus Callosum]

Gene Genie #3

 
Hsien Hsien Lei has just posted Gene Genie #3 at Genetics and Health. There are >26,000 genes in the human genome and we hope to cover them in a finite amount of time. At this rate we'll be done sometime in the Spring of 2207! Let's pick up the pace, fellow bloggers.

The next Gene Genie (#4) will be hosted right here on Sandwalk. Send me your articles by email or submit them at blogcarnival [gene genie]. You ain't never had a friend like Gene Genie!

Summary of Genes on Human Chromosomes

 
I've prepared a table of the number and types of gene on each human chromosome based on the data at the Ensembl site managed by the Wellcome Trust Sanger Institute in Cambridge UK.

The total number of genes comes to 26,290.

The different categories of gene are:

Known: The "known" protein-encoding genes are those for which there is solid full-length cDNA evidence that they are actually expressed.

Novel: The "novel" class is reserved for genes that are predicted but lack confirming evidence.

miRNA: Micro RNAs are short single-stranded RNAs that are thought to play a role in regulating gene expression.

snRNA: Small nuclear RNAs are required for a number of cellular processes such as RNA processing. Those required for splicing associate with proteins in the nucleus to form small nuclear ribonuleoprotein particles or "snurps."

rRNA: Ribosomal RNA forms the core of the ribosome.

snoRNA: Small nucleolar RNAs are required for proper processing of ribosomal RNA. The are located in the nucleolar region of the nucleus because that's where ribosomal RNA is made.

other RNA: The "other" category includes transfer RNA (tRNA) and some specialized RNAs such as 7SL RNA and P1 RNA.

Chr.	Size (kb)	Protein known	Protein novel	Pseudo- genes	miRNA	rRNA	snRNA	snoRNA	other RNA	Total     Genes
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y	247,249,719 242,951,149 199,501,827 191,273,063 180,857,866 170,899,992 158,821,424 146,274,826 140,273,252 135,374,737 134,452,384 132,349,534 114,142,980 106,368,585 100,338,915 88,827,254 78,774,742 76,117,153 63,811,651 62,435,964 46,944,323 49,691,432 154,913,754 57,772,954	2,146 1,375 1,111 828 922 1,103 984 736 921 819 1,390 1,088 358 661 657 915 1,232 293 1,428 612 271 509 878 86	54 84 47 59 63 29 68 32 38 35 52 51 10 28 65 49 60 20 49 15 23 26 37 27	159 40 45 32 23 81 48 19 66 52 61 38 41 25 34 25 56 8 45 29 9 39 80 2	43 23 24 21 19 17 31 17 26 16 19 21 14 51 15 14 32 5 71 16 7 15 58 6	42 24 21 13 22 16 14 14 11 17 19 15 9 14 6 13 10 42 6 8 10 2 19 6	178 116 89 81 74 82 64 61 43 64 51 77 29 42 43 39 47 12 14 32 5 18 64 14	60 37 30 16 18 25 27 21 15 8 40 21 12 56 95 14 29 12 12 16 5 11 25 3	93 74 66 58 67 56 62 39 47 42 47 65 34 38 35 31 52 21 18 34 6 20 48 2	2,616 1,733 1,388 1,076 1,185 1,328 1,250 920 1,101 1,001 1,618 1,338 466 890 916 1,075 1,462 401 1,598 733 325 601 1,129 140

Daisy, the Canada Goose

 
From KARE 11 News in Minneapolis, St. Paul, Minnesota (USA) [Daisy the Goose]. Why would evolution favor behaviors where a beagle, a Canada goose, and a human could get along in a boat? The video on the TV station's website is much, much better than the YouTube video. It's worth watching.

PZ's Hooked a Live One!

 
Hop on over to Pharyngula where PZ Myers is pointing out the deficiencies of an IDiot school teacher in Colorado [What's the matter with Colorado?].

This guy, Ken Poppe, has actually written a book exposing his ignorance. Look at the cover—that's supposed to be DNA but the structure is so wrong it makes you wonder if Poppe knows anything about science at all.

But here's the fun part. Ken Poppe has popped into Pharyngula to comment on PZ's post. Poppe's first comment is "I'm not afraid of your witchhunt. Bring it on, secularists. Bring it on." It goes downhill from there.

How Many Genes Do We Have?

 
The number of genes in the human genome flutuates on a monthly basis as the genome annotators add new genes and remove false positives. It's an ongoing process that's not likely to be complete in the near future.

The original draft sequences of the human genome had between 25,000 and 30,000 genes but these numbers were not reliable since they were based entirely on computer predictions. The programs were still in the testing stage for complex genomes when they were used in 2001. They are much better now but it really takes human intevention to assess whether a prediction is correct or not. The annotation process is tedious.

The latest summary from NCBI is based on the Oct. 17, 2006 genome assembly [NCBI Reference Assembly]. It lists 28,961 genes for the public genome and 26,245 for the private Celera assembly.

The Ensembl site has better data because the curation seems to be more rigorous. It lists 26,720 genes of which 3,994 have RNA products (mainly ribosomal RNA, tRNAs, and snoRNAs) [Ensembl Homo sapiens]. This is not much different than the NCBI number. It looks like the total number of genes is stabilizing at 27,000 total genes and about 23,000 protein encoding genes.

