Most of you missed the exciting Evolution Ottawa 2012 meeting earlier this month but, cheer up, you have another chance to visit Ottawa form Novermber 30 to December 2, 2012.
The meeting is called Eschaton 2012 where "eschaton" refers to the end of the world. That's because, as you all know by now, the world is going to end on December 21, 2012. The Mayans said so and so do a lot of modern kooks.
Here's an outline of the meeting.
The conference opens with a Friday night plenary session on the historical relationship between humans and our apocalypses. Saturday morning and afternoon, we have parallel tracks: 1) Talks and panels on skepticism/science/science communication (including a live recording of Ottawa Skeptics' podcast, The Reality Check) and 2) "The Immaculate Convention" - talks and panels on religion from an academic and sociological perspective. Saturday evening there will be a reception with food and drink in the early evening at the Canadian Museum of Nature (around the corner from the hotel), after which there will be a talk by PZ Myers, followed by a meet-and-greet social, with snacks, cash bar, and access to some of the galleries and exhibits. On Sunday the parallel tracks include panels and workshops on ethics, gender identity, parenting, and other exciting topics to be announced.
Here's the latest list of speakers. (I changed the order somewhat from the one on the website.)
I'm planning to talk about the accommodationist wars and why science and religion are incompatible. Hopefully, Genie Scott will represent the accommodationist position as promoted by NCSE.
Chris DiCarlo and I are teaching a course at the University of Toronto next Fall on scientific controversies and misconceptions (including evolution vs creationism). Maybe we can have a workshop on Sunday to discuss science literacy?
PZ Myers approves of this plan to cast a vote for Jesus [An excellent suggestion for the Bible-believing Christians].
Isn't there a problem? Who's going to produce a valid birth certificate?
This is a very important molecule. It's found in (almost?) all living species where it serves a very important function. What is the common name of this molecule and what role does it play in metabolism?
Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.
There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)
Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)
In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.
Winners will have to contact me by email to arrange a lunch date.
Comments are invisible for 24 hours. Comments are now open.
UPDATE: The molecule is S adenosylmethionine (SAM). It is the major methyl donor in biochemical reactions. Today's winners are Sean Ridout and William Grecia.
Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
We live in an era where almost 50% of the citizens in some Western European countries don't believe in God and a solid majority of those in Japan and Vietnam are nonbelievers [Top 50 Countries With Highest Proportion of Atheists / Agnostics].
According to some polls, about 30% of Canadians don't believe in God [Religion in Canada] and in the USA the number of nonbelievers is about 12% of the population {Atheists in America].
A recent survey by The PEW Forum on Religion & Public Life looked at the religious belief of Americans as adults and how they were raised as children. There were 1387 people who self-identified as atheists but only 131 of these were raised as atheists. Thus, 90% of the atheists were raised in a religious household but later on abandoned their belief in God(s).
That's pretty remarkable in a society that's as religious are the USA. It's not surprising that there are so many first generation atheists because a generation ago the number of atheists in the USA was less than 1% of the population.
On the other hand, there were 432 respondents who said they were raised as atheists. Only 131 of these respondents are still atheists so that means that the retention rate for atheism is only 30% and that makes it the worst "religion" at retaining childhood beliefs. The figure and the data are from Mark M. Gray who blogs at Nineteen Sixty-four. He writes ...
What these findings reflect is that in the U.S. Atheists are for the most part "made" as adults after being raised in another faith. It appears to be much more challenging to raise one's child as an Atheist and have them maintain this identity in their life. Of those raised as Atheists, 30% are now affiliated with a Protestant denomination, 10% are Catholic, 2% are Jewish, 1% are Mormon, and 1% are Pagan.
This is perceived as good news by the IDiots who were happy to pass along the information on Uncommon Descent: Why do atheists have such a low retention rate?.
Some of us are tempted to wonder whether they just grow tired of the society of Darwin’s tenure bores and the atheist troll in the mailroom. Or of the uproar around the Skepchick. Re that latter individual, at some point, surely a normal dude must wonder, what is in this for me, long term?
He might be better off with a cute, decent girl who offers free coffee and cake in the parish hall, not sexy pics. But to meet her, he has to sober up, shave, shower, and go to church … so …
So, … maybe it’s just the facts of life that catch up with some of them?
I think there's a better explanation. As we all know, many evangelicals are proud of advertising that they were raised as atheists but were "born again" as teenagers or adults. Perhaps they "misremember" certain aspects of their religious upbringing and "forget" that their parents believed in God? If a few hundred of them declared, incorrectly, that they were raised as atheists then the real retention rate would be much higher.
