I don't know where this clip comes from or when it was made but it's being promoted on YouTube as "Dr. Craig Venter Denies Common Descent in front of Richard Dawkins!" The link was posted by someone in a comment to a previous post on Sandwalk.
Everything that Ventor says is correct. He didn't need to quibble about the universality of the genetic code but it's true that there are variants.
His point about the tree of life is correct, especially in a discussion about the origin of life. It's unfortunate that Richard Dawkins repeatedly makes such an issue about the tree of life because he's on shakey ground when he does that. I assume that Dawkins hasn't studied the problem. However, he's in good company since most scientists don't understand the problems with the early tree of life. The early history of life looks more like a bush with many interconnecting branches due to horizontal gene transfer [The Tree of Life].
Here's a video of the complete debate. The relevant part, according to the creationists, begins at 9 mins.
A new book has just been published. The title is "Darwin's Dead Idea and the Man Who Helped Kill It." Here's the description on Amazon.
"Darwin’s Dead Idea and the Man Who Helped Kill It" makes for highly engaging reading. Witness the fascinating journey of a smart, inquisitive adolescent rejecting his school’s ask-no-questions religious indoctrination into a mathematician, philosopher, and scientist of the highest order, one who today is powerfully and persuasively challenging academia’s reigning answer to the questions that haunt us all: Where did we come from? Why is there something rather than nothing? A leading spokesman for the scientific theory that is shattering materialist assumptions about reality and the origin of life, Dr. William Dembski responds to probing questions from James Barham, general editor of TheBestSchools.org. That interview forms the core of DDI. Dembski’s forthright and humbly restrained responses reveal the courage, perseverance, and original thinking that have made him a lightning rod in the scientific community. The heated controversy surrounding intelligent design theory dramatically confirms Machiavelli’s observation that there is nothing more difficult to carry out nor more doubtful of success, nor more dangerous to handle, than to initiate a new order of things. DDI introduces readers to one of the stellar lights of the new order of things now emerging on the horizon.
There's a very interesting paper that's just been published online in ScienceExpress. The work is by Haung et al. (2013) from the Broad Institute at Harvard and MIT (Boston, Massachusetts, USA). These workers looked at the genomes of 70 different malignant melanomas and discovered that fifty (50) of them had mutations in the promoter region of the gene TERT (telomerase reverse transcriptase). The mutations created a new binding site for transcription factors resulting in a 2-4 fold increase in transcription of the gene.
Here's a picture of the gene from the Ensembl website [TERT]. The position of the transcription start site (P) is shown and the approximate position of the two mutations (M) is just upstream.
It's good that mutations affecting melanomas have been identified but the result isn't totally unexpected. We've known for fifty years that mutations in the promoter regions of genes can affect expression. Even in humans, such mutations have been widely studied; for example, lactase persistence is due to mutations in enhancer regions of the lactase gene.
"This new finding represents an initial foray into the 'dark matter' of the cancer genome," said Levi Garraway, senior associate member of the Broad, and associate professor of medicine at Dana-Farber, the article’s senior author.
WTF! Since when have promoters and enhancers been called "dark matter"? And why isn't it mentioned, or even hinted at, in the published paper?
Only about 1% of the human genome provides the blueprint for the body’s proteins. The remaining "non-coding" portion of the genome, sometimes referred to as dark matter, is poorly understood. Scientists have only recently begun exploring the relationship between these regions and the body’s cellular structure and processes.
We have an excellent understanding of the human genome [What's in Your Genome?]. This press release implies that only 1% of the genome is understood and the rest is mysterous "dark matter." We've known for decades that most of this DNA is junk (defective transposons). We know about pseudogenes, genes that encode functional RNAs, regulatory regions (including enhancers), introns, centromeres, defective viruses, telomeres, origins of replication, and several other functional parts of the genome.
I don't believe that the senior author of this study, Levi Garraway, actually believes what he is quoted as saying. If it were true then why didn't he put it in the paper? Why is there nothing in the paper about the importance of revealing mysterious "dark matter"?
Why do press releases have to be so misleading?
Huang, F.W., Hodis, E., Xu, M.J., Kryukov, G.V., Chin, L., and Garraway, L.A. (2013) Highly Recurrent TERT Promoter Mutations in Human Melanoma. Science published online January 24 2013 [doi: 10.1126/science.1229259
One of the take-aways here is not only the progress ID is making in scientific and general culture, but specifically among liberal thinkers. That makes it a lot harder to pigeonhole us in time-honored Darwinian fashion as right-wing Christian fundamentalists, creationists and the like. This may be the chief source of outrage from the Darwin community. Deprived of that old crutch, these guys will be forced to argue with us and explain in detail why ID, not creationism yet again, is wrong. Of course that's something that most have stubbornly, and tellingly, refused to do.