Carl Zimmer recently posted an article about the number of genes in the human genome [You Don't Miss Those 8,000 Genes, Do You?]. He referred to the PANTHER database where they quote 25,431 genes on their current website [PANTHER pie chart]. This differs considerably from the 18,308 genes shown in Zimmer's original article at this site [PANTHER filtered NP]. The difference is due to filtering the total number of genes (25,431) by showing only those that have a RefSeq entry in the Entrez database. This is an underestimate since not all genes have been assigned a RefSeq entry, particularly those that produce an RNA product rather than a protein.

[Thanks to Scientia Natura for the cartoon]

Your Hotel Key Card Contains Personal Information and Credit Card Numbers

 
Friday's Urband Legend: FALSE

I received this warning in an email message from a friend.

Ever wonder what is on your magnetic key card?

Answer:
a. Customer's name
b. Customer's partial home address
c. Hotel room number
d. Check-in date and out dates. Customer's credit card number and expiration date!

When you turn them in to the front desk your personal information is there for any employee to access by simply scanning the card in the hotel scanner.

An employee can take a hand full of cards home and using a scanning device, access the information onto a laptop computer and go shopping at your expense.

Simply put, hotels do not erase the information on these cards until an employee re-issues the card to the next hotel guest.

At that time, the new guest's information is electronically "overwritten" on the card and the previous guest's information is erased in the overwriting process.

But until the card is rewritten for the next guest, it usually is kept in a drawer at the front desk with YOUR INFORMATION ON IT!

The bottom line is:
Keep the cards, take them home with you, or destroy them.

Snopes debunks this urban myth at [Card Sharks].

They say,

In January 2006, Computerworld investigated the key card rumors by collecting and examining over 100 hotel card keys and found no personally identifiable information on any of them:

As part of a Computerworld investigation into the allegations, reporters and other staff members who traveled last fall brought back 52 hotel card keys over a six-week period. The cards came from a wide range of hotels and resorts, from Motel 6 to Hyatt Regency and Disney World. We scanned them using an ISO-standard card reader from MagTek Inc. in Carson, Calif. — the type anyone could buy online.

We then sent the cards to Terry Benson, engineering group leader at MagTek, for a more in-depth examination using specialized equipment. MagTek also gathered cards from its own staff. In all, 100 cards were tested.

Most cards were completely unreadable with an off-the-shelf card reader. Neither Benson nor Computerworld found any personally identifiable information on them. Based on these results, we think it's unlikely that hotel guests in the U.S. will find any personal information on their hotel card keys

We also purchased our own MagTek card scanner and have scanned several dozen magnetic room keys we acquired during our various hotel stays over the last few years and likewise found not a single key with any personal information stored on it.

Nevertheless, the rumor dies hard. In a followup report consumeraffairs.com claims that there have been instances of personal information stored on a hotel key card [Hotel Key Cards: Identity Theft Risk or Not? "Mythbusters" Aside, the Answer's Not Clear-Cut]. In some cases it's because thieves have stolen hotel key cards and entered stolen credit card information so the key cards can be used as fake credit cards. In other cases, it appears there were hotels that encoded personal information in the past. (These reports sound a lot like hearsay.)

Forgetfulness - Billy Collins Animated Poetry

 
I was just sent this a few minutes ago. (My wife again! Is there a message here?) I'm posting this right away, partially in hono(u)r of PZ Myers who just turned 50, but mostly so I won't forget.

How RNA Polymerase Works: The Topology of the Reaction and the Structure of the Enzyme

 
Transcription is one of the most important steps in gene expression. During the elongation phase, the transcription complex moves along double-stranded DNA creating a transcription bubble by local unwinding of the helix (Transcription). As RNA is synthesized it forms a transient DNA:RNA helix at the active site of the enzyme (How RNA Polymerase Works: The Chemical Reaction). We now know what this transcription bubble really looks like, thanks to the work of 2006 Nobel Laureate Roger Kornberg

The figure on the left is taken from a review in Science magazine written by Aaron Klug (A Marvellous Machine for Making Messages). It shows the structure of the RNA polymerase II complex (Eukaryotic RNA polymerases) associated with a DNA:RNA hybrid that Kornberg's lab synthesized. They solved the structure of the co-crystal.

The solid blue and green lines represent fragments of DNA. As you can see from the diagram it is in the form of a double helix at the front end of RNA polymerase where it enters the groove on the leading edge. (The transcription complex is moving from left to right.) The DNA is gripped by the "jaw" region near the opening of the grove.

As the double-stranded region reaches the active site (identified by the purple Mg²⁺ ion), it unwinds to a single-stranded form creating a bubble. The bubble isn't actually seen in the crystal structure but its location can be inferred (dotted green and blue lines).

It looks like the unwinding is promoted when the DNA runs into the "wall" and is forced to make a sharp upward turn before exiting near the "clamp" where the two strands of DNA come back together to form a helix.

