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Saturday, September 21, 2013

My American Dialect

I finally got to take the quiz at Dialect Quiz & Survey. The server is often overloaded and answering the 140 questions takes more than one hour because of the slow server.

My dialect is most like that of Buffalo NY, which is hardly a surprise since it's the closest American city to Toronto. (I grew up in Ottawa but I don't have much of an Ottawa Valley accent.)


Do the IDiots Really Know What Evidence Looks Like?

I've been dealing with Intelligent Design Creationists for over twenty years. I've spent a lot of time addressing their scientific misconceptions and trying to explain where they've gone wrong. A few years ago, for example, I posted a whole series of article on Jonathan Wells' book The Myth of Junk DNA. A few weeks ago I explained why Jonathan McLatchie was wrong about pseudogenes.

Lately, I been focusing on one of the chapters in Darwin's Doubt—it's the one on molecular evolution and I know something about that subject. It has been pretty easy to show why Mayer is wrong about his conclusions.

That's why it's so frustrating to read what journalist Tom Bethell said the other day on Evolution News & Views (sic) ["What Is the World Really Like?" Darwinism, Materialism, and How They Relate].
The explicit materialism of the Darwinians is the mirror image of creationism. Creationists are easy for scientific materialists to rebut, because the materialists can say, "That is just your belief. We don't have to accept that." In a parallel way, we can say to the materialists: "That is just your belief. We don't have to accept that. And it is the real basis of your evolutionism."

In between the Creationists and the Materialists we encounter the scientific evidence that makes the materialist position increasingly improbable -- the evidence that Stephen Meyer recently presented in Darwin's Doubt: information theory, insufficiency of the fossil record, epigenetics, complexity of life at the molecular level, and so on.

Increasingly, it seems to me, the Darwinians are responding to this science by saying (in effect): "Bah! We won't read that! It's creationism in disguise." They get graduate students like Nick Matzke, or incompetents like John Farrell (in National Review of all places), to do the work for them. All along the Darwinists have found that their materialism has allowed them to lie back and relax without really bothering to study the evidence.

Now that may be changing. They are being put in a position where they just might have to hit the books. I suspect it is not a prospect that they relish.
Keep in mind that this is written by a man who denies that humans cause global warming and denies that HIV causes AIDS.

He has no idea what evidence looks like.


Why Are IDiots So Nasty?

You've probably noticed that in addition to being stupid most IDiots are not very respectful of scientists (i.e. Darwinists). William J Murray1 explains why religious people have to be mean and nasty [Can We Afford To Be Charitable To Darwinists?].
I used to be one that diligently attempted to provide Darwinists charitable interaction. I tried not to ridicule, demean, or use terms that would cause hurt or defensive feelings. My hope was that reason, politely offered, would win the day. My theistic perspective is that returning the bad behavior I received at sites like TSZ would be wrong on my part. I thought I should stick to politely producing logical and evidence-based exchanges, regardless of what Darwinists did. I note that several others here at UD do the same. Lately, however, I’ve come to the conclusion that what I’m attempting to do is the equivalent of bringing a knife to a gun fight; polite reasoning with Darwinists, for the most part, is simply setting up our own failure. It’s like entering a war zone with rules of engagement that effectively undermine a soldier’s capacity to adequately defend themselves, let alone win a war. While pacifism is a laudable idea, it does not win wars. It simply gives the world to the barbarians.

And that’s the problem; a lot of us don’t realize we’re in a war, a war where reason, truth, religion and spirituality is under direct assault by the post-modern equivalent of barbarians. They, for the most part, have no compunction about lying, misleading, dissembling, attacking, blacklisting, ridiculing, bullying and marginalizing; more than that, they have no problem using every resource at their means, legal or not, polite or not, reasonable or not, to destroy theism, and in particular Christianity (as wells as conservative/libertarian values in general). They have infiltrated the media, academia and the entertainment industry and use their influence to generate narratives with complete disregard for the truth, and entirely ignore even the most egregious barbarism against those holding beliefs they disagree with.

Wars are what happen when there is no common ground between those that believe in something worth fighting for. There is no common ground between the universal post-modern acid of materialist Darwinism and virtually any modern theism. There is no common ground between Orwellian statism-as-God and individual libertarianism with freedom of (not “from”) religion. There is only war. One of the unfortunate problems of war is that certain distasteful methods must be employed simply because they are the only way to win. In this war, in a society that is largely a low-information, media-controlled battleground, logic and reason are, for the most part, ineffective. The truth is ineffective because it is drowned out by a concerted cacophony of lies, or simply ignored by the gatekeepers of low-information infotainment. What has been shown effective is the Alinsky arsenal of rhetoric, emotional manipulation, and narrative control.

