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Wednesday, September 07, 2011

Carnival of Evolution #39

This month's Carnival of Evolution (39th version) is hosted by Cromercrox, a "Celebrity Nutritionist" who lives in Cromer, Norfolk, England (United Kingdom). It blogs at The End Of The Pier Show: Carnival of Evolution #39.

The main subject headings are:
  • The Books! The Books!
  • The Birds! The Birds!
  • Tempo, Mode and the Tangled Bank
  • Genes and Jumpers
  • One Species Or Two?
  • The Brain! The Brain!
Next month's Carnival of Evolution will be hosted by Kevin Zelnio on EvoEcoLab. You can submit your postings at Carnival of Evolution.


Thursday, September 01, 2011

Canadian National Vimy Memorial

We're in Brussels babysitting my granddaughter Zoë while her parents are house hunting in Los Angeles.

Yesterday we went to see the Canadian National Vimy Memorial on Vimy Ridge, the site of an important battle in April 1917. Thousands of Canadians died in the battle.

Zoë liked climbing on the steps and statues.

There are 11,000 names engraved on the memorial. They represent Canadian soldiers who died in France during World War I and whose remains were never recovered. One of the names is Lance Corporal Robert Alexander Hood (1895 - 1917), a distant cousin of Ms. Sandwalk. He died on April 12, in 1917 during the final days of the battle of Vimy Ridge.

We found his name.



Saturday, August 27, 2011

Praise for Canadian Blood Services


Last week I criticized the Canadian Blood Services for a stupid website called "What's Your Type?" The website associated certain personality traits and diet preferences with your blood type and also gave out false information about the origin of the various blood types [Shame on Canadian Blood Services].

Many people wrote letters to the Canadian Blood Services complaining about the obvious woo. They usually received a form letter saying that the site was not meant to be serious. It was for amusement only and whenever donors showed up for typing they would be told the real science behind blood types. In response to those form letters I wrote to explain that the actual science on the website was wrong—how were they going to explain that as a form of entertainment?

I'm pleased to report that the website is gone [What's Your Type?]. Now you just get a message explaining why you should know your blood type.

I never received a replay from Canadian Blood Services but PZ Myers posts a copy of a letter that some have received.
Dr. Sher has asked me to respond to your recent e-mail regarding our What's Your Type? new donor recruitment program. I understand that you have also sent an e-mail communicating your concerns to www.whatsyourtype@blood.ca and that others from our organization have provided you with specific details in response. I can confirm that the content you object to has been removed from our web site. The marketing materials for this program are being revised.

Thanks again for sharing your views with us.

Ian Mumford
Chief Operating Officer
Canadian Blood Services
Congratulations, Canadian Blood Services. You did the right thing.


Friday, August 26, 2011

Revisiting the Central Dogma in the 21st Century

James A. Shapiro is an interesting character. He claims that he is opposed to both neo-Dawinism and Creationism (upper case "C") and he claims to offer a "Third Way." That "third way" appears to be indistinguishable from Intelligent Design Creationism although Shapiro never admits to being an advocate of intelligent design. Instead, he prefers to let his "science" do the talking and points out that it's science that leads us to the conclusion that life is designed.

Shapiro has published scientific articles with Richard Sternberg who advocates a similar position but who has become one of the poster boys of the Discovery Institute and one of the stars of the movie Expelled: No Intelligence Allowed. Like Sternberg, Shapiro is admired by IDiots [Non-supernatural ID?: University of Chicago microbiologist James Shapiro works with ID guys, dismisses Darwinism, offers third way].

One of the characteristics Shapiro shares with the IDiots is attacking evolution. In this post I want to review a paper he published in 2009 on "Revisiting the Central Dogma in the 21st Century" (Shapiro, 2009).

The correct version of the Central Dogma of Molecular Biology is:
... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)

The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. (F.H.C. Crick, 1970)
In other words, the flow of information is from nucleic acid to protein and never from protein to nucleic acid.

The incorrect version of the Central Dogma of Molecular Biology is what Crick referred to as the "Sequence Hypothesis" and what we now know as a simplified version of the standard pathway for information flow from genes that specify a protein product. The incorrect version is often presented in textbooks as the real Central Dogma although that's slowly changing [The Central Dogma Strawman].