The blue strand of the transcription bubble is the template strand and part of it is associated with a short strand of RNA (red) behind the active site. There's a large funnel at the bottom of the enzyme that serves as a pathway from the outside to the site of polymerization. This is where nucleoside triphosphates (NTPs) enter and leave the active site. It also appears to be the site where the 3′ end of the RNA is extruded when the enzyme backs up for proofreading (backtracking).

The "bridge" part of the enzyme is required for the translocation step. This is the step following addition of a ribonucleotide when the enzyme has to shift by one nucleotide (base pair) to the right. The new 3′ end of RNA has to be re-positioned at the active site during this shift. At the same time, one base pair of DNA is unwound by the "fork" region of the enzyme and one base pair is reformed at the back end of the bubble by the "zipper" region.

The "bridge" acts like a flexible ratchet allowing a shift of one base pair while maintaining a grip on the growing end of the RNA molecule. This movement is steered by the "rudder."

Most of these terms ("bridge," "rudder" etc.) refer to short α helices or loops within RNA polymerase and almost all of them are part of the conserved β and β′ subunits. The same features are seen in the bacterial enzymes although the resolution of the bacterial enzyme structures is not good enough to decipher the translocation step. This is one of the achievements of the Kornberg group in the two famous papers (Gnatt et all, 2001; Cramer et al., 2001).

Gnatt, A.L., Cramer, P. , Fu, J., Bushnell, D.A., and Kornberg, R.D. (2001) Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science 292:1876 - 1882.

Cramer, P. , Bushnell, S.A. and Kornberg, D.A. (2001) Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science 292:1863 - 1876.

Killer Pet Food?

 
Menu Foods is a company that makes pet food. Their headquarters is in Mississauga, Ontario (Canada) not far from where I live. The plants that make the pet food are located in the USA.

According to some reports, about 16 cats and dogs have died in recent weeks, allegedly of kidney failure. There are claims that nine cats and one dog died while participating in a taste test run by Menu Foods (FDA says wheat gluten may be pet death cause). Other reports say that seven animals have died (CTV News). In some reports these seven animals were supposed to have died in a test for pet food contamination run by Menu Foods.

It's very confusing. The various reports seem to suggest that there were "only" about nine pets who died from contaminated food in all of North America over the past two months. It has been reported that most (all?) were fed products made by Menu Foods. I'm not sure what the probabilities are here. It looks like Menu Foods makes just about every kind of pet food on the market.

In any case, the company acted quickly to recall all suspect cat food and dog food. This means 60 million units under 95 different brand names. They began testing the recalled food to see if there was anything wrong. The latest word is that they can't find anything wrong (Company can't explain why its pet food is fatal). The only remaining possibility is a problem with wheat glutton according to Paul Henderson, the chief executive and president of Menu Foods.

“Our hypothesis is that it is that ingredient that in fact represents the highest probability as to the cause,” Henderson said. “But we have been unable to prove that through scientific information.”

The wheat was supplied by a manufacturer in Kansas.

This is beginning to look suspicious. I'm not convinced that the known deaths were due to a problem with the food in spite of the scary headlines. Is it a case of mass hysteria or is there really something mysterious in the pet food that's killing cats and dogs?

NBC News aired a segment on the controversy where Brian Williams interviewed veterinarian Lisa Moses of Boston. You can watch the interiew on the MSNBC Website. It sounds to me like she has no evidence whatsoever that "lethal" pet food is associated with the complaints she's hearing from concerned pet owners. Nevertheless, she's looking at all cases of kidney failure in the past six months to see if the pets ate food that was manufactured by Menu Foods. (You can be certain they did.)

I'm skeptical, but Lisa Moses isn't. You can bet that angry pet owners are going to sue the pants off Menu Foods no matter what the scientific evidence says.

There are some bloggers who are convinced they know what's happening (Examining Animal Rights And Wrongs!).

It breaks my heart every time I hear of another pet dying from the 60 million tainted cans and pouches of wet dog and cat food that has been recalled. I get outraged when I realize that there is very little legal recourse that can be taken because animals are considered property rather than a member of the family. Shit! I’ve had some pets I’ve liked better than some members of my family!

It’s been a week since Menu Foods of Canada, told the public of the danger that face their pets if they eat their food sold in the the U.S. under almost 100 different names and they aren’t any closer to finding out what is causing animals to die from kidney failure! What amazes me are the stats released yesterday, which show the company tested the food months ago and one out of six animals died from eating the food! ONE OUT OF SIX! Wasn’t that enough reason to keep the product off the market?

If it's true that Menu Foods tested animals months ago and discovered that one in six were killed by their food then we have a real scandal. But I can't find any confirmation of that fact except a quotation from some FDA official who doesn't give a source.

Does anyone know the truth?

Dumping Darwin from British currency

 
Bill Dembski has just posted this on his blog [“No thanks, I’ll take two fivers” — Dumping Darwin from British currency].

British paper currency — the 10-pound note — features Charles Darwin. (The custom is that the notes all have the Queen on one side and a famous Briton on the other. The notes are in denominations 5, 10, 20, and 50; there are no 1-pound or 2-pound paper notes, these are coins).