I would find it distasteful to pick up a gun in a ground war and have to shoot others to defend my family and way of life, but I would do so. Should I not pick up Alinsky’s Rules for Radicals and employ the weapons of my adversaries, if it is the most effective way – perhaps the only way – of winning the cultural war? There comes a point in time where all the high ground offers is one’s back against the precipice as the barbarian horde advances.
I understand where he's coming from. He's a good Christian who advocates "lying, misleading, dissembling, attacking, blacklisting, ridiculing, bullying and marginalizing" because that's what his opponents do. (And because his versions of truth, logic, and reason have proven to be ineffective.)

BTW, did you notice that he forgot to pretend that the Intelligent Design Creationist movement was all about science, not religion? Oops.

Note to William Murray: If you really were trying "not to ridicule, demean, or use terms that would cause hurt or defensive feelings" then why did you call us "Darwinists"?


1. I assumed that he was the Baptist minister but apparently it's a different William J. Murray.

IDiots Love Epigenetics

I read everything posted on Uncommon Descent and Evolution News & Views. These are the most important blogs for learning about Intelligent Design Creationism. The posts on those two blogs represent the very best that Intelligent Design Creationism has to offer. Their best minds are behind the posts.

Here, for example, is Denyse O'Leary in action: Turns out some Texas media DID believe Texas bans discussion of evolution.
... epigenetics is to Darwin’s darlings what relativity and quantum mechanics are to Newtonian physics, only worse, much worse. Newtonian physics was useful within its scale. Darwin’s magical mechanism of natural selection is more like phlogiston, which supposedly produced fire the way Darwinism supposedly produces mind from mud.

And if nothing really happens that way, what becomes of Darwin’s magical mechanism? It’s phogliston, the substance that need not exist!
Seriously, that's the best of the best?

You have to imagine that there are some Intelligent Design Creationists with a modicum of intelligence. Why aren't they speaking up to muzzle people like Denyse O'Leary? She's an embarrassment to their cause.


Friday, September 20, 2013

Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different Rates

Stephen Meyer is promoting the idea that God made all the various types of animals over a short period of time about 530 million years ago. The molecular data refutes that speculation because it shows that the various phyla share common ancestors and many of those ancestors appear long before the Cambrian Explosion.

This data creates a serious problem for the IDiots so they have to discredit it in order to dismiss it. As we've seen in earlier posts, Meyer argues that the molecular data is wrong because: (a) there are no transitional fossils, and (b) different molecular phylogenies do not agree in all detail [see The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes and Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates]. He has five anti-evolution arguments altogether [Darwin's Doubt: The Genes Tell the Story?]. The third one is that different genes evolve at different rates.

On Preparing Students for the 21st Century

Yesterday I attended a meeting organized by the Ontario Ministry of Education. The theme was From Great to Excellent: The Next Phase in Ontario's Education Strategy. The idea was to promote widespread consultation before the Ontario government releases its new plan for education reform next year.


I was attending on behalf of my friend Chris DiCarlo who had to be out of town. He (and I) are promoting the concept of critical thinking; specifically, the idea that it needs to be explicitly taught in a high school philosophy course.

The Minister of Education (Liz Sandals) and several of the senior members of her ministry were there. They told us that today's students are facing unprecedented changes and that the Ontario education system has to change in order to cope. They were mostly thinking about technological change and the possibility that today's students would have new types of jobs and careers.

I'm certain that we can improve our education system but I'm not sure it's helpful, or even correct, to focus on the idea that the next generation will have to cope with situations we never faced in the past. If we could show that our existing education system did a pretty good job of preparing students for change then maybe we should turn our attention to problems other than job training and technological innovation?

Wednesday, September 18, 2013

The Quebec National Assembly Crucifix Belongs in a Museum

I'm indebted to Veronica for telling me about this petition. I stole the title of her post: La Place du Crucifix de l’Assemblée Nationale Est dans un Musée.

Sign this petition if you think the crucifix should be removed from the Quebec National Assembly.


Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates

Stephen C. Meyer believes that the rapid appearance of complex, primitive, animals in the Cambrian cannot be explained without invoking God. The fact that there are no obvious transitional forms in the fossil record means, to him, that those transitional forms don't exist and God must have created all those primitive animals over a short period of time. Presumably, God then let them evolve naturally for the next 530 million years. (Meyer isn't very clear about this.)

Scientists looked at the molecular data in order to test the hypothesis that the Cambrian animals appeared suddenly in a very rapid radiation. The molecular data did not show such a rapid radiation. The overall pattern was consistent with branching evolution spread out over many millions of years. The diagrams that Meyer shows in his book are similar to the figure shown below from Erwin et al. (2007).

Breaking News!!! Wikipedia Is Wrong! (about the Central Dogma)

I shuddered when I spotted Razib's latest post in my aggregator [see The Central Dogma goes YouTube]. "Oh, no!" I thought, "Am I going to have to point him to my post on The Central Dogma of Molecular Biology?

Imagine my surprise when I saw that he has a link to the Wikipedia article on the Central Dogma. I said to myself, "This will set him straight because I wrote some of that article."

Oops! The Wikipedia article on the Central Dogma of Molecular Biology has been changed. Apparently I haven't looked at it for nine years since the important change was made by someone named Kierano back on September 15, 2006. Kierano describes himself (in 2011) as a Ph.D. student in bioinformatics.

Here's the opening paragraphs from before Sept. 15, 2006.
The central dogma of molecular biology was first enunciated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970:
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid.
In other words, 'once information gets into protein, it can't flow back to nucleic acid.'

The central dogma is often misunderstood. It is frequently confused with the standard pathway of information flow from "DNA to RNA to protein". There are notable exceptions to the normal pathway of information flow and these are often mistakenly referred to as exceptions to the central dogma.

The standard information flow pathway can be summarized in a very short and oversimplified manner as "DNA makes RNA makes proteins, which in turn facilitate the previous two steps as well as the replication of DNA", or simply "DNA → RNA → protein". This process is therefore broken down into three steps: transcription, translation, and replication. By new knowledge of the RNA processing, a fourth step must be included: splicing.
This has undergone some edits from what I originally wrote but the main idea is there. Strictly speaking, the Central Dogma of Molecular Biology (Crick version) says only that once information gets into protein it can't flow back to nucleic acid. I thought it was important to explain the main misconception; namely, that the Central Dogma means DNA to RNA to protein. This should be referred to as "the standard information flow pathway" or something similar.

The rest of the Wikipedia article talks about transcription and translation which, strictly speaking, are not part of the Central Dogma. However, the misconception is so widespread that many people expect these to be described under "Central Dogma."

The new version posted on Sept. 15, 2006 says ...
The central dogma of molecular biology was first enunciated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970:
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid.
In other words, 'once information gets into protein, it can't flow back to nucleic acid.'

The dogma is a framework for understanding the transfer of information between information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of information-carrying biopolymers: DNA and RNA (both nucleic acids), and protein. There are 9 possible direct transfers of information that can occur between these. The dogma classes these into 3 general transfers (believed to occur normally in most cells), 3 special transfers (known to occur, but only under abnormal conditions), and 3 unkown transfers (believed to never occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA, (transcription), and proteins can be synthesized using the information in mRNA as a template (translation).

The central dogma is occasionally misunderstood as being a statement of absolute fact. If taken as such, it can be criticised, as there are well-described exceptions. It is also criticised by some systems biologists as being too reductionist.
This is the beginning of a change in emphasis. Kierano removed my statement that the basic meaning of the Central Dogma is often misunderstood. It's clear that he misunderstands it.

On March 10, 2012 someone named Nbauman addd the following statement; "Or, as Marshall Nirenberg said, 'DNA makes RNA makes protein.'" Nbauman cautioned that this was a reliable published source and should not be removed from the Wikipedia article. As far as I can tell Nbauman is not a scientist and has no training in science. In fact, she seems proud of the fact that she is ignorant of the subjects she edits. She does not seem to have noticed that her "authority" (Nirenberg) conflicts with another authority (Francis Crick).

Here's the complete version as of this morning. It's going to change as soon as I get around to it.
The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It was first stated by Francis Crick in 1958[1] and re-stated in a Nature paper published in 1970:
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.
Or, as Marshall Nirenberg said, "DNA makes RNA makes protein."[3]

To appreciate the significance of the concept, note that Crick had misapplied the term "dogma" in ignorance. In evolutionary or molecular biological theory, either then or subsequently, Crick's proposal had nothing to do with the correct meaning of "dogma". He subsequently documented this error in his autobiography.

