Friday, September 30, 2011

Evolutionary Psychology Crap in New Scientist

 
Here are the opening paragraphs of an article published in the most recent issue of New Scientist [Domestic violence gets evolutionary explanation].
What can evolution tell us about domestic violence? Two researchers in the US suggest such violence has ancient origins and that establishing evolution's role could help to better identify those at risk. Others argue that the research makes simplistic assumptions, and warn that some people will interpret the research as an excuse for violence.

Each year more than 500,000 women in the US alone report to the police violent attacks by current or former male partners. There is a reason why domestic violence is so widespread, says David Buss, an evolutionary biologist at the University of Texas in Austin: it carries a selective advantage, tied with reproductive success. In other words, men who are violent are trying to make sure that their partner has his child and not another man's.
Let's think about this for a minute.

In order for violence against women to have a selective advantage there has to be an important genetic component. Let's imagine a time back in hunter-gather days when there were two groups of men who differed in their violence-against-women alleles. One group was kind and considerate toward their female companions. They treated them with respect. The other group treated women as property and often beat them in order to prevent imagined infidelity. Somehow the violent group managed to mate more frequently and/or have more children than the kind group so the allele for kindness and respect was eliminated from the population.

Lots of things had to happen in order for this scenario to play out as the evolutionary psychologists imagine. For example, women had to prefer to have children with men who would beat them. (Or maybe they were forced to mate with the violent men.). Furthermore, there had to be no consequences for the men who beat their mates. The other members of the group had to tolerate that behavior even if they found it repulsive.

If the scenario is correct then most men—including you and I—have to carry the violence-against-women allele since it was selected in the past. This seems very strange since most men don't beat their wives.1 I guess we have learned to suppress the genetic urge. But why would we do that if it's a selective advantage to engage in domestic violence?

There's something seriously wrong with evolutionary psychology. And there's something seriously wrong with respectable science magazines who promote this crap.

There's also something seriously wrong with men who engage in domestic violence. They are assholes who deserve very little sympathy from the rest of society. I suspect they got no sympathy in ancient hunter-gather societies either. There is no gene that makes you act like an asshole. That's all due to nurture and it can be changed if we put our minds to it.


1. At least I think this is true. When was the last time you beat your wife or girlfriend?

Young Earth Creationism in the 21st Century

 

We discussed Young Earth Creationism in our last class. As most of you know, the Young Earth Creationist believes that the universe was created about 10,000 years ago and that all modern species (or kinds) were created simultaneously at that time. This view is compatible with the Genesis story in the Bible.

How is it possible for someone in the 21st century to ignore all the scientific evidence supporting an Earth that has been around for 4.5 billions years and an universe that is even older? We tried to come up with the most common ways that Young Earth Creationists can rationalize the obvious conflict.

The most obvious explanation is that they are completely unaware of the massive amount of scientific evidence that conflicts with their belief. In other words, they simply don't see a conflict between science and their religion because they have never been taught proper science. I suspect this is true of the vast majority of Young Earth Creationists.

But there's a subset of them who know the science. They have to come up with some sort of explanation that makes their position compatible with the findings of science. We identified two sorts of explanation that seem to apply.

1. Reject the scientific evidence as unreliable and try to discredit scientists. This path gives rise to talking points about the errors in carbon-14 dating and the fact that atheist scientists are blinded by their "religion."

2. Rely on faith and revelation as superior paths to knowledge. This means that the scientific "evidence" must be wrong even though the flaws aren't obvious. It must be wrong because it conflicts with God's word and there's no more reliable indicator of truth than the word of God.

(Sometimes the superiority of faith leads to the conclusion that God must have deliberately created an Earth with the illusion of age. It's not clear why God did this but we are not in a position to question God's wisdom in this matter.)

The BioLogos Foundation has, until recently, promoted theistic evolution. This worldview tends to accept scientific evidence as much as possible. Theistic Evolutionists, for example, are perfectly happy with a 4.5 billion year old Earth.

This emphasis on Theistic Evolution seems to be changing as Jerry Coyne points out in a recent article on his blog website: Templeton-Funded BioLogos cleans house, promotes young-earth creationist, begins slide into irrelevance. BioLogos now has a video promoting a Young Earth Creationist named Aaron Daly [A Young Earth Creationist Perspective].

