I don't think Dawkins does a good enough job of ignoring or discounting these arguments. They are irrational and deserve no place in debates like this. Dawkins does say, on several occasions, that just because a belief makes you feel good doesn't mean that it's true. He should have kept on saying that, and nothing else, every time Lennox brought it up.
Thursday, February 07, 2013
Dawkins vs Lennox: Has Science Buried God?
Professor Richard Dawkins debated Professor John Lennox at Oxford University. This is an old debate from about five years ago. I find it very frustrating because both sides frequently drift off-message. All of the arguments from Lennox seem to be of two sorts: (1) the argument from personal incredulity, or (2) the argument from personal satisfaction (i.e. I believe in god(s) because it makes me feel good).
I don't think Dawkins does a good enough job of ignoring or discounting these arguments. They are irrational and deserve no place in debates like this. Dawkins does say, on several occasions, that just because a belief makes you feel good doesn't mean that it's true. He should have kept on saying that, and nothing else, every time Lennox brought it up.
I don't think Dawkins does a good enough job of ignoring or discounting these arguments. They are irrational and deserve no place in debates like this. Dawkins does say, on several occasions, that just because a belief makes you feel good doesn't mean that it's true. He should have kept on saying that, and nothing else, every time Lennox brought it up.
How Linus Pauling Discovered the α-Helix
Biochemistry students have been learning this little bit of history for over fifty years. I discovered, quite by accident, that there's a video of Linus Pauling telling the story ...
[Hat Tip: The Biochemistry Questions Site]
Wednesday, February 06, 2013
Do You Want to Go to a Conference?
There's a conference in April called the Westminster Conference on Science and Faith. It takes place in a church in Philadelphia. Here's the trailer. How many of you just can't wait to register?
Annual Darwin Lecture at the University of Toronto
Brief Description: Modern day evolutionary biologists combine DNA studies with field experiments that can detect Darwinian evolution in real time. Lizards are an ideal subject for such research.
Five Million Pageviews!!!
Nevertheless, it's a significant milestone. Please help me to celebrate by reading the top five Sandwalk posts since November, 2006. Four of them are science posts! Only the non-science post generated a significant number of comments and that's because so many people tried—and failed—to meet my challenge ....
I challenge all theists and all their accommodationist friends to post their very best 21st century, sophisticated (or not), arguments for the existence of God. They can put them in the comments section of this posting, or on any of the other atheist blogs, or on their own blogs and websites. Just send me the link.
The Genetics of Eye Color
May 11, 2007
Regulating Glycogen Metabolism
June 30, 2010
Smart Crocodile Eaters?
September 25, 2012
A Challenge to Theists and their Accommodationist Supporters
August 1, 2011
Carnival of Evolution #38
There are three other posts that are inching their way up toward the top five ...
December 15, 2012
Ann Gauger Describes the Intelligent Design Creationist Version of Population Genetics
May 22, 2011
Junk & Jonathan: Part 4—Chapter 1
February 23, 2007
Genetics of ABO Blood Types
Golden Palace Egg Rolls
I've taken many friends to the restaurant and recommended it to visitors. Recently the talk.origins moderator, Dave Greig, sampled the food and pronounced it tolerable. More recently, I brought lots of food to the hotel at Eschaton 2012 and treated PZ Myers, Veronica Abbas, Chris DiCarlo, and Ophelia Benson. They all liked the egg rolls. Everyone likes Golden Palace egg rolls.
The new, 3rd generation, owner, Bill Kwong is a friend of my cousin. Bill has kept all of the traditional servings at the restaurant (you don't mess with success). But he's done one thing that the previous owners never did—he's selling Golden Palace egg rolls at hockey games!
Check out the TV report to see how the egg rolls are made: Golden Palace egg rolls score big at Scotiabank Place.
UPDATE: Ms. Sandwalk recounts how we used to get our egg rolls 50 years ago [Golden Palace egg rolls].
Saint Andrew at Work
Andrew was also interested in "Polystrate" Tree Fossils because creationists often used them as "proofs" that evolution is wrong.
Here's Andrew extracting a fossil tree from the Joggin Fossil Site in Nova Scotia (Canada). He looked a bit younger when I last saw him in Toronto in 1998.
God and the Problem of Pain
Unfortunately for Jeff, he is being subjected to a bunch of lectures from real Professors on how to rationalize belief in God with being reasonable. The latest was a lecture on God and Reason - Lecture 3 - John North - The Problem of Pain.
The argument goes like this ...
1. Assume (withou any evidence) that god(s) exist.
2. Assume (without evidence) that your favorite god is good and wouldn't allow pain.
3. Since pain exists then ...
- god is mysterious and we don't understand her motives OR
- god wants us to have free will and be capable of voluntarily choosing pain and suffering OR
- temporal pain is transitory, we will be free of pain once we reach heaven
Join Us on Friday to Discuss "Thoughts on Science: Evolution versus Intelligent Design (Part I of an indefinite number of parts)"
Here's the description form the Facebook page ...
Discussion of the controversies that lie within the question "How did organisms on earth come to be?"When I open a page of Darwin I immediately sense that I have been ushered into the presence of a great mind. ... When I read Phillip Johnson, I feel that I have been ushered into the presence of a lawyer.
Ideally, an equal number of evolutionary biologists and creationists will attend.
All are welcome, even spectators.
Richard Dawkins (1996)Please join us. The last meeting [What Is Science? - Still No Answer!] was a lot of fun.
Here's a list of some topics we could discuss. If you can only read one then choose Creationism Continuum because it helps if you understand the meaning of "creationism."
The Discovery Institute Presents the Case for Magic
Five Myths (?) About Intelligent Design Creationism
How Do Intelligent Design Creationists Define "Creationism"?
The "Intelligent Design" Version of Creationism
Creationism Continuum
Casey Luskin "Explains" Intelligent Design Creationism
A Torley Defense of Irreducible Complexity
Blown Out of the Water
"Impossible" Molecular Machines
Will the Real IDiot Please Stand up?
And here, for no particular reason, is a quote from George Orwell.