A couple of days ago the Bank of England issued a new 20-pound note, using new security features, and took the occasion to change the “famous person.” This is a news-worthy cause for British Darwin-doubters, who should urge that Darwin be dumped from the 10-pound note whenever there is a new security-upgrade version, on grounds that he is the chief prophet of the materialist religion, and his presence on the 10-pound note is an inappropriate endorsement of that materialist religion and its related anti-religious ferment. Now, it’s true that Britain has no 1st Amendment, but still, Britain is trying to be multi-cultural. A part of the effort could include a long list of choice inflammatory quotes from the new anti-religion books currently out in the bookstores (and in Darwin’s own writings — see the previous post here at UD); the effort could point out that the government, by honoring Darwin, implicitly lends its prestige to their venom.

A worthy replacement on the 10-pound note would be William Wilberforce, the anti-slavery crusader, particularly in light of the new movie. As it happens the Fabian Society is also in favor of dumping Darwin, and offers Wilberforce as a possible new famous person — at least, that is what one website says. Thus, this effort would also kick-off a comparison of what good has been brought to the world by these two people — Darwin vs. Wilberforce. Nazi Eugenics vs. the abolition of slavery. Is there really any contest?

Which brings up the reason I keep posting juicy bigotted and racist quotes by Darwin and his disciples here at UD. While the intellectual community may know them, the general public does not. Suppose the public decided that every time it accepted a “Darwin” (a 10-pound note) in payment or in change for a purchase, it was implicitly endorsing those terrible quotes? People would likely say, “No thanks, I’d rather have two fivers. I don’t take money that praises racists and bigots — and neither should you.”

In other words, promote a boycott of the Darwin 10-pound note because it promotes racism. It’s like putting Robert E. Lee on the ten-dollar bill because he was a great general, and ignoring the cause he served. This would work particularly well because the goal of the Fabians and other multiculturalists is to re-define Britain to be racially-inclusive. Thus there is a particular reason to highlight the racism of Darwin and get rid of him.

This would also be a good way to start a counter-reaction to the ‘Darwin Deification’ that we are going to get in 2009. Deifying Darwin is contrary to the multicultural goal of the British intelligentia, and it encourages the worst anti-religious bigotry of Dawkins et al.

Is it just me or has Dembski changed in the past few years? I don't think he used to be so anti-Darwin. I thought he was above the petty name-calling that has characterized many of his fellow travellers.

How RNA Polymerase Works: The Chemical Reaction

 
During the elongation step in transcription, the transcription complex consisting of RNA polymerase plus various elongation factors moves along the double-stranded DNA copying the template strand to produce a single-stranded RNA. In the example shown below the RNA product is mRNA and the enzyme would be RNA polymerase II in eukaryotes.


The transcription bubble spans about 20 nucleotides of DNA. This corresponds to the opening of two turns of the double helix. During transcription, a transient DNA:RNA double helix forms and this is sufficient to form one turn of the hybrid helix. As the complex moves down the gene from left to right, ribonucleotides are added one at a time to the growing 3′ end of the RNA. This is positioned in the active site of RNA polymerase.

The known structures of the bacterial and eukaryotic RNA polymerases have allowed workers to decipher the details of transcription in a way the wasn't possible before these structures were available. I'm going to describe the steps by which this amazing molecular machine adds nucleotides to make RNA.

Let's begin by looking at the chemical reaction. An incoming ribonucleoside triphosphate (blue) aligns with the DNA template strand to form a base pair. G pairs with C and A pairs with T/U. In the figure we use generic bases B and B′ to represent the real bases. For each addition, a number of different nucleotides need to be tested to see if they match the base on the template strand. Since there are four different ribonucleotides this means that, on average, 25% of the pairing attempts will be successful. The unsuccessful nucleotides have to be allowed to escape from the active site. Since the active site is buried deep within the enzyme, there must be a channel that allows ribonucleotides to diffuse easily to and from the active site.

Once a proper base pair has formed, the chemical reaction takes place. In technical terms this is referred to as a nucleotidyl-group-transfer reaction. It involves a nucleophilic attack by the electron-rich oxygen of the 3′ hydroxyl group on the α-phosphorus of the incoming ribonucleoside triphosphate. The result is the formation of a new phosphodiester linkage and the release of pyrophosphate. The mechanism of the reaction requires a metal ion (Mg²⁺) at the active site. Subsequent cleavage of pyrophosphate helps drive the reaction in the direction of RNA synthesis.

The rate of the reaction in eukaryotes is on the order of 50 nucleotide additions per second. This means that the precursors (nucleoside triphosphates) have to diffuse into and out of the active site very rapidly.

The stage is now set for the addition of the next ribonucleotide. Before this can happen the transcription complex has to shift by one base pair in the direction of transcription so the 3′ hydroxyl group of the most recently added nucleotide is now positioned in the active site next to the Mg²⁺ ion. Looking at the top figure you can see that several other things have to happen simultaneously. The DNA helix has to uniwind by one base pair in front of the transcription complex and rewind by one base pair at the back of the the bubble. The short DNA:RNA helix also has to unwind by one base pair. This all happens without the complex falling off the DNA because this is a highly processive reaction. (A processive reaction is one that doesn't release the polymer as it's being synthesized. )

In another post I'll show how these molecules fit into the RNA polymerase structure.

