Friday, December 6, 2013

Valley girl talk

Last summer we took a short drive through the San Fernando Valley on our way from Thousand Oaks to Griffith Park. I happened to mention "valley talk" ("uptalk") but none of us could do a good job of talking like a teenage girl from the valley.

That's a shame because now it looks like Valley girl speak is, like, on the rise! I believe it. Not only have I heard girls speak like this on the university campus here in Toronto but I've even heard this language in Ottawa and that's about as far away from California as you can get.

I hope my granddaughter and grandson don't grow up speaking like this. They live in Los Angeles.


Moon Unit Zappa Valley Girl by mrjyn


Have you ever seen the Grand Canyon? Did it make you believe in god?

Last year we took a helicopter ride to the Grand Canyon [The Magic Canyon Ride ]. None of us converted to Christianity or any other religion.

We may be the exception. According to Time magazine, "It’s hard to be an atheist when you’re looking at the Grand Canyon."

See what Friendly Atheist has to say about this: Time Magazine Says ‘There Are No Atheists at the Grand Canyon,’ Claims that ‘Awe Equals Religion’.

My son and daughter-in-law took a mule ride down into the Grand Canyon. I don't think they were converted either.

Are there any former atheists out there who were converted by the Grand Canyon? Which god(s) did you choose?


Die, selfish gene, die!

"Die, selfish gene, die!" is the provocative title of an article by science writer David Dobbs [Die, selfish gene die!].

Dobbs begins with ....
The selfish gene is one of the most successful science metaphors ever invented. Unfortunately, it’s wrong.
The article attracted the attention of Jerry Coyne who effectively dismantles the strange ideas promoted by Dobbs. Read all about it at: David Dobbs mucks up evolution, part I and David Dobbs mucks up evolution, part II.

As it turns out, this is just another example of a science writer who has been mesmerized by the latest effort to overthrow modern evolutionary theory by some scientist promoting their own work. In this case it's Mary Jane West-Eberhard.

But there's a more serious issue here and I'm not sure that Jerry Coyne recognizes it. The selfish gene metaphor can be interpreted in several different ways. Here's how Richard Dawkins describes it in the preface to the 1989 edition of The Selfish Gene.
The selfish gene theory is Darwin's theory, expressed in a way that Darwin did not choose but whose aptness, I should like to think, he would instantly have recognized and delighted in. It is in fact a logical outgrowth of orthodox neo-Darwinism, but expressed as a novel image. Rather than focus on the individual organism, it takes a gene's-eye view of nature.
Lot's of people misunderstand the selfish gene metaphor. They think it means that organisms behave selfishly but that's not what Dawkins meant at all.

Jerry Coyne explains this in his book Why Evolution Is True (p. 226) ....
As Dawkins shows clearly, the "selfish" gene is a metaphor for how natural selection works. Genes act as if they're selfish molecules: those that produce better adaptations act as if they're elbowing out other genes in the battle for future existence. And, to be sure, selfish genes can produce selfish behaviors. But there is also a huge scientific literature on how evolution can favor genes that lead to cooperation, altruism, and even morality.
There are two main criticisms of the selfish gene metaphor and both of them are quite valid. It's the reason why Dawkin's view hasn't caught on the the evolutionary biology textbooks. It usually merits nothing more than a footnote.

The most damning criticism comes from evolutionary biologists who point out that the primary unit of selection is the individual and not the gene. Stephen Jay Gould and Richard Lewontin are prominent opponents of what they see as an unnecessary reductionism in Dawkins' writing. Clearly, hierarchical theory (Gould) is inconsistent with the selfish gene metaphor because evolution can also operate at the level of groups and species (according to Gould and others). There are plenty of other evolutionary biologists who object to selfish genes for these reasons.

The second objection comes from the focus on natural selection and "Darwinism" (or neo-Darwinism). Many evolutionary biologists have a pluralistic view of modern evolutionary theory. That view includes random genetic drift where the appropriate metaphor might be "lucky gene" or "accidental gene." The problem with the Dawkins' metaphor, according to these critiques, is not that "selfish genes" don't exist, it's that the metaphor is not appropriate for evolution in general.

While I admire Jerry's take-down of Dobbs, I'm not sure that he (Jerry Coyne) fully appreciates these other criticisms of the selfish gene. Here's what Coyne wrote ...
Let me add one thing, though. I’m constantly puzzled these days by how often people argue that the neo-Darwinian synthesis is wrong, and that we need a new paradigm. Genetic assimilation, epigenetics, horizontal gene transfer—all of these buzzwords are evoked as reasons to jettison our “conventional” view of evolution. But always, when you look at the data, the evidence that these phenomena will overturn neo-Darwinism is nonexistent.

I’ve already written a lot on the epigenetics hype, and have shown that there’s no evidence that a single adaptation in nature involves the fixation in the DNA of an epigenetic alteration of the genome that isn’t initially inherited. Yet people keep banging on about epigenetics.

I’m not sure why the hype continues, but perhaps it has to do with the fact that the main paradigm of evolution—the neo-Darwinian synthesis—is largely consolidated, and is correct. Sure, there are surprises to come, and interesting new phenomena, but there’s no “quantum mechanics” of evolution on the horizon. Some theories don’t need to be overthrown because they’re generally right. Perhaps people don’t like working in a field where there’s no new “paradigm” to forge, and Kuhn has ruined us all!