The power of holding two contradictory beliefs in one's mind simultaneously, and accepting both of them... To tell deliberate lies while genuinely believing in them, to forget any fact that has become inconvenient, and then, when it becomes necessary again, to draw it back from oblivion for just as long as it is needed, to deny the existence of objective reality and all the while to take account of the reality which one denies – all this is indispensably necessary. Even in using the word doublethink it is necessary to exercise doublethink. For by using the word one admits that one is tampering with reality; by a fresh act of doublethink one erases this knowledge; and so on indefinitely, with the lie always one leap ahead of the truth.
George Orwell, Nineteen Eighty-Four
Tuesday, February 05, 2013
Goodby Penny!
Everyone is supposed to round off to the nearest nickle. That's means that things that used to cost 16 or 17 cents will now cost 15 cents and things that used to cost 18 or 19 cents will now cost 20 cents.
Monday, February 04, 2013
Reviewing the "Arseniclife" Paper
The "arsenic affair" began with a NASA press conference on Dec. 2, 2010 announcing that a new species of bacteria had been discovered. The species was named GFAJ-1 (Get Felisa a Job), by the lead author Felisa Wolfe-Simon. GFAJ-1 was grown in a medium that lacked phosphate and contained high concentrations of arsenic. The paper, published that day on the Science website, claimed that arsenic was replacing phosphorus in many of the cell's molecules, including nucleic acids.Like many other scientists, I was very skeptical from day one. The results reported in the press conference just couldn't possibly be true unless everything we knew about chemistry and DNA was very wrong.
How did this paper ever get published in Science? I was suspicious that the normal peer review process had been skipped in order to get a major discovery into press as soon as possible.
Turns out that wasn't true. There were three reviews and they were all glowing. We know this because USA Today has obtained copies of the reviews through the Freedom of Information Act in the USA [Glowing reviews on 'arseniclife' spurred NASA's embrace] [Excerpts for the "asreniclife" investigation file]. Here are excerpts from the three reviews—I've never seen such glowing reviews.
Review 1Looks like we can blame the reviewers, or perhaps the editor for choosing the wrong reviewers.
The manuscript Wolfe-Simon et al. demonstrates for the first time that a microorganism is able to use arsenic in place of phosphorus to sustain growth and life. This was done by using a rather simple initial selection on synthetic growth medium followed by a more in-depth analysis of the isolated organism with regard to the path of arsenic from uptake to incorporation into various cellular fractions using ICP-MS, 73As labeling and X-ray absorption near edge spectroscopy (XANES).
The results are exceptional as they show that arsenic, yet believed to be highly toxic for most organisms, in GFAJ-1, a member of the Halomouadaccae, can substitute for the lack of phosphate, a major building block for various macromolecules present in all cells, namely nucleic acids, lipids and proteins.
The methods applied are straightforward. The most surprising and acknowledgeable aspect of the work is its simple approach.
I have only a few minor points regarding the overall presentation.
Review 2
The manuscript by Wolfe-Simon et al. is well-written, concise, to the point and provides exciting novel results. The authors provide many lines of evidence to prove their point that the isolated novel bacterium (at least to some extent) can replace phosphate by arsenic in its biomolecules. It's a pleasure to get a well-conceived and carried-out study to review.
Review 3
Reviewing this paper was a rare pleasure. It is clearly-written and well-reasoned. The authors choose the right methods, designed the right experiments, obtain solid data supporting the conclusion that GSAJ-1 uses As in place of place of P. They use appropriate caution in interpreting results. I think the paper is just about publishable as is; my comments for revision are below. Great job! I look forward to seeing follow-up work in the future.
[Hat Tip: Michael Eisen (@mbeisen) (#arseniclife)]
Erb, T.J., Kiefer, P., Hattendorf, B., Günther, D., and Vorholt, J.A. (2012) GFAJ-1 is an arsenate-resistant, phosphate-dependent organism. Science, 337: 467-470. [doi: 10.1126/science.1218455 ]
Reaves, M.L., Sinha, S., Rabinowitz, J.D., Kruglyak, L., and Redfield, R.J. (2012) Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells. Science, 337: 470-473. [doi: 10.1126/science.1219861]
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]
Become an Atheist
How can you resist this ad from Cult of Dusty?
[Hat Tip: Friendly Athiest: The Atheist Super Bowl Ad You Didn’t See]
Saturday, February 02, 2013
Happy Groundhog Day!
Wiarton Willie says we're going to have an early Spring.
None of these groundhog festivals compare to the one in movie starring Bill Murray and Andie MacDowell. It's one of the best movies ever.
None of these groundhog festivals compare to the one in movie starring Bill Murray and Andie MacDowell. It's one of the best movies ever.
Friday, February 01, 2013
Jenny McCarthy Dumped
CTV News is now reporting that Jenny McCarthy Dumped from Bust A Move Ottawa event.
Actress Jenny McCarthy has been dumped again. McCarthy won't be in Ottawa for Bust A Move.Kudos to CFI Canada and Ottawa Skeptics. Well done!!!
The Ottawa Regional Cancer Foundation reacted today to a public backlash in signing the anti-vaccine campaigner to the Ottawa breast health fundraiser.
McCarthy was to headline a fitness class for the March 2nd fundraiser at the Ottawa Athletic Club.
Social media websites exploded with negative reaction to McCarthy's choice for Ottawa's Bust A Move celebrity.
Twitter featured hashtag #DropJenny.
McCarthy has been replaced by fitness guru Tommy Europe.
What Is a Mutation?
"Mutation"¹ is almost as difficult. First, we want to distinguish between a mutation and DNA damage. DNA damage occurs when various enzymes make a mistake and damage the nucleotides in a DNA molecule. Damage also occurs when outside forces such as X-rays or chemical mutagens attack DNA. Examples are thymidine dimers or cleavage of a base from a nucleotide. DNA can also be broken into two or more pieces.
This damage is never copied and passed on to the next generation. Either it is fixed in some way or it is lethal. When the damage is fixed it may end up being identical to the original DNA molecular or it may be altered in some way that is passed on. Thus, mutation is (semi-)permanent change that is heritable.
