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).

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Jesus and Mo

See Jesus and Mo: Sept. 18, 2013

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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?

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[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.

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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 ....

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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.

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Monday's Molecule #215

Last week's molecule was malonate (propanedioic acid). A derivative of malonate called malonyl-CoA is a key intermediate in fatty acid synthesis. Bill Chaney was the first person to identify the molecule and describe its function [Monday's Molecule #214].

Recently I've been having a discussion with the Chair of my department about whether undergraduates in introductory biochemistry courses should memorize structures. He thinks they should. I wondered whether all the professors in my department could draw the structures of some important molecules. Here are a couple of molecules that you might be able to recognize. How many of you can identify them without checking a textbook?

How many of you can identify them even with a textbook? I'll need a fairly exact identification. Be sure to specify "top" and "bottom" molecules.

Email your answers to me at: Monday's Molecule #215. I'll hold off posting your answers for 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)

Move This Book?

I noticed a couple of books in the Science section of my local bookstore. One was by a guy named Meyer (Stephan C. Meyer) and the other was by someone named Myers (PZ Myers). I bought the one by Myers because I already had the other one.

There are some people who get upset by seeing these books in the Science section. Some of these people even like to move them to other sections, such as religion and/or philosophy. I even did it myself on one or two occasions in the past. Lately, however, I've become somewhat less dogmatic about the creationist books. They are, after all, books about science even though they may try to bring religion into science. That does not mean their view are non-scientific. Many of those books are no worse than some of the other "science" books on the shelf that have nothing to do with religion.

What would you do? Here are the choices ...

1. Move the Meyer books to another section.
2. Move the Myers books to another section.
3. Move both books to other sections.
4. Leave both books in the Science section.

I'm especially interested in hearing from Jerry Coyne and his supporters who supported Diana MacPherson's successful attempt to get Amazon to reclassify Darwin's Doubt as a religious book [Reader gets ID book moved from science to religion section].

Amazon puts The Happy Atheist in the "Religion and Spirituality" category. Does it belong in the Science section of local bookstores?

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Creationist Quotes

"Quote mining" can be fun. Here are some actual quotes taken from online forums. They are spoken by atheist actors.


Someone recently asked me why I mock creationists when I should be giving them more respect.

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Sean Carroll: "What Is Science?"

I've been meaning to comment on Sean Carroll's post from last July (July 3, 2013) but there always seems to be something else that commands my attention. The issue is important, in fact I've just finished an entire book on the question (Philosophy of Pseudoscience: Reconsidering the Demarcation Problem edited by M. Pigliucci and M. Boudry).

Sean Carroll (the physicist)¹ has a view that's quite similar to my own. Read his post at: What Is Science?. Here are some key points.

Better Biochemistry: Teaching ATP Hydrolysis for the MCAT

I'm digesting the idea that many American biochemistry courses teach to the MCAT exam [see Better Biochemistry: Teaching to the MCAT?]. What this means is that the scientists who teach biochemistry are willing to let the curriculum be established by a group of American medical schools (AAMC). That organization has put up a website to guide faculty members and students in preparation for the 2015 MCAT exam [MCAT2015: Biological and Biochemical Foundations of Living Systems].

One of the links takes you to a chemwiki at the University of California, Davis: Biological Chemistry. From there you can click on several topics. I picked ATP/ADP to see what kind of information the MCAT thinks is appropriate. The information on the ATP website is provided by Tiffany Lui of the University of California, Davis so it's not something that AAMC created. Nevertheless, it is presumably indicative of the sort of thing that might appear on the MCAT exam.

Humans Are Still Evolving

Sir David Attenborough said something stupid the other day [Sir David Attenborough: Humans have stopped evolving]. (Not for the first time.) He said ...

Because if natural selection, as proposed by Darwin, is the main mechanism of evolution – there may be other things, but it does look as though that’s the case – then we’ve stopped natural selection.

We stopped natural selection as soon as we started being able to rear 95–99 per cent of our babies that are born.

We are the only species to have put a halt to natural selection, of its own free will, as it were.

The headline says that humans have stopped evolving. If that's what he really said then it's easy to prove him wrong by showing that there's a lot more to evolution than natural selection [Have Humans Stopped Evolving?].

But what about his specific claim that natural selection doesn't work on humans any more? I covered that in earlier posts but John Hawks has corrected him today [Humans are still evolving, and soon we'll know a lot more about it]. I love it when I agree with John Hawks! (That's me, visiting him in his lab in Madison, Wisconsin.)

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Better Biochemistry: Teaching to the MCAT?

Theme

Better BiochemistryI view science education as a way of teaching students how to think critically. In that sense, it's not any different than education in the arts and humanities. In my opinion, biochemistry should be taught as a bunch of fundamental concepts and principles that will help students understand the basics of life at the molecular level. The course will demonstrate how to think critically and how we come to know what we know—if we teach it correctly. I believe that biochemistry should be taught from an evolutionary perspective since that's the best way to achieve fundamental understanding.

The last thing we should be doing in an undergraduate biochemistry course is to ask students to memorize enzymes, structures, and pathways and regurgitate them on an exam. We should not just be teaching the biochemistry of humans since that does not provide students with a broad view of life and where humans came from. Such an approach also makes biochemistry seem like it's only important because it can contribute to health. We have plenty of evidence that this is the wrong way to teach.

The Happiest Countries

Why do the people of these countries think they are happy? Why isn't the USA in the top ten? [World’s Happiest Countries In 2013, According To The UN]

I recently visited #1, #2, #5, #7 and #9 and I can confirm that the citizens of those countries do, indeed, think they are happy. I also visited #17 a few months ago and the citizens of that country do not seem happy. It's probably worse today than it was a few months ago.

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