The dogma is a framework for understanding the transfer of sequence information between sequential information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and protein. There are 3×3 = 9 conceivable direct transfers of information that can occur between these. The dogma classes these into 3 groups of 3: 3 general transfers (believed to occur normally in most cells), 3 special transfers (known to occur, but only under specific conditions in case of some viruses or in a laboratory), and 3 unknown transfers (believed never to occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA (transcription), and proteins can be synthesized using the information in mRNA as a template (translation).


Jesus and Mo

See Jesus and Mo: Sept. 18, 2013

Tuesday, September 17, 2013

The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes

Darwin's Doubt is a book about the problems surrounding the Cambrian Explosion. It's written by a prominent Intelligent Design Creationist and, like most books by IDiots, the main theme is how scientists get everything wrong.

The "problem" is how to account for the very rapid appearance of complex animals about 530 million years ago. Intelligent Design Creationists think that they can ignore all of the evidence for evolution for the following 530 million years and focus on this one problem to discredit naturalistic explanations for the history of life.

You might expect that they would offer an alternative explanation. Like, perhaps, an intelligent being who visited Earth 530 million years ago, created a bunch of different animals with similar body plans, then allowed evolution to proceed for the next half a billion years?

Don't hold your breath waiting for a scientific explanation. They aren't that clever.

23andMe Sponsors a MOOC on Genetics

A private company, 23andMe sponsors a MOOC on genetics in association with UDACITY [Tales from the Genome]. Two of the instructors are employees of 23andMe.
You will learn about fundamental principles of inheritance, gene expression, mutation and variation, development of simple and complex biological traits, human ancestry and evolution, and the acquisition of personal genetic information. By the end of this course, you will be able to read and understand genetic information available from personal genetics services such as 23andMe.

What could possibly go wrong?


[HatTip: an unskeptical Blaine Bettinger: 23andMe and Udacity Partner to Offer A Free Online Genetics Course]

Atheist Freethinkers Support the Quebec Charter of Values ... with Reservations

There's a debate going on in Canada over the so-called "Charter of Values" proposed by the government of Quebec. The fact that the governing party is a separatist party (Parti Québécois) makes the debate much more interesting. (That's Premier Pauline Marois in the photo below.)

The main issue concerns how public servants present themselves to the public. The new law proposes to ban outward signs of religion on the grounds that public servants should represent a secular government. What this means in practice is that Sikh men won't be allowed to wear turbans and kirpas and Muslim women won't be allowed to wear hijabs or niqabs. Christians can't wear large crosses. Atheists can't wear a large red letter "A" on their lapel.

Opinion in Quebec is pretty evenly divided but most of the rest of Canada sees this (mostly incorrectly) as an infringement on fundamental rights and freedoms.

Atheist groups are struggling with this issue. Here's what the Atheist Freethinkers say in today's press release: The Quebec Charter of Values: A major advance towards secularism.
Montreal, 17th September 2013 — Atheist Freethinkers (LPA-AFT), an association which promotes secularism and supports the rights of atheists, welcomes the intention of the government of Quebec to adopt a so-called Charter of Values which would formally establish the secular status of the Quebec state. The project is outlined on its website www.nosvaleurs.gouv.qc.ca.

The proposed Charter would formally declare separation of religion and state, the religious neutrality of the state and the secular nature of its institutions. It would impose an ethics of restraint and religious neutrality for public servants. It would prohibit obvious religious symbols in the public service. And it would establish clear guidelines for so-called “reasonable” accommodations. Furthermore, it would make it mandatory for any client of public services to have one’s face uncovered in order to be served. All of these measures go in the direction of formalizing the secular nature of the state and assuring the independence and autonomy of the state from religion. This is very good news.

However, like most who support the proposed Charter, we do so with some reservations. Firstly, the title “Quebec Charter of Values” is very badly chosen. What Quebec requires is a Charter of Secularism, a charter which expresses values which have universal, human import, the values of the Enlightenment.

Secondly, it has not been proposed that the large crucifix be removed from the wall of the Quebec National Assembly in Quebec City. This object was installed there in 1936 by the Duplessis government of the day, with the aim of consecrating its alliance with the Catholic Church. If the crucifix is a “Quebec value,” it represents the worst possible value in this context. Its presence in the most important venue of the Quebec state is a blatant violation of secularism, a glaring symbol of non-secularism! The Charter should stipulate its removal – to a museum for instance. To leave it in place would be totally inconsistent and expose the authors of the Charter to charges of hypocrisy. However, it is important to realize that keeping the crucifix in the National Assembly is not explicitly stipulated in the proposed Charter. In fact, this crucifix is not even mentioned there.