The genetic material is DNA in most cases but RNA genomes (viruses) can also be mutated. There are many different kinds of "genomes" that have to be covered in our definition. This include virus genomes, mitochondrial genomes, chloroplast genomes, plasmids, and mobile genetic elements (mostly transposons).
Any alteration in the sequence of a genome counts as a mutation, not just those that occur in a gene (whatever that is!). This is important because some of the traditional definitions of mutation are restricted to genes.
Here's a good definition from the Wikipedia site ...
In genetics, a mutation is a change of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element. Mutations result from unrepaired damage to DNA or to RNA genomes (typically caused by radiation or chemical mutagens), from errors in the process of replication, or from the insertion or deletion of segments of DNA by mobile genetic elements.[1][2][3] Mutations may or may not produce discernable changes in the observable characteristics (phenotype) of an organism.The Understanding Evolution at UC Berkeley defines mutation as ...
A mutation is a change in DNA, the hereditary material of life. An organism's DNA affects how it looks, how it behaves, and its physiology. So a change in an organism's DNA can cause changes in all aspects of its life.This isn't good because it doesn't cover RNA genomes and it doesn't distinguish between DNA damage and fixed, heritable, change.
Theme
Mutation
-definition
-mutation types
-mutation rates
-phylogeny
-controversies
The Genetic Science Learning Center at the University of Utah offer this definition.
A mutation is a permanent change in the DNA sequence of a gene. Mutations in a gene's DNA sequence can alter the amino acid sequence of the protein encoded by the gene.That's no good because it restricts mutations to protein encoding genes.
A quick Google search will reveal many other definitions but none as as good as the Wikipedia entry.
As usual, the standard dictionary definitions are not helpful. They are usually quite poor at defining biological terms. Merriam-Webster defines mutation as ...
a relatively permanent change in hereditary material involving either a physical change in chromosome relations or a biochemical change in the codons that make up genesThis is actually better than some of the definitions from scientists. It's main deficiency is that it restricts mutations to genes.
1. The word comes from the Latin mutare, to change.
What About Grandfathers?
From these slim clues, Hawkes and her colleagues developed the "grandmother hypothesis," which holds that women past childbearing age helped not just their children, but their children's children, and lengthened the human lifespan in the process. Without babies of their own to lug around, grandmothers had both time and a very good reason to be useful. When they eked out food for their daughters' children, they reduced the chance that those children would die. That gave the grandmothers a better chance of passing on their own predisposition to longevity. (In general, grandmothers appear to have helped daughters' offspring more than sons'; evolutionary theorists explain this by pointing out that a daughter's maternity affords a surer genetic connection than a son's paternity, unless you all but imprison your daughter-in-law.2)I've written about the Grandmother Hypothesis before [The Adaptive Value of Menopause] [How Women Got Their Menopause ]. It's an adaptationist just-so story that makes no sense whatsoever as soon as you start thinking critically.
But that's not what worries me today. What troubles me is that grandfathers don't seem to figure into these stories. Why is that? Are we completely irrelevant to our children and grandchildren?
Carnival of Evolution #56
Welcome to the 56th edition of the Carnival of Evolution.If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission.
I haven’t been on holiday for a while, so for this issue I thought I’d take a trip around the world, looking in on all the exciting research and work being done in the field of evolution. There are some great posts here, from some wonderful bloggers, so go take a look!
A Fake Humanist Quiz
So is Veronica Abbas 'cause she only scored 90% as well [Are You a Humanist?]. I scored 93% but I'm angry because this isn't a test for humanism—it's a test to see whether you are an atheist.
They are not the same thing. I'm not certain that all humanists share the same values but I am certain that there's a distinct libertarian leaning in many humanist organizations. Since I'm a socialist, I reject that point of view and I could never call myself a humanist.
Here's a guest column by Crystal Jurczynski on the American Humanist Association website: Why Humanists Should Vote Libertarian. Although it's a personal opinion it seems to reflect a common perspective shared by most humanist organizations although the libertarian influence was watered down in recent Humanist Manifestos.
Humanists and Libertarians share an optimistic vision for an America where people are empowered to make their own life choices, improve their circumstances, and employ peaceful solutions to conflict. These three areas are governed by our social, economic, and foreign policies.Humanism is a worldview that goes far beyond just nonbelief in supernatural beings. You won't see much exploration of that worldview in the quiz.
Libertarians want government out of our personal lives. So, Libertarians support many humanistic causes, such as abortion rights, gay marriage, medical marijuana, and death-with-dignity. Libertarians are also faithful to the Constitution and reject curtailments of our rights, like the illegal detention of "enemy combatants" and the ironically-named "Patriot Act."
Some Humanists, however, take exception to the Libertarian rejection of social programs like Welfare, Social Security, and Medicare. These Humanists should take a hard look at the results produced by these programs. For example, we've spent trillions on poverty programs since the "Great Society" was introduced 40 years ago, but Census Bureau reports show no reduction in poverty rates. The return on the money we are forced to contribute to Social Security and Medicare is much less than can be gained on the free market (and both of these Ponzi schemes will have to be fixed soon or go broke).
Without these types of programs devouring our income, we could save more money to support ourselves as well as provide charity to those in need.
Why Is Jenny McCarthy Going to Ottawa?
The Ottawa Regional Cancer Foundation is dedicated to increasing cancer survivorship in Eastern Ontario. We unite those who want to be active in the fight for cancer survivorship, drawing on their expertise and resources to fund the gaps between what can be done and what is being done to reduce suffering and death due to cancer in Eastern Ontario. We support cancer care and research to prevent, detect, diagnose and cure cancer.Part of their yearly fundraising effort involves "Bust a Move for Breast Health," a "day-long fitness extravaganza" that usually involves a celebrity fitness person. This year they invited Jenny McCarthy the well-known opponent of child vaccinations.
To Bernice Rachkowski
Leadership Committee Chair
Bust a Move 2013
Dear Ms Rachkowski,
We are greatly disappointed to hear of your decision to select Jenny McCarthy as headliner for the Bust a Move fundraiser this year. As pointed out by the Ottawa Citizen, Ms. McCarthy is well-known for her outspoken support for deeply unscientific and anti-health claims regarding vaccination and autism. As such, she is entirely unsuitable to represent a cancer charity such as the Ottawa Regional Cancer Foundation, and we ask you to please reconsider this unwise invitation.