In any case, religion is in trouble everywhere, including the United States. In many countries, there are millions of second and third generation atheists who will never believe in imaginary supernatural beings. Those who are making a big deal of this apparent retention rate among Americans are a lot like the passengers who concentrated on rearranging the deck chairs while the Titanic was sinking.
Jeffry Shallit of Recursivity is in London, England where he recently took a train from Victoria Station to Bromley South, then a bus to Downe, and a rather dangerous walk up a narrow hedge-lined road to Down House [Larry Moran Would Approve ].
He joins a distinguished list of people whose visit to the Sandwalk has been recorded here.
Larry Moran
PZ Myers
John Wilkins
Ryan Gregory
The God Delusion
Cody
John Hawks
Michael Barton
Seanna Watson
Steve Watson
Michael Richards
Jeffrey Shallit
Chris DiCarlo
Bill Farrell and Louis C
Cody
The first atomic bomb was detonated on this day in 1945 [Trinity]. The second detonation of an atomic bomb took place over Hiroshima, Japan, on August 6, 1945.
So far, Hiroshima and Nagasaki are the only examples of a nuclear device being used in war. We've managed to avoid dropping atomic bombs on each other for 67 years. If you think about it, that's a pretty remarkable achievement.
Lots of people don't understand what we mean by a secular society. If you're one of them, watch this video by QualiaSoup. He uses a very good example—the saying of prayers at city council meetings.
Most of you have been to business and/or organization meetings of various sorts. You don't normally start those meetings with a Christian prayer in spite of the fact that you might be making some very big decisions. At the recent evolution conference in Ottawa, for example, there were five society meetings of boards of directors and (I'm told) not one of them began with a prayer!
People believe in many different gods. Evey person on the planet thinks that the vast majority are false gods that do not exist. Some of us think that applies to all gods. You have no right to promote the existence of some gods over others at public meetings in a secular society, especially a multicultural society like those that exist in most modern, industrialized nations.
Whether or not you believe in god(s), the only reasonable approach in a modern society is the secular one where religions is a private matter, not a public one.
A link to this video was sent to Katie Mahoney, city councillor for Ward 8 (my ward) in Mississauga, Ontario, Canada.
Hat Tip: Friendly Atheist
It was only a few months ago that lawyer Casey Luskin presented us with The Top Three Flaws in Evolutionary Theory. Now he's back with the top ten problems with Darwinian evolution. Here they are, read 'em and weep.
- Lack of a viable mechanism for producing high levels of complex and specified information.
- The failure of the fossil record to provide support for Darwinian evolution.
- The failure of molecular biology to provide evidence for a grand "tree of life."
- Natural selection is an extremely inefficient method of spreading traits in populations unless a trait has an extremely high selection coefficient.
- The problem that convergent evolution appears rampant -- at both the genetic and morphological levels, even though under Darwinian theory this is highly unlikely.
- The failure of chemistry to explain the origin of the genetic code.
- The failure of developmental biology to explain why vertebrate embryos diverge from the beginning of development.
- The failure of neo-Darwinian evolution to explain the biogeographical distribution of many species.
- A long history of inaccurate predictions inspired by neo-Darwinism regarding vestigial organs or so-called "junk" DNA.
- Humans show many behavioral and cognitive traits and abilities that offer no apparent survival advantage (e.g. music, art, religion, ability to ponder the nature of the universe).
I started to work on the top 1000 problems with Intelligent Design Creationism but then I realized that it was a waste of time. There are only two essential problems with Intelligent Design Creationism: (1) There's no evidence for supernatural design in nature, and (2) There's no evidence for a supernatural designer.
Many proteins bind to double-stranded DNA and most of them bind specifically to a particular target site. The lac repressor, for example, binds to a specific DNA site that blocks transcription of the genes required for lactose uptake and utilization. The lac repressor protein is a dimer of two identical subunits and each one binds a short segment with the core sequence ATTGT.1
If you look closely at the structure shown above, you can see how parts of the protein lie in the grove of double-stranded DNA where they can detect the sequence by "reading" the chemical groups on the edges of the base pairs. It's important to realize that DNA binding proteins interact with the DNA double helix and not with unwound DNA where the individual bases are exposed.
How does a DNA binding protein like lac repressor find its specific site in the genome? The most obvious explanation is that the protein binds non-specifically to any piece of DNA and checks to see if it's a specific binding site. If it is, the protein binds very tightly and doesn't fall off. If it isn't, the interaction is much weaker and the protein falls off quickly so it can check out another potential site.
