Steampunk Genetics

 

I recently learned a lot about steampunk by attending Polaris 25 last July. I'm thinking I should put together an outfit that I can wear around campus. I haven't seen a fashion statement that's as cool as steampunk since the 1960's.

John Hawks is obviously a fan as well. He's posted an article entitled Steampunk Genetics where he describes how predictions based on Victorian genetics are still more accurate than those based on genome sequences. The important point is that some heritable traits are still too complex to be attributed to specific alleles.

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Jetcat

 

Gordon Moran (my son) and his friend Kevin Forbes are building a game (app) for mobile devices. You can follow their progress on: Omnisaurus Games.

Check out the September build. They actually have a version you can play! It even has sound.

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Christian vs Christian

The Discovery Institute is the leading proponent of Intelligent Design Creationism—a form of creationism that concentrates on proving evolution is wrong and therefore the history of life must be explained by the intervention of an intelligent designer (i.e. god).

The BioLogus Foundation was founded by Francis Collins and it brings together a group of theistic evolutionists. Theistic Evolution is a form of creationism that accepts much of evolutionary biology but still postulates the the history of life requires the intervention of a creator.

Recently a Theistic Evolution-type creationist attacked Stephen Meyer, an Intelligent Design Creationist at the Discovery Institute [On Deciphering the Signature]. You can read a brief history of what happened in a guest post on Jerry Coyne's blog website: Guest post: the conflicted relationship between Intelligent Design and BioLogos.

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A New Moderation Policy: Doug Dobney Is Banned on Sandwalk

Up until now I have been proud of the fact that nobody is banned on Sandwalk. I delete all spam that consist entirely of threats and incoherent ranting (e.g. Dennis Markuze). I also delete spam that advertises products and/or commercial websites. But even the weirdest kooks are allowed to post comments as long as they don't post spam.

But there's one thing I won't tolerate and that's when people start threatening other bloggers and commenters by contacting their families or their employers. That's where I draw the line.

Doug Dobney has posted hundreds of comments on Sandwalk under "anonymous." He is apparently opposed to evolution and won't listen to reason from those who have tried to set him straight on the facts. That's fine with me. If others want to have fun with him here, then it's up to them. I've been ignoring him and so has almost everyone else.

Recently another commenter revealed that "anonymous" was, in fact, Doug Dobney, a well-known kook from Peterborough, Ontario, Canada. That made Doug very upset in spite of the fact that it was trivially easy to identify him based on his internet record where he has already admitted to his identity. (He also posts as "Socrates.")

That's fine too. What happened next is not fine. Doug Dobney sent letters to the Chair of my department and the Dean of the Faculty of Medicine complaining about me. Here's a copy of his letter.

Dear Dr. Whiteside:

I need to bring to your attention a serious problem that relates to the Department of Biochemistry.

Please see the emails below.

Not only has the problem not been addressed, but I have not even been given a response to my emails documenting this dangerous situation.

To give you some insight into this problem, here are three, of many, instances from Dr. Moran’s blog:

“Josef Gladstone said...

I don't even understand why Doug Dobney would even want to toil in anonytimity when he is doing such groundbreaking work on organism development, especially in the new field of pterosaur to bird development. He is truly one of the great minds of the 21st century.

Doug Dobney will eventually be viewed in the same light as Darwin by the time the history of organism development is written.

And of course, to quote the great Mr. Dobney, this is certainly not worth arguing about! (both his wonderful wife Angela and myself get a great chuckle out of this whenever he says it, which is quite often!)

“AND

Ddobney@moffathouse.ca said...

Hey Doug Dobney, do guests at the Moffat House know you're insane?

AND if your stomach is up to it, there is this link on the blog:

http://socratesisdougdobney.blogspot.com/

I would appreciate your attention to this serious problem.

Yours sincerely,

Douglas Dobney

That's something I will not tolerate. Doug Dobney has earned the distinction of being the very first person to be banned on Sandwalk

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My Dean is a very busy person but I'm sure she enjoys a little chuckle now and then when these kook emails turn up in her mailbox. I'll have to ask her if she remembers Doug Dobney next time I see her in the line for coffee downstairs.

Conspiracy Theories

 

There are kooks everywhere. Some people believe they have been abducted by UFOs and others believe that the moon landings never happened. There are many who believe that the 9/11 tragedy was a conspiracy of the United states government.

One thing that all kooks have in common is their ability to completely detach themselves from reality. Wanna see a good example?

David Klinghoffer posts on the Intelligent Design Creationist website Evolution News & Views. His latest display of kookdom is to try and link evolutionary biology with 9/11 truthers [Darwinism and 9/11 Conspiracy Theories: The Parallels].

I hope the Discovery Institute has a full-time psychologist on their staff.

With the approaching 9/11 anniversary, Slate has been running a series tracing the rise and ongoing evolution of 9/11 Truth theories that try to show how the attacks 10 years ago were really an inside job. According to this thinking, 9/11 was no attack by Islamic terrorists. Rather, the towers were detonated by an expertly covered-up collusion among Zionists and U.S. government operatives. You might have expected these notions would, if entertained at all, be dispelled by the exhaustive debunking job that Popular Mechanics did with its 5,500-word article on the subject back in 2005. Not so, as those who take an interest in conspiracy culture know well.

What I found striking about the first installment in the Slate series, by Jeremy Stahl, is the parallels with what we know about the thought and writings of Evolution Truth activists: our ever-loving friends in the Darwin Lobby. You may recall the news of a few months back that Glenn Branch, deputy director of the Darwin-lobbying National Center for Science Education, had collaborated with 9/11 Truth conspiracist James H. Fetzer in editing a special number of the journal Synthese on "Evolution and Its Rivals." That issue of the journal became so notorious for the incivility of its contributions that a whole fracas broke out and made the pages of the New York Times.

It may have seemed just a delicious coincidence at the time to find Branch and Fetzer teaming up so comfortably. Yet consider the features of 9/11-style paranoid thinking and some similarities to its evolutionary counterpart ...

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Keep the Faith—but not in Our Schools

Coalition Calls for Defunding of Catholic Boards, End to Discrimination Against Gays in Publicly Funded Schools
KEEP THE FAITH—BUT NOT IN OUR SCHOOLS

The Canadian Secular Alliance and its allies are hosting a rally in front of the Legislature at Queen's Park on Sunday, September 18 from 1:30-3:30 p.m. to demand:

• The end of the over $500 million taxpayer subsidization for the promotion of the Roman Catholic religion. Public funding for the expensive duplicate school system must be eliminated to provide one secular publicly funded school system.

• The protection of equality rights for all students—including gay students—by ending the constitutional privilege afforded Roman Catholics to overrule legislation and the courts in favour of religious dogma.

"Equality for all students means ending privileged access to public schools for favoured religious services," says CSA President Greg Oliver.

Speakers represent a cross section of the religious and non-religious.

More information: Canadian Secular Alliance

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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.

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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.

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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.

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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.

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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."

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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.

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.

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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.

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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.