Watch the video and see if you can figure out how a seemingly rational person can believe in something that is totally discredited by science.


Wednesday, September 28, 2011

John Hawks on the Sandwalk

 
I post pictures of anyone on the Sandwalk. Technically speaking, John Hawks isn't exactly "on" the Sandwalk but I assume he went for a stroll shortly after this picture was taken.


Larry Moran
PZ Myers
John Wilkins
Ryan Gregory
The God Delusion
Cody


Is WiFi Harmful to Children?

 
There are many things that are harmful to children—poverty and war come to mind. There's also superstition and ignorance.

Believe it or not, there are many parents who think that electromagnetic radiation from WiFi transmitters is harming their children. They want it removed from schools because their children are becoming sick when they are at school.

Steve Thoms at Skeptic North has a post on this issue [Why, Wifi? Why?]. He explains why some people believe stupid things and how they go about defending those beliefs in a scientific society. He also raises questions about the "evidence" of illness caused by WiFi.

Worth reading—especially for the students in my course.


Tuesday, September 27, 2011

Should Creationism Be Banned?

 
A bunch of British scholars have issued a Joint statement on creationism and evolution in schools. The list of signatories include all the usual suspects: Richard Dawkins, David Attenborough, Steve Jones, Michael Reiss, Steven Rose, John Sulston, Lewis Wolpert, etc.
Creationism and "intelligent design" are not scientific theories, but they are portrayed as scientific theories by some religious fundamentalists who attempt to have their views promoted in publicly-funded schools. There should be enforceable statutory guidance that they may not be presented as scientific theories in any publicly-funded school of whatever type.

But this is not enough. An understanding of evolution is central to understanding all aspects of biology. The teaching of evolution should be included at both primary and secondary levels in the National Curriculum and in all schools.
Nobody can argue with the second part of the statement; of course evolution should be taught.

I want to challenge the first part of the statement. Should the British government pass a law banning the teaching of creationism and/or Intelligent Design Creationism as science?

The first thing that troubles me is the idea of a legal ban on teaching anything at all. I don't think this is a good idea even for ridiculous ideas such as homeopathy or astrology. Do we really want lawyers and legislators making decisions about what should be taught as science and what shouldn't? Neither of those groups are competent to make such decisions.

Besides, enforcing a legal prohibition against teaching Intelligent Design Creationism as science only plays into the hands of the creationists. What are we afraid of? Are we worried that the creationist challenge is so strong that science may not be able to withstand the assault without protection from the courts?

There's another issue that's even more troubling. We could read between the lines of the joint statement and come up with the following logic ...
We the undersigned have adopted a particular version of what science is and we have adopted a particular definition of intelligent design. We agree on a particular (unstated) definition of "scientific theory." According to these views and definitions, intelligent design is not science and should not be taught as science in our schools.
Problem is, there are many different definitions of science and why should we believe this group of signatories over another? There are also many different ways of defining intelligent design and some of the definitions fit my view of what science is. It may be horrible science but it can't just be dismissed as non-science.

On this blog we often discuss books by Intelligent Design Creationists. Most of what's in The Myth of Junk DNA or The Edge of Evolution, for example, is pure science by any definition. It turns out to be bad science—or a very misleading version of science—but on the surface it seems to apply rational thought, evidence, and skepticism to the problem of evolution.

I'm very uncomfortable with the idea that those books should be banned from science classes.

There's another reason why banning bad science is wrong. Study after study has shown that in order to correct student misconceptions you need to address those misconceptions directly. For example, if a student comes into a classroom thinking that creationism is correct, they will not be swayed by simply presenting the evidence for evolution. That's necessary but not sufficient. You also have to show them why their creationist views are wrong and that means bringing up those incorrect views in science class.

Take irreducible complexity as an example. If students think that irreducible complexity refutes evolution then you aren't ever going to change their minds by ignoring irreducible complexity in class. What you have to do is explain the concept and demonstrate why it's bad science (or non-science if you prefer). You can't do this if you are legally prohibited from mentioning intelligent design in a science class.

We need to teach students what science is and what science isn't. The appropriate place to do this is in science class. You can't teach this concept without giving some examples of non-science or pseudoscience and that's a good thing because it directly addresses any misconceptions students might have.