None of this should be a problem for someone who is writing a scholarly article for the scientific literature since we expect such a person to have read the relevant references (Crick, 1958; Crick, 1970). They should get it right. Let's see how Shapiro does when he says ...
The concept was that information basically flows from DNA to RNA to protein, which determines the cellular and organismal phenotype. While it was considered a theoretical possibility that RNA could transfer information to DNA, information transfer from proteins to DNA, RNA, of other proteins was considered outside the dogma and "would shake the whole intellectual basis of molecular biology [Crick, 1970].
That sounds pretty good but the first part is a little troubling. Which version does Shapiro actually believe he's "revisiting"?

Chris Talks to God


Chris DiCarlo tries to teach God about philosophy. He doesn't do so well.

Chris is coming to Toronto (from Guelph) on Sept. 9th to talk about his book, "How to Become a Really Good Pain in the Ass" [Centre for Inquiry]. He'll also be visiting/has visited Vancouver, Kelowna, Kamloops, Calgary, Edmonton, Saskatoon, Ottawa, and Montreal.




Thursday, August 25, 2011

Junk & Jonathan: Part 11—Chapter 8

This is part 11 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."


The title of Chapter 8 is "Some Recent Defenders of Junk DNA." It is Wells' attempt to deal with a very small percentage of the criticisms of his claim.

He begins with a reference to a 2003 paper that reported on transcription of a pseudogene and proposed a function for that transcript. He then references a 2006 paper that refutes the earlier study showing that the pseudogene transcript has no function. Good for Wells. That means he is aware of the fact that some of the work he references has not been reproduced. It's bizarre that Wells devotes three paragraphs to the discredited reference in Junk & Jonathan: Part 7—Chapter 4 and only mentions in passing that the result has been challenged.

He returns to this result in Chapter 8 and all but admits that the original result—so prominently presented in Chapter 3—is no longer valid. However, Wells can't leave it at that. The 2006 paper by Gray et al. went on to point out that some creationist literature had written up the earlier incorrect result and claimed that this was support for functional "junk DNA" and support for intelligent design creationism. The authors conclude their paper with ...
Furthermore, because Mkrn1-p1 is a nonfunctional pseudogene and does not trans-regulate its source Mkrn1 gene as claimed (6–9), our work reestablishes the evolutionary paradigm supported by overwhelming evidence that mammalian pseudogenes are indeed inactive gene relics.

Wednesday, August 24, 2011

Darwinian Theory in a Nut




GilDodgen (remember him?) lets us know what a typical IDiot thinks of "Darwinian Theory" [Darwinian Theory in a Nutshell: Random Events Can Produce the Antithesis of Randomness]. Thanks Gil.
Boiled down to its essentials, Darwinian theory is a bizarre cult-like belief that random events can produce the antithesis of randomness.

In no other area of science would such obvious nonsense be accepted without scrutiny or dissent.

One can learn the essentials of Darwinian theory and its claims in a few hours. It’s really just that shallow.

Those of us who are involved in real science — in which rigor is demanded, and in which fantastic, evidentially and rationally unsupported stories like those proposed by Darwinists are laughed at — recognize this shallowness and the transparently absurd claims made on behalf of the theory.
BTW, some of you might have forgotten that Gil Dodgen is involved in real science. Here's a reminder: Gil Dodgen Explains the Salem Conjecture.


Tuesday, August 23, 2011

What He Said


Believe it or not, I often try not to make fun of Americans people in other countries. I'm not always successful.

Richard Dawkins has an article on the Washington Post website where he can't help himself. I agree with everything he says [Attention Governor Perry: Evolution is a fact].
There is nothing unusual about Governor Rick Perry. Uneducated fools can be found in every country and every period of history, and they are not unknown in high office. What is unusual about today’s Republican party (I disavow the ridiculous ‘GOP’ nickname, because the party of Lincoln and Theodore Roosevelt has lately forfeited all claim to be considered ‘grand’) is this: In any other party and in any other country, an individual may occasionally rise to the top in spite of being an uneducated ignoramus. In today’s Republican Party ‘in spite of’ is not the phrase we need. Ignorance and lack of education are positive qualifications, bordering on obligatory. Intellect, knowledge and linguistic mastery are mistrusted by Republican voters, who, when choosing a president, would apparently prefer someone like themselves over someone actually qualified for the job.
There's lots more. Enjoy, no matter what country you live in.