McCarthy has claimed for years that vaccines cause autism, ignoring copious scientific evidence that there is no such connection. She has used her celebrity to spearhead a public campaign to discredit childhood vaccination, a medical advance responsible for saving millions of lives every year. Her celebrity status - which you cite as the reason for your invitation - has helped her to persuade large numbers of parents to leave their children defenceless against potentially lethal illnesses such as measles and whooping cough. The dangers of such reckless misinformation have become increasingly apparent in recent years with the tragically unnecessary resurgence of several of these diseases.
McCarthy’s campaign against vaccinations should be of particular concern to the ORCF, for declining vaccination rates have an impact on cancer and cancer survival rates. The HPV vaccine, which shows great promise in reducing the incidence of cervical and other cancers, has met with resistance and disappointingly low uptake rates, in part because of the public distrust of vaccination sown by celebrities such as Jenny McCarthy. Moreover, the reduction in herd immunity caused by wide-scale refusal to vaccinate children poses a very real threat to the survival of immunocompromised cancer patients.
By inviting Jenny McCarthy to participate in your fundraiser, you raise her profile within the community, and implicitly give support to her anti-vaccination efforts. Even though she may not mention these views as part of your event, she will gain credibility from association with such a reputable and well-liked charity as the Ottawa Regional Cancer Foundation. At the same time, you bring yourself into disrepute by inviting such a controversial figure to play a prominent part in your campaign. As members of the medical, scientific, and skeptical communities, we cannot help but question the judgement of an organization that would extend such an invitation.
It is not too late. You are reported in the Ottawa Citizen to have said that you would be surprised if people were upset by your invitation of Ms McCarthy. This was clearly a miscalculation. We hope that you will recognize the error that you have made and restore public trust in your organization by rescinding this invitation.
Sincerely,
Michael Payton, National Executive Director, Centre for Inquiry Canada
Iain Martel and Steve Livingston, Co-chairs, Committee for the Advancement of Scientific Skepticism
Chris Hebbern, Chair, Ottawa Skeptics
Seanna Watson, Chair, Centre for Inquiry Ottawa
Dear Freethinkers,
The upcoming fundraising event "Bust a Move", held regionally in Ottawa is planning to host Anti-Vaccination Advocate Jenny McCarthy as a headline speaker. McCarthy's writings have contributed substantially to the belief that Vaccines cause Autism and Cancer. Together with CFI Ottawa, CASS and our allies at Ottawa Skeptics we have released the statement below.
Here are three great ways to help motivate the organizers at "Bust a Move" to rethink their choice of speaker:
1) Tweet your thoughts to the event organizers at @OttawaCancer and be sure to use the hashtag #dropjenny
2) Read - the Ottawa Citizen's excellent coverage here and leave a comment expressing your dissatisfaction
3) Write to Ottawa Cancer CEO Linda Eagen - leagen@ottawacancer.ca and voice your opinion.
Thursday, January 31, 2013
Theme: Mutation
This is a collection of Sandwalk posts on mutation starting in 2007. The latest ones are at the bottom of the list.
March 27, 2007
Silent Mutations and Neutral Theory
Neutral Theory and random genetic drift explains variation and it also explains molecular evolution and the (approximate) molecular clock. There are no other explanations that make sense and nobody has offered a competing explanation since Motoo Kimura (1968) or Jack King and Thomas Jukes (1969) published their papers almost fifty years ago. (Aside from occasional nitpicks, of course. There are always scientists who like to show that some mutations that were thought to be neutral are actually beneficial or deleterious. None of them have mounted a serious claim that most variation or most of molecular evolution can be explained by natural selection.)
April 19, 2007
Haldane's Dilemma
This is very interesting. Dembski has teamed up with Walter ReMine, demonstrating once again that the old addage "opposites attract" does not apply to kooks.
ReMine has an article on Uncommon Descent where he pushes his usual whine about evil scientists and how their world-wide conspiracy has kept him from revealing the fatal flaw in evolution [Evolutionist withholds evidence on Haldane’s Dilemma]. I can see how similar this is to Intelligent Design Creationism.
Silent Mutations and Neutral Theory
Neutral Theory and random genetic drift explains variation and it also explains molecular evolution and the (approximate) molecular clock. There are no other explanations that make sense and nobody has offered a competing explanation since Motoo Kimura (1968) or Jack King and Thomas Jukes (1969) published their papers almost fifty years ago. (Aside from occasional nitpicks, of course. There are always scientists who like to show that some mutations that were thought to be neutral are actually beneficial or deleterious. None of them have mounted a serious claim that most variation or most of molecular evolution can be explained by natural selection.)
April 19, 2007
Haldane's Dilemma
This is very interesting. Dembski has teamed up with Walter ReMine, demonstrating once again that the old addage "opposites attract" does not apply to kooks.
ReMine has an article on Uncommon Descent where he pushes his usual whine about evil scientists and how their world-wide conspiracy has kept him from revealing the fatal flaw in evolution [Evolutionist withholds evidence on Haldane’s Dilemma]. I can see how similar this is to Intelligent Design Creationism.
Dramatic Irony
Irony (from the Ancient Greek εἰρωνεία eirōneía, meaning dissimulation or feigned ignorance) is a rhetorical device, literary technique, or situation in which there is an incongruity between the literal and the implied meaning....The funny thing about irony (and sarcasm) is that there are so many people who are irony-deficient. They just don't get it. They seem to be incapable of recognizing anything other than the literal meaning of a statement. Look at the example given in the Wikipedia article (right figure). Then look at yesterday's Jesus and Mo cartoon (below). Both are excellent examples of intended irony.
In dramatic irony, the author causes a character to speak or act erroneously, out of ignorance of some portion of the truth of which the audience is aware. In other words, the audience knows the character is making a mistake, even as the character is making it. This technique highlights the importance of a particular truth by portraying a person who is strikingly unaware of it.
