Jeffrey Shallit is making a heroic sacrifice. He's attending a series of lectures on God and Reason. This is a legitimate dichotomy, either you believe in God or you accept reason. You can't do both.
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
This is an example of Christian reasoning? Jeff, you have my sympathies ... and thanks for reporting on the best that sophisticated theology has to offer.
Rufina Kim has organized the second meeting of her group Thoughts on Science. We will meet on Friday, February 8, 2013 at 5 pm in room 5253 of the Medical Sciences Building on the University of Toronto St. George campus. The meeting is scheduled to end at 7:30 pm.
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?"
Ideally, an equal number of evolutionary biologists and creationists will attend.
All are welcome, even spectators.
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.
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
Beginning yesterday the Canadian penny is being removed from circulation.
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.
Many of you will remember the "arsenic affair" from a couple of years ago. Here's what I wrote in February 2012 once we knew that the main result of the paper had been disproven by Rosie Redfield. We now know that there was no arsenic in the DNA (Erb et al. 2012, Reeves et al., 2012).
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 1
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.
Looks like we can blame the reviewers, or perhaps the editor for choosing the wrong reviewers.
[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]
How can you resist this ad from Cult of Dusty?
[Hat Tip: Friendly Athiest: The Atheist Super Bowl Ad You Didn’t See]
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.
Wow! That was quick. I just wrote my letter a few hours ago and just posted to my blog at 11am [Why Is Jenny McCarthy Going to Ottawa?]. 
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.
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.
Kudos to CFI Canada and Ottawa Skeptics. Well done!!!
I've said it before and I'll say it again, biology is messy. It's really hard to rigorously define simple terms because there are always exceptions. Just think of the problems we've had trying to define a gene [What Is a Gene?].
"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.
In the example shown here, the damage is deamination of cytosine, a very common spontaneous reaction. It is usually repaired fairly quickly but if the DNA is replicated before repair it will result in a switch from a G/C base pair to an A/T base pair at the same site. This change is inherited in all subsequent generations ... it is a mutation.
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 genes
This 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.
Judith Shulevitz is a journalist with no particular science background as far as I can tell. Her latest work is a piece published in The New Republic with a provocative title: Why Do Grandmothers Exist? Solving an evolutionary mystery. She writes ...
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?
This month's Carnival of Evolution is hosted by Shuna E.Gould (Lab Rat) at Scientific American blogs [Lab Rat]. Read it at: The Carnival of Evolution: World Travel Edition!
Welcome to the 56th edition of the Carnival of Evolution.
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!
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.
The British Humanist Association has an online quiz called Are You a Humanist?. PZ Myers took the test and discovered that he is only 90% humanist [I think I got an A-]. He's disappointed.
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.
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.
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.
The Ottawa Regional Cancer Foundation raises money to support cancer research and treatment. Here's their Mission Statement.
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.
As you might imagine, this move has not been universally praised by rational people. The Ottawa Citizen wrote an interesting piece questioning the wisdom of inviting a quack to an event sponsored by a cancer society [Anti-vaccine crusader Jenny McCarthy to headline Bust a Move Ottawa]. The Center for Inquiry, Canada, and Ottawa Skeptics sent the following letter to the organizers of "Bust a Move."
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.
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.
From Wikipedia [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....
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.
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.
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.]