Similarly, if Intelligent Design Creationism is mostly bad science (instead of non-science) then the best way to teach the difference between good science and bad science is to use examples and Intelligent Design Creationism is an excellent example because so many students think it's good science. Banning it from the science classroom is just bad pedagogy.

It's also counter-productive. By protecting it from direct critical analysis in a science class you are actually giving a free pass to the anti-science forces outside the classroom.


Monday, September 26, 2011

The Protein Engineer

 
Two former undergraduate students of mine have started a blog called The Protein Engineer.
A blog started by two graduate students, 11000 kilometres apart, on a quest to discover, or otherwise invent, the holy grail of bioengineering: rational protein design.

Our blog consists of weekly reviews of important papers within the cutting edge field that is an amalgam of theoretical and experimental biology, fused with a heavy dose of computational engineering. At the same time, our posts are accessible to even the keen undergraduate in science or engineering.

In nature, new proteins are created by means of mutations and recombination in the DNA, a process that can take thousands of years, and only then, whose purpose serves only strengthen the fitness of the host organism, a purpose often ill-suited for industry or medicine. Protein engineering aspires to create new proteins within a year or less, using powerful computational and experimental techniques such as simulation and directed evolution to create custom-tailored proteins designed especially for industry or medicine.

But more importantly, we hope to fascinate our readers with the immense possibilities of protein engineering. So that perhaps one day, you too, will become a proteneer.


Thursday, September 22, 2011

Countries That Execute Their Own Citizens

 
Most civilized, democratic countries have abolished capital punishment. This is especially true of those countries with a Christian tradition.

The last execution in Canada took place in 1962 and the last one in Mexico was in 1961. Here's a short list of other countries with the last year of execution: Australia (1967), Israel (1962), Brazil (1876), Argentina (1916), United Kingdom (1964), France (1977), and Italy (1947).

[Blue: capital punishment abolished for all crimes; Green: abolished for all crimes expect some committed in exceptional circumstances; Brown: abolished in practice; Red: legal form of punishment]

The United States differs from its geographical and cultural neighbors. Why does the United States still carry out executions in 2011 when the practice has ceased in all those countries with a similar cultural and religious background?


Saturday, September 17, 2011

When Will They Ever Learn?

 
In my class on Scientific Misconceptions and Controversies we discuss the ways in which scientific reasoning is used and misused in debates and discussions.

As a general rule, you can divide scientific debates into two main categories: (1) genuine scientific controversy that hasn't been resolved, or (2) misconceptions or misunderstandings of the science by one or more of the sides. The third category is genuine fraud.

Sometimes it's really hard to decide when a misconception turns into lying (fraud). This is particularly true in the evolution/creation debate where some of the most outlandish claims by the creationists have been refuted again and again but continue to be used. Are those creationists so stupid that they just don't understand why they are wrong or is it more likely that they know they are wrong but are just taking advantage of the ignorance of their audience to promote a good-sounding talking point?

Here's an example from Denyse O'Leary, one of the leading IDiots based right here in Toronto [Darwin lobby: We have the bumper sticker. We win.].
In August we noted that National Center for Science Education was running a bumper sticker contest

They may have declared their winner. Folk have been seeing this bumper sticker around town:

We have the fossils. We win.

That would be good news for Darwin, who didn’t think the fossil record supported him, but hoped it would, one day.

The trouble is, that has been the trade secret of paleontology (Stephen Jay Gould) that it doesn’t support him. It supports sudden, rapid emergence, which almost certainly means a non-Darwinian origin for change in life forms.
The issue is whether the fossil record, taken as a whole, supports the transformation of one type of organism into another. The answer is overwhelmingly "yes." There are dozens of excellent examples including our own species.

These examples have been described in detail in an attempt to educate the creationists but all this to no avail. They continue to repeat the myth that the fossil record does not support evolution in spite of the enormous efforts made by evolution supporters to correct their ignorance.

At some point we need to stop attributing this behavior to mere stupidity and ignorance and start recognizing it for what it is—a lie. Denyse knows the truth but continues to repeat a false claim.