Wednesday, January 30, 2013
Citation Chart
This is pretty cool. You can ask Google Scholar to collect all citations to your published articles and display them as a chart [Citations]. I don't have a lot of citations but it's still fun to see them.
[Hat Tip: Ford Denison of This Week in Evolution: A citation a day keeps ideas in play. He has hundreds of citations every year.]
Defending Homeopathy?
Allow me to lay my admittedly love-of-science, rant-tainted cards on the table. In general, the services provided by naturopaths reside either in the realm of commonsense lifestyle advice (get lots of sleep, eat well and stay active) or they have little empirical evidence to support their use. In fact, many naturopathic practices are based on a semi-spiritual theory (the healing power of nature), and have no foundation in science. They reside largely in the realm of pseudoscience.There are people who don't live in the material world and they always pop out of the woodwork whenever their favorite superstitions are questioned. In this case, it's a homeopath named Karen Wehrstein who was given space on the newspaper website to respond to Timothy Caulfield [Homeopathy offers hope]. Wehrstein is described as ....
Am I being too harsh? I recently worked with a University of Alberta colleague on an analysis of the websites for the naturopaths in Alberta and British Columbia. We wanted to get a sense of what is being offered to the public. In Alberta, the number one most commonly advertised service is homeopathy.
Homeopathy has been around for hundreds of years. The basic philosophy behind the practice is the idea of “like cures like.” A homeopathic remedy consists of a natural substance — a bit of herb, root, mineral, you get the idea — that “corresponds” to the ailment you wish to treat. The “active” agent is placed in water and then diluted to the point where it no longer exists in any physical sense.
In fact, practitioners of homeopathy believe that the more diluted a remedy is, the more powerful it is. So, if you subscribe to this particular worldview, ironically, you want your active agents to be not just non-existent, but super non-existent.
The bottom line: For those of us who reside in the material world, where the laws of physics have relevance, a homeopathic remedy is either nothing but water or, if in capsule form, a sugar pill.
Karen Wehrstein is the executive director of the Canadian Consumers Centre for Homeopathy (homeocentre.ca), an organization formed in 2011 to educate the public about homeopathy and advocate for freedom of choice in health care.In other words, she's a lobbyist for quackery. She runs the Homeopathy Centre of Muskoka. Here's part of what she has to say ...
Homeopathy’s big stumbling block to acceptance is that its medicines are diluted so much that people outside of the field can’t understand how they can possibly have an effect. There are, however many scientists who do have that expertise. So many, that there is an entire journal devoted to the field, the International Journal of High Dilution Research. And they seem to be getting intriguingly close to providing definitive answers.Students who have taken my course will recognize this kind of response. Science is so overwhelmingly respected these days that nobody can afford to be on the wrong side of scientific evidence. If you are defending quackery then you only have two choices; either you discredit the evidence against you or you make up scientific evidence to support your position. Most quacks do both. They end up simultaneously disparaging and praising scientists who work in the field.
Opponents of homeopathy claim that homeopathic medicines are “just plain water” with no medicinal properties. But increasing numbers of scientific findings are making it harder to maintain such as stance. One study has found that solutions prepared in the traditional homeopathic way — through repeated dilutions by mechanical shaking — have properties unlike plain water, with elements of the dissolved material. Another study suggests the solutions have an affect on living cells in vitro. Yet another study shows that solutions can be distinguished from each other, using the right equipment to determine their contents. And emerging research suggests that homeopathic solutions actually contain nanoparticles of the original dissolved material.
If you're interested in the scientific truth and why Karen Wehrstein is so very wrong, then you can do no better that read what Diane Sousa has to say on Skeptic North where she takes apart all of Wehrstein's claims [A Response to Karen Wehrstein: Homeopathy Offers Hope but Delivers Only Sweet Nothings].
Should Chilliwack BC Permit Distribution of Bibles in Public Schools?
Sign the Petition. You will have to identify yourself but that shouldn't be a problem if you really believe in a secular school system.Recent secular victories in Chilliwack are at risk.
On November 13th, the Board of the Chilliwack School District deleted Regulation 518 that stated, "The Board approves the distribution of Gideon Youth Testaments to Grade 5 pupils with parental consent." At the same meeting, the Board agreed to draft a new policy to permit the "distribution of materials" by March 2013.
This new policy represents an attempt to use public schools for religious proselytizing in BC public schools.
Superintendent Evelyn Novak intends to gather feedback through February to draft the new policy. While this feedback may not be open to the public, secular voices will be heard.
Please sign the petition below to send the message to the Chilliwack School Districts that BC schools should remain secular.
[Hat Tip: Veronica Abbas at Canadian Atheist.]
Monday, January 28, 2013
Guelph Biology Students
Here are the biology students at the University of Guelph (Guelph, Ontario, Canada) dancing and singing to "Anna Sun" by Walk the Moon.
I love this stuff. Some of these students are going to be scientists some day.
I love this stuff. Some of these students are going to be scientists some day.
[Hat Tip: Ryan Gregory, Professor, University of Guelph.]
Sunday, January 27, 2013
New Premier of Ontario: Kathleen Wynne
Kathleen Wynne represents the leftish wing of the Liberal Party of Ontario and that's the view I support. Wynne becomes the first women Premier of Ontario and she joins five other women who lead provincial/territorial governments in Canada. As of today, almost 90% of Canadians live in provinces headed by a woman!
Kathleen Wynne is also the first openly gay person to head a provincial government. She is married to Jane Rounthwaite.² Her sexual orientation wasn't really much of an issue during the campaign. Here she is, thanking her partner Jane during the acceptance speech last night.
1. Subject to approval by the Lieutenant Governor.
2. Same-sex marriage has been legal in Ontario since 2002.
Friday, January 25, 2013
How Many Genomes Have Been Sequenced?
There are several types of genome sequence. Some are relatively incomplete and they don't really count. Others have been thoroughly sequenced and we have a good permanent draft sequence. The best ones are the "finished" genome sequences where the preliminary drafts have been checked and gaps have been filled.