The Faculty of Medicine at my university runs a Youth Summer Program (Medicine) for high school students. There are four one-week modules: Human Physiology, Molecular Biology & Genetics, Pharmacology & Toxicology, and Microbiology. The final module is two weeks of working in a research lab.
One of the modules that takes place in my building is the analysis of forensic evidence at a mock crime scene [The Science Behind CSI]. Here's the description from the website.
From stem cell research to criminal convictions, the science of molecular biology and genetics is at the centre of many of today’s most contentious issues. In this module, students learn about DNA fingerprinting, forensic investigations, and genetic transformation through a variety of hands-on laboratory activities and lectures from world-class speakers. Highlighting the program is the mock crime scene investigation where students collect and analyze crime scene evidence. After students have collected the appropriate evidence, they move into the laboratory to perform their analysis and, assuming they have collected the correct pieces of evidence, solve the case.
I can understand why students might find this appealing but there's a problem. One of my goals is to teach students, including high school students, about the wonder and excitement of science as a method of knowing. I would like students to appreciate the knowledge for it's own sake. I would like them to be excited when they learn how life operates at the molecular level (i.e molecular biology & genetics).
One of the major impediments to this goal is the widespread belief that science is just a tool and the main objective is not knowledge for its own sake but applications of science. According to this view, you only learn about molecular biology and genetics because it will somehow cure cancer, detect genetic diseases, and solve crimes.
I think it's wrong to reinforce this belief when we have a chance to educate a select group of high school students. I would much prefer to teach them about molecular evolution, how genes are expressed, and how we solve the structure of proteins.
This isn't going to happen in a program with such a heavy emphasis on medicine and medical applications but, in the long run, science will lose out when these bright students enter medical schools or forensic programs instead of pure science programs.
What's the appropriate balance between catching and holding the attention of students by having them solve a "crime" and trying to teach them the value of scientific discovery for its own sake?
Ms. Sandwalk sent me the link to this video. She knows that I love this sort of thing. It makes me happy.
Basic, fundamental research in Canada is in big trouble. The current government, led by Stephen Harper's Conservatives, have cut back on the funding of basic research while promoting applied research of various sorts. The consequences in academic departments have been nothing short of disastrous. In university biochemistry and molecular biology departments, for example, there are hundreds of mid-career scientists who have lost their grants and many of them will never get back funding for their basic science projects. This means that research technicians are being fired, graduate students and postdocs can't complete their projects, and PI's find themselves unable to do what they've been hired to do, with 15-20 years before retirement age.
The recent protest on Parliament Hill [Protest on Parliament Hill] highlighted some of these problems with science funding in Canada. That prompted a response from Gary Goodyear, Minister of State for Science and Technology (see below). Recall that Gary Goodyear is a chiropractor and a creationist [Gary Goodyear "Clarifies" His Stance on Evolution].
Here's the Harper Government's1 response to criticism that it has neglected basic research in favor of applied research.
The Harper government has made historic investments in science, technology and research to create jobs, grow our economy and improve the quality of life for Canadians.
Support for science and technology has been a fundamental priority of our government since 2006. This year, through Economic Action Plan 2012, we enhanced federal government support for leading-edge research.
As a world leader in post-secondary research with a highly skilled workforce, Canada has strong fundamentals for innovation. While several countries around the world are reducing funding in science and research, our government continues to invest in research, development and technology. In fact, Canadian higher-education research and development expenditures are higher than any other G7 country, as a percentage of GDP.
While the government is returning to a balanced budget, science, technology and innovation remain a strong priority with an added $1.1-billion investment over five years. University presidents, academic leaders and industry leaders have praised our government's leadership in recognizing the important role that research and innovation play in our economic prosperity.
Economic Action Plan 2012 funding allocated to science, technology and innovation includes:
- $12 million per year to make the Business-Led Networks of Centres of Excellence program permanent.
- $6.5 million over three years for a research project at McMaster University to evaluate team-based approaches to health care delivery.
- $17 million over two years to further advance the development of alternatives to existing isotope production technologies.
- $105 million over two years to support forestry innovation.
- $37 million annually starting in 2012-13 to the granting councils to enhance their support for industry-academic research partnerships.
- $60 million for Genome Canada to launch a new applied research competition in the area of human health and to sustain the Science and Technology Innovation Centres until 2014-15.
- $10 million over two years to the Canadian Institute for Advanced Research to link Canadians to global research networks.
- $500 million over five years, starting in 2014-15, to the Canada Foundation for Innovation to support advanced research infrastructure.