The Oldest Cells

I was going to write about the discovery of the oldest fossil cells but Jerry Coyne beat me to the punch [Newly found: the world’s oldest fossils!]. The new fossil bacteria are thought to be 3.4 billion years old and they were discovered in Australia only a few kilometers from the site where the so-called "cyanobacteria" fossils were discovered almost twenty years ago. Those fossils were reported to be even older (3.5 billion years) but the discovery has been completely discredited. The "fossils" aren't fossils [Did Life Arise 3.5 Billion Years Ago?]. That makes this discovery the oldest known cells (Wacey, 2011).

Interestingly, the senior author on this paper is Martin Brasier and he was one of the scientists who challenged the earlier result of William Schopf. Read all about it on Jerry Coyne's blog website.

The fossils are associated with a sulfur-rich mineral called pyrite. This mineral is produced by modern sulfate-reducing bacteria and it's reasonable to assume that the primitive bacteria detected in these ancient rocks also carried out sulfate reduction. That's not surprising since there wasn't much oxygen in the deep ocean 3.5 billion years ago.

Monday, August 22, 2011

Junk & Jonathan: Part 10—Chapter 7

This is part 10 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links below. For other postings on junk DNA check out the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

What Ever Happened to Freya?


Freya was one of the important Norse gods.
In Norse mythology, Freya is a goddess of love and fertility, and the most beautiful and propitious of the goddesses. She is the patron goddess of crops and birth, the symbol of sensuality and was called upon in matters of love. She loves music, spring and flowers, and is particularly fond of the elves (fairies). Freya is one of the foremost goddesses of the Vanir.
How can you not love a god who is fond of eleves?

Where has Freya gone now that nobody believes in her any more? Did she die? Is she buried somewhere?

These are important questions because there are hundreds of extinct gods and we don't know what's happened to them. Jerry Coyne tries to come up with an answer [Where are all the dead gods?] but I fear that his knowledge of religion isn't sufficient for such a complex topic.

Maybe we should ask one of those sophisticated Christians that we hear so much about?

Do you remember William Lane Craig? [Why Reasonable People Should Not Debate William Lane Craig] He tried to educate Jerry Coyne about science and religion. Listen to his broadcast and see how Jerry responds at: William Lane Craig goes after me for ignorance of religion and science.



Don't you just love it when those sophisticated Christians teach us about sophisticated science? Perhaps he would do better if he got another degree. So far he only has a Ph.D. (Philosophy) and a Doctor of Theology (Th.D.). Poor old Jerry Coyne only has a single Ph.D. (under Richard Lewontin). Jerry is completely outclassed in the sophisticated department but I bet he wears better boots!


Be a Proud Atheist


We Are Atheism Campaign from the Richard Dawkins Foundation.
This is your chance to finally be heard. This is our chance to stand up, speak out, and be counted. We want to provide a platform for atheists around the globe to see that they are not alone. Atheists come in all shapes, sizes, ages, and backgrounds. The only thing that we all have in common is that we don’t see any credible evidence to believe in a god. It’s ok to be an atheist, and we want the world to know.
  • Provide an outlet for atheists to feel comfortable to come out of the closet.

  • Always let visitors know there are other people out there that are non-believers.

  • Help people find other atheists like them in their state, city, and even neighborhood.

  • Give access to local, national, and international organization to become involved in the secular community.

  • Empower people to start their own organization in areas that does not already have one.
We are not just here to let you watch movies; these are real people living real lives as atheists. We want the world to know we exist and we will not be ignored. We will stand up, speak out, and be counted.



Despicable Rhett S. Daniels


EpiRen is the pseudonym of a blogger who about public health issues, including vaccinations and various forms of quackery. He works for a state public health department in the United States. At some point EpiPen crossed paths with Rhett S. Daniels and Daniels didn't like what he heard.

So what did Daniels do? He had EpiPen investigated and "outed" him to his employers. The employers told EpiPen to stop blogging about these issues or be fired. EpiPen complied—as we all would under such circumstances. Read all about it at: The consequences of blogging under one's own name] [A Public Servant, Blogging and Tweeting Under His Own Name, Has Been Silenced By His Employers].