How many "finished" or permanent draft complete genome sequences have been published?
How many of them are eukaryotes?
Here are the answers from: GOLD
(Apologies for the Three Domain influence.)
Archaea: 181
Bacteria: 3762
Eukaryotes: 183
Why are there so few eukaryotes? Because many eukaryotic genomes are very large and it takes a lot more work to sequence that much DNA. Furthermore, many eukaryotic genomes are full of junk DNA and it's difficult to sequence and assemble repetitive regions in order to get a complete chromosome. The bottom line is money—for most labs it's too expensive to sequence the genome of their favorite eukaryote but it can be quite cheap these days to sequence a bacterial genome.
How many "finished" or permanent draft complete genome sequences have been published?
How many of them are eukaryotes?
Here are the answers from: GOLD
(Apologies for the Three Domain influence.)
Archaea: 181
Bacteria: 3762
Eukaryotes: 183
Why are there so few eukaryotes? Because many eukaryotic genomes are very large and it takes a lot more work to sequence that much DNA. Furthermore, many eukaryotic genomes are full of junk DNA and it's difficult to sequence and assemble repetitive regions in order to get a complete chromosome. The bottom line is money—for most labs it's too expensive to sequence the genome of their favorite eukaryote but it can be quite cheap these days to sequence a bacterial genome.
[Hat Tip: Jonathan Eisen]
Why You Should Become a Postdoc Instead of Taking a Job in the Private Sector
Eric Lewellyn is an enthusiastic postdoc in the Drubin/Barnes Lab at US Berkeley. (They work on membrane trafficking.)
Eric tries to convince you to stay in university using song and dance. He describes all the good things aboutslaving away enjoying science in a research lab. I don't know Eric but I have met his mother—she's the cousin of one of our best friends.
Eric tries to convince you to stay in university using song and dance. He describes all the good things about
What Does the Liberal Party of Canada Stand For?
I've long been a supporter of the Federal Liberal Party of Canada. It's the party of Mike Pearson and Pierre Elliot Trudeau—two Prime Ministers that I greatly admire. I even like Jean Chrétien!
Lately I'm having trouble understanding what the Liberal Party stands for. They've just had two leaders (Michael Ignatieff, and Bob Rae) who are complete mysteries to me. I really don't know what they stand for, or what they're passionate about.
Apparently I'm not alone. Here's the view of Thomas Walkom from a column in the Toronto Star a few days ago [Do Canada’s, or Ontario’s, Liberals matter any more?].
Omar sent us a link to this video. It's obvious that Justin is avoiding the question. He stands for some trivial issues like legalizing marijuana but what about the bigger issues? How do I tell the difference between the Liberal Party and Conservative Party or the New Democratic Party? I don't think I can vote for Justin Trudeau or for any of the other leadership candidates. In fact, I'm not sure I can vote for the Liberal in the next election. The NDP is looking very attractive.
Lately I'm having trouble understanding what the Liberal Party stands for. They've just had two leaders (Michael Ignatieff, and Bob Rae) who are complete mysteries to me. I really don't know what they stand for, or what they're passionate about.
Apparently I'm not alone. Here's the view of Thomas Walkom from a column in the Toronto Star a few days ago [Do Canada’s, or Ontario’s, Liberals matter any more?].
On the other hand, it’s not clear what the Liberals represent any more. They would like voters to think of them as the non-Conservatives — the alternative to Stephen Harper federally or to Tim Hudak in Ontario.We've been discussing this issue with our former Liberal MP, Omar Alghabra, who happens to be a member of Justin Trudeau's team. Justin, for those of you who don't follow Canadian politics, it the son of Pierre Elliot Trudeau and he's running for the leadership of the Federal Liberal Party. We want Justin, and all the other candidates, to speak out on what the Liberal Party stands for.
But are they?
Paul Adams, an astute political observer writing in iPolitics, argues that the federal Liberals have transformed themselves into the old Progressive Conservatives, socially progressive but fiscally to the right.
I’d go further. I reckon the old PCs of Joe Clark would find federal Liberal leadership candidate Martha Hall Findlay’s talk of dismantling farm marketing boards a bit too right-wing for their tastes
Similarly, Liberal front-runner Justin Trudeau’s enthusiastic embrace of the Alberta oilsands would probably be seen as a tad naive by the Red Tories of former Ontario premier Bill Davis, most of whom believed that strong business required equally strong regulation.
As a party, the Liberals haven’t had a new idea since the 1980s. Individual party members have (Stéphane Dion’s green shift comes to mind).
But the party, as a whole never signed onto Dion’s environmental agenda. Nor has it signed onto anything else.
The Liberals talk of holding policy conventions that would replicate that golden period of the 1960s, when the party embraced medicare, public pensions and welfare reform.
But they never do. Former federal leader Michael Ignatieff hosted a thinkers’ conference that headlined prominent conservatives. Nothing came of it.
The conventional wisdom among Liberals is that strong policy positions should be avoided at all costs in order to avoid alienating voters. Instead, Liberals prefer to talk about what they call values.
Omar sent us a link to this video. It's obvious that Justin is avoiding the question. He stands for some trivial issues like legalizing marijuana but what about the bigger issues? How do I tell the difference between the Liberal Party and Conservative Party or the New Democratic Party? I don't think I can vote for Justin Trudeau or for any of the other leadership candidates. In fact, I'm not sure I can vote for the Liberal in the next election. The NDP is looking very attractive.
Thursday, January 24, 2013
What Is Science? - Still No Answer!
We had a fun meeting last night thanks to Rufina Kim [WTF Is Science?]. A bunch of students showed up along with Steve Livingston, the new co-Chair of CASS (Committee for the Advancement of Scientific Skepticism), and David Bailly, Chair of The Association for Science and Reason (Skeptics Canada).
Unfortunately we were not able to come to an agreement on "What Is Science."
Now we have to meet again in a couple of weeks!
We talked about whether there was a scientific method and whether falsifiability is part of the definition of science. The Wikipedia article on falsifiability is a good place to look for background information. Here are two sections from that article to get you started.