Lab Times Screws Up the Discussion of Junk DNA

 
Lab Times is a magazine that reports on news for life scientists in Europe. Their current issue (Sept. 14, 2011) has an "analysis" called Past, present and future Everything you ever wanted to know about the non-coding stretches of DNA. The author is Frederick Gruber who appears to be a science writer drawing on information supplied by various researchers.

You know the article is going to be misleading as soon as you read the opening paragraph.
When the first draft of the human genome finally became available, there were many surprises, one of them being the ridiculously large amount of DNA that did not code for proteins – or anything at all. It seemed like the genome was just a huge chaotic mess sprinkled with tiny nuggets!
The reason this is misleading is because it totally misrepresents the history of the human genome. It's been four decades since we first became aware of the fact that only 1-2% of the human genome encoded proteins. This was hardly a surprise—in fact it was one of the principle arguments against sequencing the human genome. (What was the point of wasting all that money on DNA sequences that were mostly junk?)

One of the unfortunate characteristics of the junk DNA deniers is that they are completely unaware of the historical arguments in favor of junk DNA (e.g. False History and the Number of Genes, Genetic Load, Neutral Theory, and Junk DNA). Everyone who understood the problem was quite happy to find verification when the first draft of the human genome was published. It's exactly what the knowledgeable experts predicted.

The article raises the standard question that seems to have only recently occurred to some researchers; namely, what is all that DNA doing? It's mostly junk—at least that's the conclusion reached by many scientists back in the 1970s and most of what we've discovered since then has supported that view.

Friday, September 16, 2011

Transposon Insertions in the Human Genome

Transposons are mobile genetic elements that jump around in our genome (and the genomes of every species). They are known by various names such as "jumping genes" or mobile genetic elements.

Our genome has several different types of transposons [Transposons: Part I, Transposons: Part II, Retrotransposons/Endogenous Retroviruses]. Most of them are defective in one way or another so they can no longer "jump" to another location but some subfamilies have remained functional and these will spread to new locations. About 44% of our genome consists of active transposons and (mostly) defective transposons [What's in Your Genome?]. Most of these sequences have no function—they are junk DNA.

The development of new, cheap, sequencing technologies and the availability of an annotated standard human genome reference sequence has made it possible to look for new transposon insertions in a large number of individuals. The results can help confirm or refute the idea that most of our genome is junk.

A recently published article in PLoS Genetics describes the results of such an analysis (Stewart et al. 2011). It's part of the 1000 Genomes Project.

They detected a total of 7,310 insertions that were present in only a subset of the 179 genomes that were analyzed. About 85% of these were Alu elements, 12% were L1 LINES, and 3% were SVA's. This is consistent with earlier work that catalogued the number of active transposons in the human genome. As expected, very few of these insertions occurred in exons (39) and only 3 occurred in coding regions. This strongly suggests that there is strong selection against disruptions of coding regions. It implies that most of the detectable insertions occur in regions where disruption of the sequence has no effect on the viability of the the individual. In other words, insertions occur predominantly in junk DNA.

The authors examined the sequences of two families in order to assess the frequency of new transposon insertions. Earlier data indicated that a new insertion arises only once in every twenty births so it's not a surprise to find that the offspring in these two families showed no new insertions relative to their parents.

A data set of this size allows for an assessment of the rate of fixation of various new mobile element insertion (MEI) alleles in the population. The authors conclude,
MEI alleles propagate within population groups much like other predominantly neutral polymorphisms. MEI allele frequency spectra from the low coverage samples are in general agreement with expectations from the standard neutral model for allele drift in a population.
What this means is that most (perhaps all) of the insertion alleles are segregating as though they have no effect on the fitness of the individuals that carry them. This is further support for the idea that large parts of the genome are junk.


Stewart, C., Kural, D., Strömberg, M.P., Walker, J.A., Konkel, M.K., Stütz, A.M., Urban, A.E., Grubert, F., Lam, H.Y., Lee, W.P., Busby, M., Indap, A.R., Garrison, E., Huff, C., Xing, J., Snyder, M.P., Jorde, L.B., Batzer, M.A., Korbel, J.O., Marth, G.T. (2011) A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet. 2011 Aug;7(8):e1002236. Epub 2011 Aug 18. [doi:10.1371/journal.pgen.1002236]

Steampunk Genetics

 
I recently learned a lot about steampunk by attending Polaris 25 last July. I'm thinking I should put together an outfit that I can wear around campus. I haven't seen a fashion statement that's as cool as steampunk since the 1960's.