No sex for 40 million years? No problem

 
My wife sent me a link to this story [No sex for 40 million years? No problem].

I didn't know she had been following the debate on the evolution of sex. I guess all that science talk around the house is finally having an effect. John Logsdon is already on top of the story [Bdelloid Rotifers-Ancient Asexuals?]. I wonder who told him about it?

The Heterosexual Agenda: Exposing the Myths

 
Read this eye-opening exposé of the heterosexual lifestyle [The Hetereosexual Agenda: Exposing the Myths]. Don't believe the nonsense you've been hearing about the heterosexual lifestyle. It is not harmless. It threatens the family and has the potential to bring down our society. Now is the time to take action against heterosexuals. Should they be allowed to marry?

Those of us who have fallen into the sinful lifestyle of heterosexuality need to think seriously about changing. It's not genetic. You do have a choice!

Heterosexuals have rebelled against the norms that have held civilization together for all of human history. This rebellion has become the defining characteristic of the heterosexual community. Its members have no common language, religion, music, or other typical unifying norm. What heterosexuals have in common is the one thing that makes them different from everyone else — their sexual preference.

Heterosexuality is becoming increasingly more difficult to ignore. It is being forced upon us through legislation, taught to our children in school and promoted in the powerful arts/entertainment complex. If it is true that heterosexuality has the destructive effects on the individual and society that many believe, then it behooves us to know our enemy and forestall any further advance of heterosexuality by understanding what it is, what the heterosexual community is up to, and how to answer their arguments in the open marketplace of ideas.

What Heterosexuals Do

Heterosexuals would have you believe that the heterosexual lifestyle is perfectly normal. They will tell you that their lifestyle choice should be the benchmark for society. But a closer look shows that their lifestyle isn’t as safe or as desirable as heterosexual militants say it is.

[Hat Tip: Monado]

Nobel Laureate: Roger Kornberg

 

The Nobel Prize in Chemistry 2006.

"for his studies of the molecular basis of eukaryotic transcription"


Roger Kornberg won the Nobel Prize in 2006 for describing for the first time the structure of eukaryotic RNA polymerase II at the atomic level. The presentation speech summarizes this achievement.

This year's Laureate in Chemistry, Roger Kornberg, has studied what the transcription apparatus looks like in eukaryotes, organisms with cells that have a defined nucleus, which include all fungi, plants and mammals, human beings as well. In choosing the model system for his studies he swam against the stream and selected baker's yeast, which is one of the simplest eukaryotes. This was a crucial choice, as yeast cells offer a number of advantages in this endeavour compared to the cells from mammals that had previously been used. For instance, it is possible to cultivate yeast on a large scale and to benefit from the simplicity with which yeast cells can be modified genetically. The transcription apparatus in yeast cells is very similar to the corresponding system in mammal cells, which suggests that it came into being at a very early stage of development.

By combining biochemical methods and a depiction technique called X-ray crystallography, Roger Kornberg succeeded in producing particularly detailed molecular models of the transcription apparatus in yeast cells. These models are so detailed that individual atoms can be discerned. Through the study of a host of different models of the transcription apparatus both on its own and while fully engaged in copying DNA to RNA, Kornberg has been able to draw new, important conclusions about the mechanisms of transcription and how it is regulated. As a result of his study we now understand, for instance, how the transcription apparatus chooses where to start copying on the DNA strand, how it selects the correct RNA building blocks and how it moves along the DNA strand while the copy is being made.

This was such an important result that it easily made the cover of Science magazine when the structure was published in June, 2001. There were two back-to-back papers from the Kornberg lab in that issue. (The papers were available online in late April.) As the presentation speech says, they choose to work with the enzyme from yeast because it is easy to manipulate genes in yeast cells. The first paper presented the structure of yeast RNA polymerase II in the form it would take during intitiation. The second paper described the elongation form of the enzyme [see Transcription].

RNA polymerase II [see Eukaryotic RNA Polymerases] is a complex molecule with 12 different subunits. Two of them are dispensible and they were not present in the crystals that Kornberg solved. The core of the enzyme is formed from the large subunits Rpb1 and Rpb2. These are the homologues of the β and β′ subunits of the bacterial enzyme and homologous subunits are found in RNA polymease I and RNA polymerase III. The other subunits (e.g., Rbo5, Rpb9) are much smaller. They make numerous close contacts with the large core subunits to form a very compact structure.

The technical achievement represented by these structures cannot be underestimated. While there are other examples of large complexes whose structures have been solved by X-ray crystallography, this was a particularly difficult case and it took about ten years to get the result that was published in the June 2001 issue of Science.

Roger is the son of Arthur Kornberg who won the Nobel Prize in 1959 for the discovery of DNA polymerase. This is the seventh parent-offspring set of Nobel Prizes—a remarkable statistic, if you think about it. Roger's brother is Tom Kornberg who studies Drosophila development at the University of California, San Francisco. They have another brother Ken—the smart one!—who's an architect.

The Stanford University site has a photo of Roger with his father and a short video clip of Roger Kornberg at the Press Conference.