Rhett Daniels showed up in the comments section on the second blog and started issuing more threats.
i am mr. x; first, i am not anti-vax; second, i didn't want epiren to stop posting, but rather to take down the defamatory blog; third, i am not done going after every individual who defames me.

you think you are safe, but all i have to do is file a john doe - or hire a cyber investigator. these courses of action cost less than $10,000 each; which means every person who is afraid of the light can be exposed.

i will not tolerate harassment, defamation, or any such action by any of you. i am very aware of all of you, and have the capital and the will to go after each and every one of you ONLY IF you defame or slander me.

i am self employed if you count owning 11 pharmaceutical companies with cum gross sales over 1/2 billion.

....

actuall, to save me $9,000 i will offer $1,000 for identify info that leads to an address where i can serve anarchic teapot (legally serve as in sheriff delivers court papers).
Who is this despicable person? It's a little tricky to find out since he's in the process of erasing his blog, his twitter account, and several other internet references. His YouTube videos on folate have been made inaccessible and the websites of some of his companies seem to be undergoing routine maintenance. But there are still traces of him on the internet as PZ Myers discovered: Rhett S. Daniels, litigious bully.

I'm doing my bit to create an internet presence for Rhett Daniels—I'm sure he'll thank me when he gets a chance. Let me make it clear that I am not slandering Rhett Daniels. I'm merely stating what the evidence strongly suggests; namely, that he is a despicable, cowardly, bully who will use his money to legally harass anyone who dares to criticize his treatments.

Bits and pieces of his blog are still accessible on Google cache: cigaRHETT - Toxicological Insight. From there you can link to his Blogger profile where you discover that his favorite movie was Top Gun and one of his two favorite books is the Bible. (Why are we not surprised that such a despicable man would like the Bible?) He lives in Fort Myers, Florida, United States.

Here's more,
Activist, philanthropist and entrepreneur. Highly skilled executive who excels at taking small struggling companies from low to high revenues in short periods. Boast an impressive record of the most pharmaceutical drug products ever developed by one person (over 400) in the history of pharma - surpassing my idol, Robert Stockstad from Lederle Pharma (he developed folic acid in 1947). One of the most successful non-lawyer ProSe litigants in history. As of July 18, 2011, total product sales since July 18, 2006, are: $590,635,984 (and 22,728,724 units sold!). politics: www.linkedin.com/in/RhettSDaniels ViaDiem Holdings (Founder): www.viadiem.com Captiva Pharma (CEO): www.CaptivaRx.com Goals: (1) To lead a small pharma company from less than $20 million/yr to over $1 billion/yr in revenues; (2) To feed 82 million Africans with my new unique ingredients that purifies water while provided demographic and staple-deficient based vitamins to provide min RDA based on regional disparities;

You get to ride the big roller coaster three times in a row. What will keep your dad from taking a bite out of your candy apple?

Doing the Good versus doing the Right. Somethings can be Right that are not Good; and there are many things that are Good that are not Right. Right means legally, and Good means natural law.
Rhett Daniels seems to have forgotten that there are some things that are both wrong and evil.

There are several things wrong here. Daniels behaved badly by taking the disagreement to EpiPen's employer. The employer behaved badly by threatening EpiPen if he didn't stop blogging. We should aim for a society where neither of those behaviors are acceptable and everyone can speak freely without fear of retaliation. This is not a good time to criticize the employers but we can make sure Rhett Daniels appreciates the consequences of his behavior. Judging by his defensive reactions on the internet, I think he might be learning a lesson ....

UPDATE: Read the "warning letter" that Liz Ditz received from Rhett Daniels. If this weren't so sad it would be funny.

Here's a list of posts on Keeping Up with #EpiGate. Lots of people are trying to help Rhett S. Daniels have a visible presence on the internet. He will be very grateful.


Sunday, August 21, 2011

Chitty Chitty Bang Bang Bang Bang



We recently learned that Prager University was instrumental in converting GilDodgen from obnoxious atheist to obnoxious theist [How to Convince an Atheist to Become an IDiot]. GilDodgen liked to two "courses" in particular. One was a "course" on "The Most Important Verse in the Bible." All five minutes of the course were taught by Dennis Prager.

The other "course" is taught by Frank Pastore, a former atheist and a former baseball player. He's now the host of a Christian talk show in Los Angeles. Pastore is a high school graduate. (Pastore was "converted" by some other Cincinnati Reds baseball players.)

