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.
We had a fun meeting last night thanks to Rufina Kim [WTF Is Science?]. A bunch of students showed up along with Steve Livingston, the new co-Chair of CASS (Committee for the Advancement of Scientific Skepticism), and David Bailly, Chair of The Association for Science and Reason (Skeptics Canada).
Unfortunately we were not able to come to an agreement on "What Is Science."
Now we have to meet again in a couple of weeks!
We talked about whether there was a scientific method and whether falsifiability is part of the definition of science. The Wikipedia article on falsifiability is a good place to look for background information. Here are two sections from that article to get you started.
Paul Feyerabend examined the history of science with a more critical eye, and ultimately rejected any prescriptive methodology at all. He rejected Lakatos' argument for ad hoc hypothesis, arguing that science would not have progressed without making use of any and all available methods to support new theories. He rejected any reliance on a scientific method, along with any special authority for science that might derive from such a method. Rather, he claimed that if one is keen to have a universally valid methodological rule, epistemological anarchism or anything goes would be the only candidate. For Feyerabend, any special status that science might have derives from the social and physical value of the results of science rather than its method.
...
In their book Fashionable Nonsense (published in the UK as Intellectual Impostures) the physicists Alan Sokal and Jean Bricmont criticized falsifiability on the grounds that it does not accurately describe the way science really works. They argue that theories are used because of their successes, not because of the failures of other theories. Their discussion of Popper, falsifiability and the philosophy of science comes in a chapter entitled "Intermezzo," which contains an attempt to make clear their own views of what constitutes truth, in contrast with the extreme epistemological relativism of postmodernism.
Sokal and Bricmont write, "When a theory successfully withstands an attempt at falsification, a scientist will, quite naturally, consider the theory to be partially confirmed and will accord it a greater likelihood or a higher subjective probability. ... But Popper will have none of this: throughout his life he was a stubborn opponent of any idea of 'confirmation' of a theory, or even of its 'probability'. ... [but] the history of science teaches us that scientific theories come to be accepted above all because of their successes." (Sokal and Bricmont 1997, 62f)
They further argue that falsifiability cannot distinguish between astrology and astronomy, as both make technical predictions that are sometimes incorrect.
There's no such thing as a universal scientific method and falsifiability doesn't describe how the scientific way of knowing actually works.
I made up an example of a Professor of English whose research focuses on how the English language actually sounded in the time of Geoffrey Chaucer (about 1370)¹. Is she doing science? If not, what kind of way of knowing is she using?
1. This is roughly the time of World Without End. If the characters actually spoke in 14th century dialect we probably wouldn't have understood a word.
Think about that. In the early days of developmental biology, we didn’t even know whether there was differential gene activity or not; it was considered a reasonable possibility that all the genes were just doing their work, whatever it was, all the time in every cell, and that differences between cells emerged farther downstream, in biochemical interactions. But they knew this was an important question. They knew that we had to look at the activity of individual genes…they just didn’t have the tools yet. So it was back to hacking up embryos and trying to infer causes from aberrations.
The change emerged gradually, but there were a couple of watershed moments where everyone looked up and noticed that hey, we do have ways of looking at genes directly. One was the work of Ed Lewis, a most excellent geneticist who used the tools of genetics to look directly at mutations that caused changes in fly morphology, in the 1960s. This was amazing stuff — the papers he wrote were beautiful and complex and very, very genetical — but it was written in a language that most developmental biologists of the day were unprepared to read. They were genetics papers. But I think they laid a foundation: if you want to do development, you’d better learn about genetics.
The second big event was the saturation mutagenesis screen of Christiane Nusslein-Volhard and Eric Wieschaus, about 20 years later. This work was also built on an understanding of genetics, but also used the tools of molecular biology. It was another lesson: if you want to do development, you’d better learn about molecular biology.
I used to teach this stuff in the 1980s and I certainly agree with PZ that you need to understand molecular biology and gene expression.
When it came time to write my first textbook I incorporated the examples I had used in class. The first ones I described were: the early to late switch in gene expression in bacteriophage T4, sporulation in Bacillus subtilis, and the genetic switch in bacteriophage lambda. These were well-studied examples from experiments carried out in the 1970s. They teach fundamental concepts in developmental biology and they have an additional advantage; namely, they get students thinking about species that aren't animals.
These are still excellent examples that are well-understood at the molecular level. They are much easier to understand than Drosophila or plants. Unfortunately, we've educated an entire generation of developmental biologists who have never heard of these elegant examples.
Is this a good thing or a bad thing? Do students need to know the real history of developmental gene expression as worked out by scientists who studied phage and bacteria?
Here's a short paragraph containing three sentences from my textbook (page 584). Is there anything wrong with any of these sentences?
Under physiological conditions, double-stranded DNA is thermodynamically much more stable than the separated strands and that explains why the double-stranded form predominates in vivo. However, the structure of localized regions of the double helix can sometimes be disrupted by unwinding. Such disruption occurs during DNA replication, repair, recombination, and transcription.
Having trouble seeing where I went wrong, according to some people? Check out this and this.
Everyone knows about TED talks (Ideas Worth Spreading). They know that TED talks are "riveting talks by remarkable people." Or at least that's what they would like to believe [TED Tries to Clean Up Its Act].
Here's some worthy competition to TED talks from The Onion. It's title is Using Social Media To Cover For Lack Of Original Thought.