Eukaryotic RNA Polymerases

There are several different kinds of RNA that can be made when RNA polymerase copies a gene. The most common kind is messenger RNA (mRNA), which then goes on to be translated into protein by the translation machinery.

Another abundant RNA is ribosomal RNA (rRNA) of which there are three different versions in prokaryotes (23S, 16S, 5S) and four in eukaryotes (28S, 18S, 5.8S, 5S). Ribosomal RNA makes up the bulk of a ribosome and it is the catalyst of the reaction joining amino acid residues.

The third well-defined class of RNA is transfer RNA (tRNA). These are the molecules that carry amino acid residues into the active site of translation. They are responsible for the correct translation of mRNA sequence according to the genetic code.

The fourth class is a catch-all category called small RNAs. It includes a variety of RNA molecules that are involved in RNA processing, regulation, etc. Some of these RNAs are also catalytic RNAs.

All types of RNA are made by a single RNA polymerase in bacteria. The genes for each of the various types have distinct promoters but the bacterial RNA polymerase can bind to all of them with the help of specific transcriptional activators. This is not what happens in eukaryotes.

In eukaryotes there are five different RNA polymerases. RNA polymerase I has become specialized for transcription of the genes for the large ribosomal RNAs (class I genes). Eukaryotic cells need massive amounts of ribosomal RNA and they have many copies of ribosomal RNA genes arrayed head to tail. The electron micrograph below shows RNA polymerase I molecules in the act of transcribing adjacent ribosomal RNA genes (TU = transcription unit, NTS = non-transcribed spacer). Apparently, it was advantageous to select for a specialized RNA polymerase concentrating on producing ribosomal RNA.

RNA polymerase II is responsible for transcribing protein-encoding genes to produce mRNA (class II genes). It has evolved some special features that allow it to be coupled to the processing of mRNA precursors. Unlike bacteria mRNA, eukaryotic mRNA is modified at the 5′ and 3′ ends and the mNA precursor can be spliced.

The cartoon on the left illustrates another important difference between prokarotic and eukaryotic RNA polymerases (in this case RNAP II). The eukaryotic enzymes are all related to each other and to the bacterial enzymes. They share the same large subunits. But in addition to the homologous subunits the eukaryotic RNA polymerases have many more secondary subunits so they are quite a bit larger than their bacterial counterparts.

The eukaryotice enzymes also interact with a greater variety of transcription factors. In the example shown, the RNAP II core enzyme is associating with several transcription factors (TF) that are required for transcription initiation.

RNA polymerase III makes transfer RNA (tRNA), small ribosoma RNA (5S RNA) and most of the small RNAs that make up the fourth class of RNA (class II genes).

The 4th and 5th types of eukarytic RNA polymerases are the mitochondrial and chloroplast versions. As you might expect, these are similar to bacterial enzymes since they were transferred to eukaryotic cells during the endosymbiotic events that gave rise to mitochondrial and chloroplasts.

In the beginning it was confusing to sort out the various RNA polymerase activities in eukaryotic cells. The problem became much simpler when it was discovered that the mushroom toxin α-amanitin (left) (Mushrooms for Dinner) specifically inhibited RNA polymerase II and not RNA polymerase I. RNA polymerase III is somewhat inhibited in mammals but not in fungi or insects. This differential inhibition allowed workers to sort out the various RNA polymerases and their specificities.

This Is Your Brain on Drugs

 
Denyse O'Leary has been telling us for months that she's preparing a new book in collaboration with Mario Beauregard, a researcher at the Université de Montréal in Montreal, Quebec, Canada.

The first publicity for this upcoming book has been spotted by an astute reader at the HarperCollins website. The title of the book is The Spiritual Brain: A Neuroscientist's Case for the Existence of the Soul. It's due to be published any day now and you can already order advance copies at Amazon.com. Here's the description.

The Spiritual Brain
Beauregard, Mario with Denyse O'Leary

THE SPIRITUAL BRAIN is a study of the scientific evidence or otherwise for the existence of a human soul. It seeks to answer the question: Did God create the brain, or did the brain create God? Mainstream neuroscience has long held that mind, consciousness, and the soul are simply by-products of electrochemical brain processes. Thoughts, feelings, and desires are all merely random by-products of the activity of the brain as an organ, and spiritual/mystical experiences are simply delusions created by the brain.

But with THE SPIRITUAL BRAIN, University of Montreal neuroscientist Mario Beauregard challenges this basic doctrine, and for the first time, a highly regarded neuroscientist seeks not to debunk traditional spiritual beliefs, but rather to support them. Using brain imaging technology on Carmelite nuns, known for going into deep prayer and trance, who agreed to have their brains monitored during these mystical experiences, Beauregard argues that spiritual experiences are actual connections to a presence outside ourselves, and that their power to transform our lives is a power which derives from an authentic encounter with an outside reality.

Rights sold: Portuguese (Brazil)/Record; English(Canada only)/HarperCanada
Publication: September 2007 (MP)
Estimated length: 288 pages

Mario Beauregard earned his Ph.D. at the Université de Montréal in 1991. His first postdoc was at the University of Texas Medical School (Houston) and his second was in neuroimaging at the Neurological Institute in Montreal (1994-1996). He is currently a researcher (chercheur agrégé) in the Departments of Psychology and Radiology at the Université de Montréal.