The "neo-Darwinism is dead" trend may have to do with ambition, or perhaps with boredom. I don’t know. What I do know is that the many recent challenges to neo-Darwinism have all failed to hold water, but people keep pouring liquid into that sieve.
The problem here is that Jerry doesn't really say what he means by "neo-Darwinism." Most of his writing suggests that he's talking about natural selection, albeit updated by a knowledge of genetics. He does mention, from time to time, random genetic drift and other aspects of modern evolutionary theory but I'm not sure if he appreciates the fact that some legitimate evolutionary biologists really do think that neo-Darwinism is dead.

Here's the Wikipedia description of neo-Darwinism. It illustrates the problem.
Neo-Darwinism is the 'modern synthesis' of Darwinian evolution through natural selection with Mendelian genetics, the latter being a set of primary tenets specifying that evolution involves the transmission of characteristics from parent to child through the mechanism of genetic transfer, rather than the 'blending process' of pre-Mendelian evolutionary science. Neo-Darwinism can also designate Darwin's ideas of natural selection separated from his hypothesis of Pangenesis as a Lamarckian source of variation involving blending inheritance.
I think we should refer to modern evolutionary theory as "modern evolutionary theory" in order to make sure we're not talking about "Darwinism," "neo-Darwinism," or the hardened version of the "Modern Synthesis." Modern evolutionary theory includes an important role for random genetic drift, Neutral Theory, and population genetics.

We could clarify a lot of discussion if we stopped talking about extending "Darwinism" or extending the Modern Synthesis or proclaiming once again that the selfish gene has died. In fact, the selfish gene has died, it died almost thirty years ago but most people don't know that. RIP.


Do you understand this Nature paper on transcription factor binding in different mouse strains?

I've published a few papers on the regulation of transcription of a mouse gene and students in my lab have done the standard promoter-bashing experiment to define transcription factor binding sites. I did ny Ph.D. in a lab that specialized in DNA binding proteins. I've kept up with the basic ideas in eukaryotic gene expression in order to teach undergraduate courses on that topic and in order to write appropriate information in my textbook.

I've been interested in genome organization for several decades and I've been following the literature on pervasive transcription and transcription factor binding in whole genome studies. I'm reasonably familiar with the techniques although I've never done them myself.

I'm not bragging; I'm just saying that I know a little bit about this stuff so when I saw this paper in one of the latest issues of Nature I decided to look more carefully.
Heinz, S., Romanoski, C., Benner, C., Allison, K., Kaikkonen, M., Orozco, L. and Glass, C. (2013) Effect of natural genetic variation on enhancer selection and function. Nature 503:487-492. [doi: 10.1038/nature12615]
Read more »

Wednesday, December 4, 2013

Jason Rosenhouse defends Chris Mooney

Jason Rosenhouse read Chris Mooney's article on 7 Reasons Why It's Easier for Humans to Believe in God Than Evolution and liked it. Mooney was arguing that it's easier to believe in god(s) than in evolution because our evolutionary history selected for traits that predisposed us to think more like IDiots than like scientists.

I disagreed [Why don't people accept evolution? ]. Here's what I wrote last week ....
Read more »

Cherry picking and the safety of low level electromagnetic radiation

While I was researching the previous article on the safety of GM foods, I came across the website of Magda Havas. Here's how she describes herself ...
Magda Havas is Associate Professor of Environmental & Resource Studies at Trent University where she teaches and does research on the biological effects of environmental contaminants. Dr. Havas received her Ph.D. from the University of Toronto, completed Post-Doctoral research at Cornell University, and taught at the University of Toronto before going to Trent University in Peterborough, Canada.

...

Dr. Havas’s research since the 1990s is concerned with the biological effects of electromagnetic pollution including radio frequency radiation, electromagnetic fields, dirty electricity, and ground current. She works with diabetics as well as with individuals who have multiple sclerosis, tinnitus, chronic fatigue, fibromyalgia and those who are electrically hypersensitive. She also conducts research on sick building syndrome as it relates to power quality in schools.

Since the mid 1990s Dr. Havas has taught about electromagnetic pollution in several courses at Trent University and has supervised Reading Courses and Honours Thesis Projects in this area. One of the courses deals specifically with the biological effects of electromagnetic fields and electromagnetic radiation. This is one of the few courses available in North America at a senior undergraduate level critically examining the effects of non-ionizing radiation.
Here comes the fun part. She has made a video in which she explains why we need to pay attention to all the scientific studies showing harmful effects of power lines, cell phones, WiFi etc. She uses Popper's criterion of falsifiability to justify her rejection of all articles that show no harmful effect and she turns cherry-picking completely upside down to support .... cherry-picking!

Don't you just love the title of this video?


In case you don't get it, here's a bit of extra reading.
Magda Havas’ New EHS Study Has Serious Flaws
Trust Me, I’m A Doctor: Magda Havas And WiFi


Is there any reliable scientific evidence that genetically modified food poses a health risk?

I recently had a discussion about the safety of food derived from genetically modified organisms. My opponent, whose identity I will conceal (hi Rachel!), argued that GM foods are unsafe and that there's scientific evidence to back this up. Naturally, this evidence is being concealed by Monsanto and other private companies in the same way that tobacco companies tried to hide the evidence that smoking causes lung cancer.

My position is that I'm not aware of any reliable scientific studies showing that GM foods are dangerous to your health and, furthermore, in a free and open democracy with a free press it seems highly unlikely that such evidence is being suppressed. It seems even more unlikely that scientists would be part of this conspiracy.

Read more »