John Hawks is obviously a fan as well. He's posted an article entitled Steampunk Genetics where he describes how predictions based on Victorian genetics are still more accurate than those based on genome sequences. The important point is that some heritable traits are still too complex to be attributed to specific alleles.


Jetcat

 


Gordon Moran (my son) and his friend Kevin Forbes are building a game (app) for mobile devices. You can follow their progress on: Omnisaurus Games.

Check out the September build. They actually have a version you can play! It even has sound.


Thursday, September 15, 2011

Christian vs Christian


The Discovery Institute is the leading proponent of Intelligent Design Creationism—a form of creationism that concentrates on proving evolution is wrong and therefore the history of life must be explained by the intervention of an intelligent designer (i.e. god).

The BioLogus Foundation was founded by Francis Collins and it brings together a group of theistic evolutionists. Theistic Evolution is a form of creationism that accepts much of evolutionary biology but still postulates the the history of life requires the intervention of a creator.

Recently a Theistic Evolution-type creationist attacked Stephen Meyer, an Intelligent Design Creationist at the Discovery Institute [On Deciphering the Signature]. You can read a brief history of what happened in a guest post on Jerry Coyne's blog website: Guest post: the conflicted relationship between Intelligent Design and BioLogos.


Friday, September 09, 2011

A New Moderation Policy: Doug Dobney Is Banned on Sandwalk

Up until now I have been proud of the fact that nobody is banned on Sandwalk. I delete all spam that consist entirely of threats and incoherent ranting (e.g. Dennis Markuze). I also delete spam that advertises products and/or commercial websites. But even the weirdest kooks are allowed to post comments as long as they don't post spam.

But there's one thing I won't tolerate and that's when people start threatening other bloggers and commenters by contacting their families or their employers. That's where I draw the line.

Doug Dobney has posted hundreds of comments on Sandwalk under "anonymous." He is apparently opposed to evolution and won't listen to reason from those who have tried to set him straight on the facts. That's fine with me. If others want to have fun with him here, then it's up to them. I've been ignoring him and so has almost everyone else.

Recently another commenter revealed that "anonymous" was, in fact, Doug Dobney, a well-known kook from Peterborough, Ontario, Canada. That made Doug very upset in spite of the fact that it was trivially easy to identify him based on his internet record where he has already admitted to his identity. (He also posts as "Socrates.")

That's fine too. What happened next is not fine. Doug Dobney sent letters to the Chair of my department and the Dean of the Faculty of Medicine complaining about me. Here's a copy of his letter.
Dear Dr. Whiteside:

I need to bring to your attention a serious problem that relates to the Department of Biochemistry.

Please see the emails below.

Not only has the problem not been addressed, but I have not even been given a response to my emails documenting this dangerous situation.

To give you some insight into this problem, here are three, of many, instances from Dr. Moran’s blog:

“Josef Gladstone said...

I don't even understand why Doug Dobney would even want to toil in anonytimity when he is doing such groundbreaking work on organism development, especially in the new field of pterosaur to bird development. He is truly one of the great minds of the 21st century.

Doug Dobney will eventually be viewed in the same light as Darwin by the time the history of organism development is written.

And of course, to quote the great Mr. Dobney, this is certainly not worth arguing about! (both his wonderful wife Angela and myself get a great chuckle out of this whenever he says it, which is quite often!)

“AND

Ddobney@moffathouse.ca said...

Hey Doug Dobney, do guests at the Moffat House know you're insane?

AND if your stomach is up to it, there is this link on the blog:

http://socratesisdougdobney.blogspot.com/

I would appreciate your attention to this serious problem.

Yours sincerely,

Douglas Dobney
That's something I will not tolerate. Doug Dobney has earned the distinction of being the very first person to be banned on Sandwalk


My Dean is a very busy person but I'm sure she enjoys a little chuckle now and then when these kook emails turn up in her mailbox. I'll have to ask her if she remembers Doug Dobney next time I see her in the line for coffee downstairs.