You need to watch this video. Here's how it's described in the Prager University calendar.
Who takes the greater leap of faith -- the atheist or the believer? Best selling author and award-winning radio talk show host, Frank Pastore, poses this question in this compelling Prager University video course.

WARNING: Parts of this video may be harmful to the rational mind. Viewer discretion is advised.




How Does Something Get into a Textbook?


A recent paper in Molecular Cell involved the study of nucleosome assembly in vitro (Torigoe et al. 2011). The authors were looking for intermediate stages in the assembly of nucleosome after DNA replication. Here's the abstract of their paper ...
Chromatin assembly involves the combined action of histone chaperones and ATP-dependent motor proteins. Here, we investigate the mechanism of nucleosome assembly with a purified chromatin assembly system containing the histone chaperone NAP1 and the ATP-dependent motor protein ACF. These studies revealed the rapid formation of a stable nonnucleosomal histone-DNA intermediate that is converted into canonical nucleosomes by ACF. The histone-DNA intermediate does not supercoil DNA like a canonical nucleosome, but has a nucleosome-like appearance by atomic force microscopy. This intermediate contains all four core histones, lacks NAP1, and is formed by the initial deposition of histones H3-H4. Conversion of the intermediate into histone H1-containing chromatin results in increased resistance to micrococcal nuclease digestion. These findings suggest that the histone-DNA intermediate corresponds to nascent nucleosome-like structures, such as those observed at DNA replication forks. Related complexes might be formed during other chromatin-directed processes such as transcription, DNA repair, and histone exchange.
Interesting but hardly Earth-shattering. More work needs to be done to confirm this result and see if it's significant in vivo. At least that's what you would think if you just looked at the paper.

You get a very different perspective if you read the press release from the University of California at San Diego: Biologists' Discovery May Force Revision of Biology Textbooks: Novel Chromatin Particle Halfway Between DNA and a Nucleosome.1
Basic biology textbooks may need a bit of revising now that biologists at UC San Diego have discovered a never-before-noticed component of our basic genetic material.

According to the textbooks, chromatin, the natural state of DNA in the cell, is made up of nucleosomes. And nucleosomes are the basic repeating unit of chromatin.
That's correct. All the textbooks have a diagram similar to the one shown here from my textbook. It shows the organization of nucleosome core particles and the completed nucleosome on DNA.

What the new result shows is that there's an intermediate stage where the core particle is bound to DNA but the DNA isn't wrapped around the core particle. That's not a big surprise and it's not going to make it into most textbooks, even if it's true.
"This novel particle was found as a precursor to a nucleosome," said James Kadonaga, a professor of biology at UC San Diego who headed the research team and calls the particle a "pre-nucleosome." "These findings suggest that it is necessary to reconsider what chromatin is. The pre-nucleosome is likely to be an important player in how our genetic material is duplicated and used."

The biologists say that while the pre-nucleosome may look something like a nucleosome under the microscope, biochemical tests have shown that it is in reality halfway between DNA and a nucleosome.

These pre-nucleosomes, the researchers say, are converted into nucleosomes by a motor protein that uses the energy molecule ATP.

"The discovery of pre-nucleosomes suggests that much of chromatin, which has been generally presumed to consist only of nucleosomes, may be a mixture of nucleosomes and pre-nucleosomes," said Kadonaga. "So, this discovery may be the beginning of a revolution in our understanding of what chromatin is."
This is mostly hype and none of this speculation is found in the actual paper. Unfortunately, this sort of press release has become the norm and that's got to stop.

This work isn't even close to making into the textbooks for a number of reasons. The most obvious is that it needs to be confirmed. Textbook writers do not immediately put new findings into their books because we've been burned too many times. But there's another reason why this ain't gonna make it—it's not important enough.

Textbooks are not encyclopedias. They will only contain information that undergraduates need to know in order to understand the basic concepts and principles in the field. I know that every scientist thinks his or her most recent discovery is Nobel Prize work and I'm sure they would like every biochemistry undergraduate to know about it. At some point a textbook author has to decide what's really important and, unfortunately, those choices mean that 99.99% of everything that's published in a given year doesn't make the cut.

It can't be any other way.


1. It even seemed important enough for Richard Dawkins.net: Biologists' Discovery May Force Revision of Biology Textbooks: Novel Chromatin Particle Halfway Between DNA and a Nucleosome.