I made up an example of a Professor of English whose research focuses on how the English language actually sounded in the time of Geoffrey Chaucer (about 1370)¹. Is she doing science? If not, what kind of way of knowing is she using?
Unfortunately we were not able to come to an agreement on "What Is Science."
Now we have to meet again in a couple of weeks!
We talked about whether there was a scientific method and whether falsifiability is part of the definition of science. The Wikipedia article on falsifiability is a good place to look for background information. Here are two sections from that article to get you started.
Paul Feyerabend examined the history of science with a more critical eye, and ultimately rejected any prescriptive methodology at all. He rejected Lakatos' argument for ad hoc hypothesis, arguing that science would not have progressed without making use of any and all available methods to support new theories. He rejected any reliance on a scientific method, along with any special authority for science that might derive from such a method. Rather, he claimed that if one is keen to have a universally valid methodological rule, epistemological anarchism or anything goes would be the only candidate. For Feyerabend, any special status that science might have derives from the social and physical value of the results of science rather than its method.There's no such thing as a universal scientific method and falsifiability doesn't describe how the scientific way of knowing actually works.
...
In their book Fashionable Nonsense (published in the UK as Intellectual Impostures) the physicists Alan Sokal and Jean Bricmont criticized falsifiability on the grounds that it does not accurately describe the way science really works. They argue that theories are used because of their successes, not because of the failures of other theories. Their discussion of Popper, falsifiability and the philosophy of science comes in a chapter entitled "Intermezzo," which contains an attempt to make clear their own views of what constitutes truth, in contrast with the extreme epistemological relativism of postmodernism.
Sokal and Bricmont write, "When a theory successfully withstands an attempt at falsification, a scientist will, quite naturally, consider the theory to be partially confirmed and will accord it a greater likelihood or a higher subjective probability. ... But Popper will have none of this: throughout his life he was a stubborn opponent of any idea of 'confirmation' of a theory, or even of its 'probability'. ... [but] the history of science teaches us that scientific theories come to be accepted above all because of their successes." (Sokal and Bricmont 1997, 62f)
They further argue that falsifiability cannot distinguish between astrology and astronomy, as both make technical predictions that are sometimes incorrect.
I made up an example of a Professor of English whose research focuses on how the English language actually sounded in the time of Geoffrey Chaucer (about 1370)¹. Is she doing science? If not, what kind of way of knowing is she using?
1. This is roughly the time of World Without End. If the characters actually spoke in 14th century dialect we probably wouldn't have understood a word.
Wednesday, January 23, 2013
Teaching Developmental Biology
Think about that. In the early days of developmental biology, we didn’t even know whether there was differential gene activity or not; it was considered a reasonable possibility that all the genes were just doing their work, whatever it was, all the time in every cell, and that differences between cells emerged farther downstream, in biochemical interactions. But they knew this was an important question. They knew that we had to look at the activity of individual genes…they just didn’t have the tools yet. So it was back to hacking up embryos and trying to infer causes from aberrations.I used to teach this stuff in the 1980s and I certainly agree with PZ that you need to understand molecular biology and gene expression.
The change emerged gradually, but there were a couple of watershed moments where everyone looked up and noticed that hey, we do have ways of looking at genes directly. One was the work of Ed Lewis, a most excellent geneticist who used the tools of genetics to look directly at mutations that caused changes in fly morphology, in the 1960s. This was amazing stuff — the papers he wrote were beautiful and complex and very, very genetical — but it was written in a language that most developmental biologists of the day were unprepared to read. They were genetics papers. But I think they laid a foundation: if you want to do development, you’d better learn about genetics.
The second big event was the saturation mutagenesis screen of Christiane Nusslein-Volhard and Eric Wieschaus, about 20 years later. This work was also built on an understanding of genetics, but also used the tools of molecular biology. It was another lesson: if you want to do development, you’d better learn about molecular biology.
When it came time to write my first textbook I incorporated the examples I had used in class. The first ones I described were: the early to late switch in gene expression in bacteriophage T4, sporulation in Bacillus subtilis, and the genetic switch in bacteriophage lambda. These were well-studied examples from experiments carried out in the 1970s. They teach fundamental concepts in developmental biology and they have an additional advantage; namely, they get students thinking about species that aren't animals.
These are still excellent examples that are well-understood at the molecular level. They are much easier to understand than Drosophila or plants. Unfortunately, we've educated an entire generation of developmental biologists who have never heard of these elegant examples.
Is this a good thing or a bad thing? Do students need to know the real history of developmental gene expression as worked out by scientists who studied phage and bacteria?
What's Wrong with These Sentences?
Here's a short paragraph containing three sentences from my textbook (page 584). Is there anything wrong with any of these sentences?
Oh, and don't forget this.
Under physiological conditions, double-stranded DNA is thermodynamically much more stable than the separated strands and that explains why the double-stranded form predominates in vivo. However, the structure of localized regions of the double helix can sometimes be disrupted by unwinding. Such disruption occurs during DNA replication, repair, recombination, and transcription.Having trouble seeing where I went wrong, according to some people? Check out this and this.
Oh, and don't forget this.
Tuesday, January 22, 2013
Onion Talks: Social Media
Everyone knows about TED talks (Ideas Worth Spreading). They know that TED talks are "riveting talks by remarkable people." Or at least that's what they would like to believe [TED Tries to Clean Up Its Act].
Here's some worthy competition to TED talks from The Onion. It's title is Using Social Media To Cover For Lack Of Original Thought.
Here's some worthy competition to TED talks from The Onion. It's title is Using Social Media To Cover For Lack Of Original Thought.
[Hat Tip: Mike the Mad Biologist]
The Revisionaries Is Coming to Television
The Revisionaries is a documentary about the Texas state board of education and their attempt to suppress science in Texas public schools.
It will be aired on PBS starting January 28th. It's due to be broadcast in my area (WNED) on Feb. 3, 2013 at 11pm and on Feb. 8, 2013 at 4am.
[Hat Tip: Mike the Mad Biologist]
Monday, January 21, 2013
Monday's Molecule #198
This week's molecule is very strange looking but it serves a very important role in some species. What is the molecule, what species have it, and what does it do?