Thirdly, the proposed ban on state employees wearing religious symbols while on duty has been poorly formulated. The plan is to include an official dress code in the Charter of Rights and Freedoms. However, this Charter is a quasi-constitutional document and should stipulate only the principle that public servants must exercise restraint – so that public services remains neutral with respect to religion – and establish a mechanism for the implementation of this principle. The dress code and other aspects of the behaviour of public servants belong to the implementation of this principle and should not be included in the Charter of Rights and Freedoms itself. In that way, the details and timing of the implementation would remain open to democratic debate.

The draft Charter was released barely a week ago and we continue to study it. Other aspects of the project may require critical analysis. Moreover, a completely secular charter would include several provisions not included in the announced project – such as cutting public funding to private religious schools; banning prayer at municipal council meetings; banning prayer rooms in government buildings; ending religious accommodations granted for ritual slaughter of animals; prohibiting mutilation of the human body without valid medical reasons and without the consent of the adult concerned; withdrawal of the Ethics and Religious Culture program from public schools; and removal of tax incentives to religious institutions and members of religious orders. These omissions remain to be addressed.

The organization Atheist Freethinkers commends the government for its courage. We note that the government is not responsible for the inflammatory and demagogic excesses of the exaggerated political opposition that arose against its attempt at secularization, even if such excesses could have easily been predicted. This project is not an exercise in identity politics. The numerous accusations of intolerance, xenophobia and even racism are extremely dishonest and even defamatory. Nevertheless, the government could have prevented the worst and minimized the damage by avoiding any measure which the opposition might use as an excuse. Excluding religious symbols is necessary in order to ensure not only the religious neutrality of the public service but also the perception of neutrality. By the same token, the government must not only avoid identity politics but also the perception of such politics. If the proposed Charter had specified the removal of the crucifix from the National Assembly, if its authors had chosen a title with more universal scope, if the plan for gradual removal of religious symbols had been better presented, then the intellectual vacuity of the opposition would have been obvious and that opposition would have been greatly defused.

Despite our reservations, we support the proposed Charter. It could serve as a model for other Canadian provinces and jurisdictions, each adapting the Charter appropriately and provided of course that the model is improved upon – in particular by avoiding the failings discussed above.

As atheists, we greatly value freedom of religion because atheists and apostates are often among the first victims when that freedom is violated. We know that freedom of religion is incomplete or even hollow if it does not include freedom from religion. Thus secularism is important not only for us as atheists but also for believers: it is essential that public institutions, i.e. state institutions, be independent of any religion and, at the same time, that total freedom to practice the religion of one’s choice, or to practice none, be protected in the private sphere and in the public sphere outside of such institutions.


Monday, September 16, 2013

Replacing Textbooks with MOOCs

John Hawks read the article that I discussed in an earlier post [On the High Price of Textbooks]. he outlines his solution to the high cost of textbooks [Textbook troubles].
I'm building the groundwork for a project that will do something about this, at least in the area of biological anthropology. I've been following stories like this for years. Developing the MOOC, I have the tremendous opportunity to make connections with people all over the world. Most of the people signed up are nowhere near the traditional U.S. college textbook market (MOOC international enrollment numbers). I face a problem that can't be solved by textbooks today, and limited-use "rental" text that will go away at the end of the course is not a valid solution.

So I'm doing something about it. The idea has many moving parts, but at its base is the need to supply quality educational content cheaply, with a way to get articles freely outside the usual college system. I'm going to be calling for help, so keep watching this space.
This is refreshingly honest. Of the many claims about MOOCs (Massive Open Online Course), the only one that makes sense to me is to use them as a possible replacement for textbooks. They can be used as a supplemental resources in a student-centered classroom.

MOOCs are good at delivering information—the sort of information you can get from a textbook.

Now I'm waiting to see if anyone creates a MOOC that comes close to the depth and quality of university science textbooks. I imagine that it can be done but it ain't going to be cheap.

John Hawks is an expert on anthropology but I find it difficult to imagine that he's going to be able to create drawings and figures of textbook quality for no cost. I don't see how he's going to ensure high quality editing and reviewing for free. I can't imagine how he's going to mount his course on servers and provide easy access for thousands of students without incurring some costs. He's going to have to pay for permissions to use photos and figures just like the textbooks do. Maybe he'll do all the administrative work himself or maybe somebody will work for him for no salary.