His website shows images of brains under different stimulation conditions. He lists one of his research interests as the neurobiology of the mystical experience. There are three projects in this category. One of them is to examine the brains of Carmélite nuns while they are haivng mystical experiences. Another is to look at patients who have survived clinical death experiences. The third study will look at the functional neuroanatomy of love.

There's nothing wrong with examining the activity of the brain while people are experiencing different states of mind. What's troubling about the book blurb is the implication that Marion Beauregard has scientific evidence that "spiritual experiences are actual connections to a presence outside ourselves, and that their power to transform our lives is a power which derives from an authentic encounter with an outside reality." I'm betting that he has no such evidence. Instead he's interpreting the bahvior of the nuns in terms of what he'd like to believe and not what he actually observes.

It will be interesting to see how the Canadian scientific community responds to the book when it comes out in a few days. This is the same community that has been highly critical of social scientists for merely hinting that intelligent could be taken seriously when a McGill Professor was denied a grant [Research Council Endorses Intelligent Design]. I can't wait to see how they treat a scientist who publishes with a genuine IDiot like Denyse O'Leary.

God and Evolution (2nd notice)

 
This is the second notice of God and Evolution, a talk about the effect of intelligent design on our education system. The lectures are in my building. I'm going. Email me if you want to meet for dinner before it starts. Several people have signed up already. You can buy tickets at the door.

The lectures are sponsored by the Centre for Inquiry, Ontario [see Standing Room Only].


Brian Alters

Dan Brooks

Mushrooms for Dinner

Julia was fed up with her husband. He was cruel and abusive and obviously preferred his own son by a previous marriage to her own son by a previous marriage. They were fighting constantly and he was heard complaining about his wife to his friends and threatening to divorce her.

She couldn't let that happen. It would mean a huge change in lifestyle. Julia decided to poison her husband by serving him mushrooms for dinner. She choose the "delicacy" Amanita phalloides because it was known to act quickly. By dawn the following day, her husband was dead.

Julia's husband was Tiberius Claudius Caesar Augustus Germanicus, Emperor of Rome, and the date was October 13, 54. Julia, better known as Julia Agrippina or Agrippina the Younger, moved quickly to install her son, Nero Claudius Caesar Augustus Germanicus on the throne.

Some mushrooms of the genus Amanita contain a deady poison called α-amanitin [Monday's Molecule #18: thanks to Matt for being the first to name the molecule]. α-amanitin is a potent inhibitor of eukaryotic RNA polymerase thus blocking transcription and preventing the expression of essential genes.

The story may not be true. Nobody knows for certain that Claudius was poisoned but by all acounts it seems likely. Nobody knows for certain that Agrippina prepared the meal herself but it seems very likely she was behind the assassination.

The story has entered the list of tales told in biochemistry class because it illustrates the importance of α-amanitin. It's rarely repeated in textbooks because of the historical uncertainties, but there's a famous telling of the tale in an earlier edition of Modern Biology by Postlethwait and Hopson. On page 229 they have a Box titled Caesar Experiments with RNA Synthesis,

For the first ten hours after Casear ate this delicacy, all seemed well. But as he digested the fungus, the α-amanitin entered his bloodstream and was absorbed by his liver and kidneys, where it began to block transcription. About 15 hours after his repast, with no new mRNA to make new proteins Caesar's liver cells stopped functioning, and nausea, diarrhea, and delirium began to hit him. Two days later, he died of liver failure. It is highly doubtful that Caesar learned to appreciate the valuable role of RNA polymerase in DNA transcription. But perhaps, in a general way, Agrippina did.

How's It Working So Far in Iraq?

 
ABC News reports on the latest poll results from Iraq [Voices From Iraq 2007: Ebbing Hope in a Landscape of Loss].

Violence is the cause, its reach vast. Eighty percent of Iraqis report attacks nearby — car bombs, snipers, kidnappings, armed forces fighting each other or abusing civilians. It's worst by far in the capital of Baghdad, but by no means confined there.

The personal toll is enormous. More than half of Iraqis, 53 percent, have a close friend or relative who's been hurt or killed in the current violence. One in six says someone in their own household has been harmed. Eighty-six percent worry about a loved one being hurt; two-thirds worry deeply. Huge numbers limit their daily activities to minimize risk. Seven in 10 report multiple signs of traumatic stress.

And how do they feel about the troops who are there to help them?

The survey's results are deeply distressing from an American perspective as well: The number of Iraqis who call it "acceptable" to attack U.S. and coalition forces, 17 percent in early 2004, has tripled to 51 percent now, led by near unanimity among Sunni Arabs. And 78 percent of Iraqis now oppose the presence of U.S. forces on their soil, though far fewer favor an immediate pullout.

That's not a good sign. But at least they're better off than they were under Saddam Hussein, right?

Given all this, for the first time since the 2003 war, fewer than half of Iraqis, 42 percent, say life is better now than it was under Saddam Hussein, whose security forces are said to have murdered more than a million Iraqis.

Forty-two percent think their country is in a civil war; 24 percent more think one is likely. Barely more than four in 10 expect a better life for their children.