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.
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.)
Vote for Your Favorite Theory of Evolution!
So far there are almost 200 votes and "EvoDevo" is leading the pack (Boo!). I'm delighted to see that "Nonadaptive Evolution of Complexity" is getting a substantial number of votes. It suggests that there are people who really do understand Michael Lynch and Eugene Koonin (among others).
"Epigenetics" is way too popular. It is NOT an addition to evolutionary theory, in my humble opinion.
Nobody has voted for "Theistic Evolution."
VOTE NOW!
WTF Is Science?
Join us for a discussion about science and its relevance in the real world. This group will meet regularly every few weeks and it's open to everyone.
The topic for the first meeting is "What Is Science?" Check out the facebook page at: WTF Is Science?.
Wednesday, January 23, 2013 at 6pm.
Room 5243, Medical Sciences Building (5th floor)
You are welcome to bring food and (non-alcoholic) drinks.
Here are some definitions of science from the Oxford English dictionary.
The topic for the first meeting is "What Is Science?" Check out the facebook page at: WTF Is Science?.
Wednesday, January 23, 2013 at 6pm.
Room 5243, Medical Sciences Building (5th floor)
You are welcome to bring food and (non-alcoholic) drinks.
Here are some definitions of science from the Oxford English dictionary.
- The state or fact of knowing; knowledge or cognizance of something specified or implied; also, with wider reference, knowledge (more or less extensive) as a personal attribute.
- Knowledge acquired by study; acquaintance with or mastery of any department of learning. Also +pl. (a person's) various kinds of knowledge.
- A particular branch of knowledge or study; a recognized department of learning.
- In a more restricted sense: A branch of study which is concerned either with a connected body of demonstrated truths or with observed facts systematically classified and more or less colligated by being brought under general laws, and which includes trustworthy methods for the discovery of new truth within its own domain.
- The kind of knowledge or of intellectual activity of which the various `sciences' are examples. In early use, with reference to sense 3: What is taught in the schools or may be learned by study. In mod. use chiefly: The sciences (in sense 4) as distinguished from other departments of learning; scientific doctrine or investigation. Often with defining adj. as in 4 b.
Saturday, January 19, 2013
Herd Immunity
Have you ever heard anyone say that they don't need to get a vaccination because they never get the disease and, even if they do, it's never very serious?
That's fine if the only person you care about is you. Maybe you live in a cave. Maybe you never visit old people in a retirement home. Maybe you are never near babies. Maybe you don't have a spouse or a partner. (I can't imagine why such a self-centered person would not have a partner.)
Or maybe you just don't understand the concept of herd immunity. Ignorance can be cured ....
That's fine if the only person you care about is you. Maybe you live in a cave. Maybe you never visit old people in a retirement home. Maybe you are never near babies. Maybe you don't have a spouse or a partner. (I can't imagine why such a self-centered person would not have a partner.)
Or maybe you just don't understand the concept of herd immunity. Ignorance can be cured ....
[Hat Tip: Mike's Weekly Skeptic Rant]
Friday, January 18, 2013
That's Extraordinary! Homeopathy
Here's a new video from Centre for Inquiry, Canada. Homeopathy is ridiculous, pseudoscientific, nonsense. It's about time that all intelligent people recognized this fact. Tell your friends.
Thursday, January 17, 2013
The NRA Anti-Obama Ad
If you live outside of the USA you may not have seen this television ad paid for by the National Rifle Association.
It's tantamount to a declaration of war on the issue of gun control. What this means is that there is no compromise or middle ground with these people. I hope Obama accepts the challenge and takes on the gun lobby. Last I heard, they were not a democratically elected part of the legislature.
BTW, if members of the NRA are really interested in protecting their children from the risk of being killed by guns then they should send them to school in the UK. Even Canada would be better.
Here's another version of the ad.
It's tantamount to a declaration of war on the issue of gun control. What this means is that there is no compromise or middle ground with these people. I hope Obama accepts the challenge and takes on the gun lobby. Last I heard, they were not a democratically elected part of the legislature.
BTW, if members of the NRA are really interested in protecting their children from the risk of being killed by guns then they should send them to school in the UK. Even Canada would be better.
Here's another version of the ad.
[Hat Tip: Pharyngula]
Which subjects need to be added to current evolutionary theory to create a new extended synthesis?
I'm not going to explain all of them because that would take many posts and a lot of time. Besides, most of them have been openly debated on numerous blogs over the past decade or so.
Choose the one(s) that you think are the most important.
50th Anniversary of Ramachandran Plots
This year marks the 50th anniversary of the publication of Ramachandran plots (Ramachandran 1963).
Don't know what I'm talking about? Read Ramachandran Plots.
THEME:
More posts on
Protein StructureChirag Vora was kind enough to alert me to this anniversary. Check out his blog at: Golden Jubilee of Ramachandran Plot.
Don't know what I'm talking about? Read Ramachandran Plots.
THEME:
More posts on
Protein StructureChirag Vora was kind enough to alert me to this anniversary. Check out his blog at: Golden Jubilee of Ramachandran Plot.
Ramachandran, G. N., Ramakrishnan, C. T., and Sasisekharan, V. (1963) Stereochemistry of polypeptide chain configurations. Journal of molecular biology, 7:95-99.
Wednesday, January 16, 2013
Drive-Thru at Timmy's
It's been ages since I've posted anything about the Canadian institution known as Tim Hortons. Here's a photo from cheezeburger.
[Hat Tip: David Schuller.]
Why Do the IDiots Have So Much Trouble Understanding Introns?
Most eukaryotic genes have introns. Introns make up about 18% of the DNA sequences in our genome. Most of these sequences are junk but introns are functional and up to 80bp of each intron is required for proper splicing. The essential sequences contain the 5′ splice site (~10 bp); the 3′ splice site (~30 bp): the branch site (~10 bp); and enough additional RNA to form a loop (~30 bp). The branch site and the splice sites are where specific proteins bind to the mRNA precursor [Junk in Your Genome: Protein-Encoding Genes]. It turns out that within introns about 0.37% of the genome is essential and about 17% is junk.
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