- $40 million over two years to support CANARIE's operation of Canada's ultra-high-speed research network.
Our government is investing in science and research that is leading to breakthroughs that are strengthening our economy and the quality of life of all Canadians. Our investments are enabling Canadian scientists in universities, colleges, businesses and other organizations to help secure Canada's prosperity today and into the future.
Does that sound like a government that understands the importance of basic research and knows the difference between research and "innovation"? He forgot to mention that these "increases" in spending are not on top of existing funding but often instead of support for fundamental research. That's why scientists all over the country are losing their grants unless they can find a way to make them sound applied or translational.
UPDATE: See how Denyse O'Leary manages to turn this into whining about Darwinists at Scientists, including evolutionary biologists, carry coffin through streets in Canada, to protest cuts to funding?.
1. Before Stephen Harper took over, it was common to refer to the "Government of Canada" in press releases. Now, it's always the "Harper Government."
Blogs have been around for more than a decade but it's still not clear what purpose they serve (if any). We still don't know how to distinguish a science blog from other types of blogs—perhaps it's foolish to try.
Bora Zivkovic of A blog Around the Clock has written a short history of science blogging [Science Blogs – definition, and a history]. It's well worth reading since Bora has been active for a long time and he's very well connected to the science blogging community.
Here's how he describes the category that applies to Sandwalk.
The earliest science bloggers were those who started out doing something else online – updating their websites frequently, or participating in Usenet groups – then moving their stuff to blogging software once it became available in the late 1990s and early 2000s.
As much of the early online activity focused on countering anti-science claims, e.g., the groups battling against Creationism on Usenet, it is not surprising that many of the early science bloggers came out of this fora and were hardly distinguishable in form, topics and style from political bloggers. They brought a degree of Usenet style into their blogs as well: combative and critical of various anti-science forces in the society.
In my case the usenet groups were talk.origins and sci.bio.evolution. Both of those groups are hosted on a server in my office; talk.origins is still very active but sci.bio.evolution isn't.
PZ Myers is the most famous talk.origins veteran. He's the one who convinced me to start a blog back in 2006 when I realized that blogs had many advantages over usenet, especially images. I don't know how many other talk.origins veterans have a blog. Can you help me out? Here's a partial list. (Some of these blogs are not science blogs.)
PZ Myers: Pharyngula
John Wilkins: Evolving Thoughts
Jeffrey Shallit: Recursivity
Jim Lippard: The Lippard Blog
various people: Panda's Thumb
John (catshark) Pieret: Thoughts in a Haystack
Troy Britain: Playing Chess with Pigeons
I know there are many more but I just can't remember them right now.
The other thing that Bora points out is that many science bloggers were connected to each other in different ways. Often we had met in person—this is certainly true of the talk.origins veterans. The early blogs were characterized by in jokes and incestuous cross links.
This has now disappeared as a whole new generation of science bloggers have entered the blogosphere, although there's still a certain amount of personal contact (see Evolution and Poutine and Beaver Tails.) I don't know if this is important or not. Blogger cliques can be a good thing and a bad thing.
Prime Minister Stephen Harper is destroying basic research in Canadian universities. His government is also shutting down government research facilities and muzzling government scientists. The current Canadian government is famous for ignoring science and evidence on many issues.
Several student organizations and scientists decided to take advantage of Evolution Ottawa 2012 to organize a protest based on the theme "No science, no evidence, no truth, no democracy." The protest took the form of a funeral for the death of evidence.
We gathered at the Conference Centre and marched across Confederation Square, up Wellington Street, and onto Parliament Hill.
Ryan Gregory and I had a good view from the steps of Parliament Hill.
There were about a dozen speakers who addressed the crowd. They included the President of the Canadian Society for Ecology and Evolution, Jeffrey Hutchings (left), Maude Barlow (centre), and Liberal MP Ted Hsu (right). (Ted Hsu has a Ph.D. in physics form Princeton University and he worked at Atomic Energy of Canada's Chalk River Laboratories (AECL) before becoming a member of parliament.
The crowd of 1100 was well-behaved. The police were bored. Everyone had a good time. I've never been to a protest that emphasized good science and support for evidence-based policy. That's the message that all the speakers supported.
Ryan Gregory has more pictures, and a video [Pro-science rally on Parliament Hill].
Ford Denison was there ... check out the photo at: Thousands protest suppression of science in Canada -- the "Death of Evidence" rally.