I have been arguing with these IDiots for over twenty years. They stubbornly, and tellingly, refuse to listen. Isn't that strange?
PZ Myers posted an article last week that was part of an ongoing discussion about the role of atheism in the skepticism movement. The title of his post was: Atheists are skeptics. I covered that debate in an earlier post [Skeptics Must Be Atheists].
Now I want to discuss whether all atheists must be skeptics.
The answer is "no." Atheists are people who don't believe in any god(s). There are millions of atheists all around the world who have grown up without any belief in god(s). Their parents didn't believe, their grandparents didn't believe, and they live in a secular culture. Many of these atheists are taken in my homeopathy, fear of GMOs, and various conspiracy theories. They aren't critical thinkers and they aren't skeptics.
Let's not fall into the trap of assuming that all atheists have grown up as believers and have recently lost their faith. That's just not accurate.
The skeptic movement has been in a bit of a turmoil over the past few years. One of the problems concerns the role of atheism in the movement. Many people think that outspoken criticism of religion (i.e. Gnu Atheism) is not a necessary part of skepticism. I agree—just as you don't have to be an outspoken critic of chiropractors to be a skeptic.
However, that doesn't mean that belief in god(s), or belief in the grandiose claims of chiropractors, is compatible with skepticism. They aren't.
PZ Myers and Steve Novella are debating this issue. The latest round is from last week on Pharyngula: Atheists are skeptics. (His title is wrong ... more about that in another post.¹) Novella is one of those skeptics who think that skepticism requires scientific thinking [Bigfoot Skeptics, New Atheists, Politics and Religion] but he also believes that the scientific way of knowing has limits and that belief in god(s) falls outside of those limits. The "limit" is, as we all know, methodological naturalism. (Novella's main interest is quack medicine.) Here's how he describes one of the attributes of a skeptic ...
Scientific societies are made up of groups of scientists who band together for various legitimate purposes such as organizing meetings, publishing journals, promoting their speciality, and lobbying for funds. The credibility of a society depends on its area of expertise. They lose credibility when they take positions on issues outside of their discipline.
That's why many of us have been opposed to the accommodationist positions of the American Association for the Advancement of Science (AAAS) and other societies. These societies have no special expertise in epistemology/philosophy or religion yet they openly proclaim that science and religion are compatible. They should be neutral on that question. A (slight) majority of Sandwalk readers agree, according to a poll I took a few years ago [What Should Scientific Organizations Say about Religion?].
I wasn't alone in adopting this position. Jerry Coyne and PZ Myers also think that scientific societies should keep their nose out of areas that are outside of their mandate. We are united when it comes to opposing accommodationism.
Here's the video of last week's debate at the Cambridge Union debating society. The main event pitted Richard Dawkins against Rowan Williams, former Archbishop of Canterbury. The motion was that "This House Believes Religion Has No Place In The 21st Century." At the end of the debate a majority decided that religions does, indeed, have a place in the 21st century.
Jonathan Wells has just been named to the Encyclopedia of American Loons: #409: Jonathan Wells. He joins another Discovery Institute Fellow, #411 John West.
Appallingly inane crackpot, infuriatingly dense, and reprehensibly dishonest, Wells’s lack of insight and inability to even pretend to begin to understand anything before he starts criticizing it based on personal dislike, is of almost epic proportions. Yet he continues to be shockingly influential.
Less than ideally honest chucklehead, and a prime case of every strand of cognitive bias channeled into a single-minded force of rage against reality. West should not be underestimated, however, as he has made serious contribution to undermining science and education.
I received this email message today from Leslie Maloy, (lmaloy@hastingsgroup.com). It's stupid. It's an example of scientific illiteracy. There's no chance than food from genetically modified crops will do you any harm. You may want to oppose GMO crops for other reasons but to pretend that GMO crops will endanger your health is a lie.
It's stuff like this that's giving the environmental movement a bad reputation. Their anti-science positions are losing them support from the scientific community.
National Coalition Calls on Hershey and Mars to Label GMOs in Chocolates, Other Candy . Or Get Them Out Completely.
Washington DC -- February 7, 2013 -- What will you get your loved one this Valentine's Day? If genetically modified organisms (GMOs) in chocolates are not on your shopping list, you will want to know about GMO Inside's new push to get the nation's largest candy manufacturers-Hershey and Mars-to break up with GMOs in 2013.
GMO Inside, a campaign dedicated to advancing the right of consumers to know whether or not foods are genetically engineered, is calling on Hershey and Mars to either stop putting GMOs in Valentines candy and other products . or to start labeling the products as containing GMOs.