It's possible to overcome all these difficulties and provide free high quality MOOCs that will replace textbooks. So far, nobody has come close in any of the subjects that I'm interested in. Most existing biochemistry MOOCs are horrible.

Holding my breath ....


On the High Price of Textbooks

Once again we have a relatively uninformed journalist writing about the high cost of college textbooks ['Required reading': As textbook prices soar, students try to cope].

I am a textbook author so I'm not totally impartial. However, it's worth pointing out that I don't defend textbooks because I'm a textbook author. Instead, I became a textbook author because I value textbooks. I still have all my college textbooks and I still refer to them from time-to-time. The oldest ones were purchased 50 years ago.

Let's look at what Martha C. White has to say.
Already grappling with skyrocketing tuition and fees, college students also must contend with triple-digit inflation on the price of textbooks. With the average student shelling out $1,200 a year just on books, students, professors and policy groups are searching for ways to circumvent the high cost of traditional textbooks.
It may be true that the average student has to spend $1200 per year on required textbooks but the NBC News Business website didn't do themselves any favors by showing a photo of 21-year-old Priya Shivraj with a stack of textbooks that she presumably had to buy in a single year. She is supposed to be a combined major in biology, Spanish and pre-med and one would guess from her age that she's in her third or fourth year of university.

Here are some of the books in her stack: Introductory Biology, Introductory Chemistry, Organic Chemistry, Introductory Biochemistry, and Immunobiology. Is it possible that a student at NYU would take all those courses in a single year?

But let's not quibble. Many science textbooks cost about $150 and I can easily imagine that a student might have to purchase as many as six of them in a single year.
The College Board found that the average student at a four-year public college spends $1,200 on “books and supplies,” or nearly $1,250 if they go to a private school. On the public policy blog of the American Enterprise Institute, where he is a fellow, University of Michigan-Flint economics professor Mark J. Perry highlighted a chart showing an 812 percent increase in the cost of college textbooks since 1978, a jump even higher than the percentage growth in the cost of health care.
This paragraph says that the "average" includes supplies and it appears to cover four years. What does that mean?

Let's use our critical thinking skills to examine the claim that textbook prices have increased by 812% since 1978. According the the US Bureau of Labor Statistics CPI Inflation Counter there should be a 358% increase in price due to inflation alone. Thus, the real cost has about doubled in 35 years.

I addressed this issue a few years ago in: PZ Rants About Science Textbooks. Here's an updated version of what I said in 2007 ...
So let's understand and agree that the original price of a textbook is not unreasonable. My biochemistry textbook in 1965 was Conn & Stumpf and it cost $9.95. This works out to $73.79 in 2013 dollars using the handy-dandy inflation calculator on the US Dept. of Labor website. The 1965 textbook was much smaller, covered less material, and had no color figures. Modern biochemistry textbooks cost about $150 and they are very much better than the books published 50 years ago.
So the price of biochemistry textbooks has doubled in constant dollars but there's a huge increase in the amount and quality of the material in modern textbooks.

Martha White continues ....
“Students are, in essence, a captive market,” said Ethan Senack, higher education associate at the U.S. Public Interest Research Group. “The publishing industry is dominated by five companies that dominate upwards of 85 percent of the market.”

“I think part of it is the consolidation… There’s less competition now,” Perry said.
This sort of complaint comes up quite often. It suggests that publishers are conspiring to keep the cost of textbooks at least twice as high as they were decades ago. It also assumes that publishers are making outrageous profits at the expense of university students. Let's use our critical thinking skills to ask whether large public companies in the publishing industry are making huge profits. Since these are public companies whose stock is trading on the stock market, it should be possible to test this idea. One of the quickest ways is to simply look at the stock prices, they should be going through the roof if the assumption is correct. They aren't. The textbook publishing industry is making a profit but it's not much different than the profits made by most other companies.

There may be lots of things wrong with making students buy textbooks but it's ridiculous to pretend that the major publishing companies are ripping off students. It's also ridiculous to pretend that the retail price paid by students at their bookstore goes directly to the publisher. The wholesale price of a $150 textbook may be only $100. The bookstores have to make money too. You can buy my book for about $110 on Amazon.

See also: Free/Cheap Textbooks for Students.