Rosie Redfield gave a talk on Sunday night. She described the work she did on the so-called "arsenic-incorporating" strain of bacteria that was made famous in a NASA press release and a subsequent Science paper last year [Arsenic and Bacteria] [Arsenic-associated bacteria (NASA's claims)] ["This Paper Should Not Have Been Published"].
You might recall that Rosie was among the first scientists to point out the flaws in the original paper and this led to a delay in its publication. When it finally was published there were several critical comments—including one from Rosie—that appeared in the same issue.
Rosie obtained the GFAJ-1 strain and tested its growth characteristics. She determined that it absoltutely required phosphate for growth and growth stopped when the phosphate in the medium was depleted. The strain did tolerate high levels of arsenic in but there was no evidence that it could replace phosphorus.
Rosie purified DNA from cells grown in the presence of arsenic and sent it to her collaborators. There was no arsenic in the DNA. (Carl Zimmer takes you through a blow-by-blow summary of Rosie's talk at Live-blogging Arsenic Life].)
The work was submitted to Science and the paper was accepted for publication It was due to be published on July 26th which meant that, under the conditions imposed by Science, Rosie wasn't allowed to talk about her work until then. Rosie informed Science that she intended to violate the embargo and describe her results at this meeting. Science responded by moving the publication date forward and posting the paper on their website at 8pm Sunday night [Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells]. Carl Zimmer was watching the website as Rosie spoke and at one point in her talk she turned to Carl to ask if the paper was up—it was.
The audience recognized that this was a major victory for open science. As the moderator put it at the end of her talk, you can mess with NASA, you can mess with Science, but don't mess with Rosie Redfield!
There are two papers being published in Science. The other one [GFAJ-1 Is an Arsenate-Resistant, Phosphate-Dependent Organism] says essentially the same thing as Rosie's paper.
The bottom line here is that the original paper by Wolfe-Simon et al. (2011) was deeply flawed and should never have been published by Science. More importantly, the latest results show that Felisa Wolfe-Simon was dead wrong when she claimed at the NASA press conference that GFAJ-1 incorporated arsenic into its DNA. You can watch her say this in the video I posted at: The Arsenic Affair: No Arsenic in DNA!.
You may be wondering how NASA and the authors of the original paper are handling this issue. In spite of the fact that they held a public press release and in spite of the fact that Felisa Wolfe-Simon was interviewed multiple time in the press and even gave a TED talk, they maintain that the only proper forum to discuss criticism of their paper is in the peer-reviewed literature! (I hate hypocrites.)
When Wolfe-Simon heard that Rosie's paper was in press she said [Arsenic-based life finding fails follow-up] ...
Wolfe-Simon, who says she can’t comment in detail until Redfield’s results appear in a peer-reviewed journal, wrote in an email that her original paper never actually claimed that arsenate was being incorporated in GFAJ-1’s DNA, but that others had jumped to that conclusion. “As far as we know, all the data in our paper still stand,” she wrote. “Yet, it may take some time to accurately establish where the [arsenic] ends up.”
She's right about the fact that the original paper never actually said that arsenic replaced phosphorus in DNA but it did strongly imply that this was the logical conclusion. However, in her press conference, Wolfe-Simon explicitly talked about arsenic replacing phosphorus in DNA and nobody who listened to that talk could have come away with any other impression. You didn't have to "jump to that conclusion" after hearing the presss conference.
So what are they saying today? Read Rosie's blog at: NASA's cowardly responses to their #arseniclife FAIL. And here's what Wolfe-Simon is saying, quoted at: New Studies Say No, Life Can't Live on Arsenic Alone.
These Science authors have made it clear that they are convinced they have tightly shut the door on arsenic incorporation into biomolecules. Yet, low amounts of arsenic incorporation may be challenging to find and unstable once cells are opened," she writes, "so may merit comprehensive and systematic efforts with other assays and conditions.
I don't think it's reasonable to expect Wolfe-Simon to apologize but I do think the scientific community should continue to apply pressure on NASA.
Here's a very good account of what happened and why NASA should be ashamed: Scientist in a Strange Land. It also expresses some sympathy for Felisa Wolfe-Simon.
Photo courtesy of Seanna Watson.
Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D. and Oremland, R.S. (2011) A bacterium that can grow by using arsenic instead of phosphorus. Science. 332:1163-1166. Published online 2 December 2010; published in Science magazine Jun 3, 2011 [doi: 10.1126/science.1197258]
Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D. and Oremland, R.S. (2011) Response to comments on "A bacterium that can grow by using arsenic instead of phosphorus". Science. 332:1149. [doi: 10.1126/science.1202098]