Three in 10 say they'd leave Iraq if they could.

It's time for the foreign troops to leave. Get out as fast as possible.

[Hat Tip: Canadian Cynic]

Transcription

 
Transcription is the process where a gene (DNA) is copied into single-stranded RNA. The enzyme responsible for this process is called RNA polymerase. (DNA polymerase is the enzyme that copies DNA during DNA replication. They are very different enzymes even though they carry out similar reactions.)

Transcription can be divided into three steps: initiation, elongation, and termination. It's easiest to describe the process in bacteria because it's simpler than eukaryotic transcription. The basics are the same in all species.

The bacterial enzyme is called the RNA polymerase holoenzyme because it's actually a complex of RNA polymerase and an activator protein. The initiation step involves assembling a transcription initiation complex at the beginning of the gene. The site of initiation is called the promoter.

The first thing that happens is that RNA polymerase binds to any old sequence of DNA then it slides along the DNA looking for a promoter sequence. The non-specific binding of E. coli RNA polymerase holoenzyme is weak and it dissociates after about three seconds. However, during that time it can slide about 2000 base pairs looking for a promoter sequence. This one-dimensional search allows it to find the start of a gene and initiate transcription much more quickly than if it had to bind directly to a promoter.

Promoters have specific DNA sequences that are recognized by the activator protein. Recall that the activator protein is part of the hololenzyme complex. In E. coli the bound activators are called σ (sigma) factors. Different σ factors recognize different promoters. In other species the activator proteins may bind to the promoter first and the RNA polymerase will encounter it when it slides along DNA. The net effect is the same whether the activator binds first to DNA or to the promoter: a transcription initiation complex assembles at the promoter.
The actual initiation event requires opening the double-stranded DNA to make a transcription bubble. Then the first few nucleotides of RNA are synthesized by copying one of the strands of DNA.

At this point the activator protein releases the RNA polymerase, which is now tightly bound to the transcription bubble. Various elongation factors join the complex and transcription proceeds along the gene copying one of the strands into RNA. As the complex moves the RNA unwinds behind the RNA polymerase and the DNA reforms a double helix. The transcription bubble moves along the gene. In the example shown below the major elongation factor (NusA) is binding to RNA polymerase as the σ factor is ejected.

Note that the shift from initiation complex to elongation complex is a crucial step in initiation. The activation protein is tightly bound to the promoter and the complex would not be able to leave the promoter if it didn't dissociate from the activator protein (σ factor, in the case of E. coli).

At the end of the gene, the elongation complex encounters a specific termination signal where specific termination factors catalyze the dissociation of RNA polymerase from DNA and the completed RNA is released.

Whether or not a gene is transcribed depends on the promoter sequence. If there's an activator protein in the cell that binds to that promoter then the gene will be transcribed. The rate of transcription will depend on how much of the activator protein is present because the more activator there is the more quickly it will find and bind to the promoter.

The rate of transcription will also depend on the strength of the promoter. If the promoter sequence is a perfect match to the ideal binding site of the activator then the gene will be transcribed often. On the other hand, if the promoter sequence is similar to the ideal binding site but not a perfect match then it will be transcribed less often because the activator won't bind as tightly. Selection will favor the appropriate promoter strength—not all promoters are ideal binding sites because not all genes need to be transcribed at maximum rate.

Gene and Transcription Orientation

 
The DNA double helix consists of two strands of DNA wound around each other to form the classic helical structure. One of the most important insights into solving the structure was when Watson and Crick realized that the two strands had to run in opposite direction. The ends of each strand are identified by the carbon atom on the deoxyribose sugar. One end is called the 5′ (five prime) end because the 5′ carbon atom is exposed. The other end is called the 3′ (three prime) end because the 3′ carbon atom is exposed.

RNA (and DNA) can only be synthesized from the 5′ to the 3′ direction. What this means is that at the beginning of the gene when the transcription bubble forms it's the template strand that's copied into RNA and the beginning of the template strand is the 3′ end. (It's the opposite orientation of the newly synthesized RNA.) [see Transcription]

The complementary strand of DNA is called the coding strand because it represents the sequence of the gene product. In other words, it's the same sequence as the RNA. By convention the orientation of the gene is determined by the coding strand and not the template strand. Thus, the beginning of a gene is called the 5′ end and the end of a gene is the 3′ end;.

The electron micrograph below shows E. coli ribosomal RNA genes being transcribed. The thin line (upper right) is the Double-stranded DNA strand. Transcription of the genes begins at the initiation site (lower left). This is the 5′ end of the genes.

RNA polymerase first bound to the initiation site and began transcribing in the 5′ to 3′ direction as shown. As the transcription complex moves along the gene the RNA product gets longer. In this case it is bound to protein so it looks compact. About halfway along the genes the RNA is processed by cutting and that's why it seems to get shorter near the middle of the gene.

The large ribosomal RNA is in the second half of the transcribed region. You can see that the RNA in the second half is larger than the small ribosomal RNA in the first half.

Note that there are many transcription complexes transcribing this region at the same time. In fact, they are about as closely packed as they can possibly be. These genes are being transcribed at the maximum possible rate. They have a very strong promoter.