Conspiracy Theories

 

There are kooks everywhere. Some people believe they have been abducted by UFOs and others believe that the moon landings never happened. There are many who believe that the 9/11 tragedy was a conspiracy of the United states government.

One thing that all kooks have in common is their ability to completely detach themselves from reality. Wanna see a good example?

David Klinghoffer posts on the Intelligent Design Creationist website Evolution News & Views. His latest display of kookdom is to try and link evolutionary biology with 9/11 truthers [Darwinism and 9/11 Conspiracy Theories: The Parallels].

I hope the Discovery Institute has a full-time psychologist on their staff.
With the approaching 9/11 anniversary, Slate has been running a series tracing the rise and ongoing evolution of 9/11 Truth theories that try to show how the attacks 10 years ago were really an inside job. According to this thinking, 9/11 was no attack by Islamic terrorists. Rather, the towers were detonated by an expertly covered-up collusion among Zionists and U.S. government operatives. You might have expected these notions would, if entertained at all, be dispelled by the exhaustive debunking job that Popular Mechanics did with its 5,500-word article on the subject back in 2005. Not so, as those who take an interest in conspiracy culture know well.

What I found striking about the first installment in the Slate series, by Jeremy Stahl, is the parallels with what we know about the thought and writings of Evolution Truth activists: our ever-loving friends in the Darwin Lobby. You may recall the news of a few months back that Glenn Branch, deputy director of the Darwin-lobbying National Center for Science Education, had collaborated with 9/11 Truth conspiracist James H. Fetzer in editing a special number of the journal Synthese on "Evolution and Its Rivals." That issue of the journal became so notorious for the incivility of its contributions that a whole fracas broke out and made the pages of the New York Times.

It may have seemed just a delicious coincidence at the time to find Branch and Fetzer teaming up so comfortably. Yet consider the features of 9/11-style paranoid thinking and some similarities to its evolutionary counterpart ...


Keep the Faith—but not in Our Schools

Coalition Calls for Defunding of Catholic Boards, End to Discrimination Against Gays in Publicly Funded Schools

KEEP THE FAITH—BUT NOT IN OUR SCHOOLS

The Canadian Secular Alliance and its allies are hosting a rally in front of the Legislature at Queen's Park on Sunday, September 18 from 1:30-3:30 p.m. to demand:

• The end of the over $500 million taxpayer subsidization for the promotion of the Roman Catholic religion. Public funding for the expensive duplicate school system must be eliminated to provide one secular publicly funded school system.

• The protection of equality rights for all students—including gay students—by ending the constitutional privilege afforded Roman Catholics to overrule legislation and the courts in favour of religious dogma.

"Equality for all students means ending privileged access to public schools for favoured religious services," says CSA President Greg Oliver.

Speakers represent a cross section of the religious and non-religious.

More information: Canadian Secular Alliance




Wednesday, September 07, 2011

Carnival of Evolution #39

This month's Carnival of Evolution (39th version) is hosted by Cromercrox, a "Celebrity Nutritionist" who lives in Cromer, Norfolk, England (United Kingdom). It blogs at The End Of The Pier Show: Carnival of Evolution #39.

The main subject headings are:
  • The Books! The Books!
  • The Birds! The Birds!
  • Tempo, Mode and the Tangled Bank
  • Genes and Jumpers
  • One Species Or Two?
  • The Brain! The Brain!
Next month's Carnival of Evolution will be hosted by Kevin Zelnio on EvoEcoLab. You can submit your postings at Carnival of Evolution.


Thursday, September 01, 2011

Canadian National Vimy Memorial


We're in Brussels babysitting my granddaughter Zoë while her parents are house hunting in Los Angeles.

Yesterday we went to see the Canadian National Vimy Memorial on Vimy Ridge, the site of an important battle in April 1917. Thousands of Canadians died in the battle.

Zoë liked climbing on the steps and statues.

There are 11,000 names engraved on the memorial. They represent Canadian soldiers who died in France during World War I and whose remains were never recovered. One of the names is Lance Corporal Robert Alexander Hood (1895 - 1917), a distant cousin of Ms. Sandwalk. He died on April 12, in 1917 during the final days of the battle of Vimy Ridge.

We found his name.