Hershey and Mars combined comprise nearly 70 percent of the U.S. chocolate market. The two companies are not shy about their love affair with GMOs; together they spent more than a million dollars to oppose GMO labeling in California in the November 2012 election. Hershey is reported to have spent $518,900 to defeat Prop 37 and Mars spent $498,350.
The reason these companies oppose GMO labeling so strongly is due to the fact that GMO ingredients are in their sweets; a label would surely make a consumer think twice about eating their favorite candy bar.
For example, these popular candies contain the following GMO-risk ingredients:
* Reese's Peanut Butter filled Hearts (Hershey) contain sugar, soy lecithin, and cornstarch
* Hershey Hugs contain sugar, soy lecithin and corn syrup solids
* Valentine's Colored M&M's (Mars) contain sugar, soy lecithin, cornstarch, and corn syrup
* Valentine's Snickers (Mars) contain soy lecithin, corn syrup, sugar, and partially hydrogenated soybean oil
GMO Inside also released a "Valentine's Day Villains" shopping guide for consumers who want to avoid GMOs treats for their Valentines. Go to www.GMOinside.org to get a list of candies to watch out for and also some non-GMO alternatives for your loved one
Genetically modified organisms have never been proven safe for consumption, and a growing body of studies is raising concerns around the health effects of eating them. GMOs are also increasing the use of toxic herbicides and causing harm to farmers in the US and abroad.
In Europe, where genetically modified ingredients are already required to be labeled, Hershey and Mars have adapted their recipes to formulate Kisses and M&Ms without GMOs. According to Confectionery News, Hershey products made for distribution in Europe will be formulated without GMO ingredients, in order to meet the requirements of major retailers which ban the sale of products with genetically modified ingredients and to satisfy increasing consumer concern about the safety of GMOs.
"Unless you can buy Hershey or Mars products in Europe, there is a high chance you could be giving your Valentine a treat with GMOs that endanger their health and the environment," said GMO Inside Campaign Director Elizabeth O'Connell, "To be safe, you should choose organic certified or Non-GMO Project Verified chocolate to show the loved ones in your life you really care."
Beyond the issue of GMOs, Hershey also has problems with child labor in the cocoa it sources. Though the company committed to certify its supply chain as 100 percent sustainable in October of 2012, there has been no further information about how the company plans to deliver on its promise to remove forced child labor from its supply chain over the next seven years.
"Consumers have a choice -- there is delicious chocolate from companies that are organic or verified through the Non-GMO Project, said Alisa Gravitz, president of Green America. "And you can make it doubly sweet by also looking for fair trade options. You'll be showing your sweetheart you care in every way. Refuse to buy GMO-laden chocolate this Valentine's Day."
Climate change has been very good to Toronto because the increase in temperature during the winter is just enough to avoid snow. In the past decade we've had several winters where I hardly ever had to shovel.
That's all about to change. Tomorrow we're going to get hit with a big storm that's supposed to dump about 25 cm of snow. It's another one of those situations where bad things come from our neighbor to the south.
The city can cope—this is, after all, Canada—but it's probably not going to be a pleasant day. I'm planning to declare a personal snow day and stay home.
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.
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 ...
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?
The Department of Ecology & Evolutionary Biology and the Royal Ontario Museum present the Annual Darwin Lecture: Darwin, Lizards, and Evolutionary Biology in the 21st Century. The speaker is Jonathan Losos and the lecture takes place tomorrow, Thursday, February 7, 2013 in the Earth Science Centre Auditorium, Room 1050, at 8pm.
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.
This is just a little blog. It's taken me more than six years to reach five million pageviews. The big guns get that many every month.
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.
I've been getting Chinese food (Canadian style) at the Golden Palace restaurant for over fifty years. The restaurant is on Carling Avenue in Ottawa (Ontario, Canada) in the neighborhood where I grew up.
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!
Andrew MacRae used to be very active on talk.origins. At the time he was studying Burgess Shale fossils and his expertise was much appreciated. He earned the nickname "Saint" Andrew because he was kind to, and patient with, most creationists. Many of us weren't.
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.
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.
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.
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."
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.
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.
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]
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.
-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.
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)
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?
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 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
What can you do? Here's some of the things you can do. I've already written to Linda Eagan.
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.
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.
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.
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.
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 ....
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.
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.
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.
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.
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.
Last night the Liberal Party of Ontario selected a new leader, Kathleen Wynne. Since it's the governing party, she automatically becomes the Premier of Ontario.¹ I was hoping she would be chosen but in the last few weeks it looked like her opponent, Sandra Pupatello, was going to win.
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.
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?
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.
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 about slaving 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.
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.
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.
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.
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.
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.
