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.
