Monday's Molecule #43

 
We have a winner!!! (see comments)


Today's molecule is a real biologically relevant molecule but it's a bit unusual. You have to supply the common name and the complete IUPAC name. There's an obtuse, indirect connection between this molecule and Wednesday's Nobel Laureate(s). (Hint: The Nobel Prize winner did not go to Sweden to get the prize.)


The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this Wednesday's reward. Both of them are waiting to collect their prize this week or next week. The prize is a free lunch at the Faculty Club.

Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

PZ Rants About Science Textbooks

This is a posting about science textbook publishing. I have a vested interest in this debate because I'm the co-author of two biochemistry textbooks published by Pearson/Prentice Hall—one of the largest textbook publishers in the world.

PZ Myers posted an article about the high cost of textbooks [Textbooks, again]. He says,

Everyone in academia knows it: textbook publishers abuse the system. Jim Fiore decries the high cost of college textbooks, and I have to agree completely. Basic textbooks at the lower undergraduate levels do not need a new edition every year or two, not even in rapidly changing fields like biology.

There are two points here. The cost of textbooks is determined by the market and lots of other factors. As a general rule, the publishers are not making outrageous profits on individual college textbooks. They try to make their money on volume.

Most people don't understand that a large part of the cost of a textbook is due to the mark-up at the retailers. Much of the rest of the price is due to the cost of production and marketing. Look at the list of people who contribute to a textbook. You'll usually find them listed on the back of the title page. There are artists and editors as well as people who manage the project and people who market the books. Each new edition of a major textbook like biology can cost close to $1 million dollars these days. You have to sell more than 20,000 copies just to recover the production costs. (Really popular books will sell more than 100,000 copies but the difference isn't all profit.)

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 $65.80 in 2007 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 $120-150 and they are very much better than the books published 40 years ago.

Even if we didn't want to make substantive changes in each edition and even if there were no second-hand market, we would still be forced to update our books because of pressure from competitors. Those other authors are hard at work revising and improving their books and if you don't follow suit you'll soon end up having no market share. What I'm saying here is that there are many reasons for new editions and it's very simplistic to attribute the cause to ripping off students. That's not how it works.

PZ's second point is more complex. Textbooks come out with new editions every few years. A typical cycle is four years—not the "year or two" that PZ suggests. While it is true that some of the pressure to produce new editions comes from a desire to eliminate the second-hand book market, that's not the only reason. There really is new material to add and new ways to approach the subject. In my case we're into the 4th edition of my Principles of Biochemistry textbook. The dates of publication are: 1992, 1996, 2002, and 2006. The next edition is scheduled for 2010. We're just about to start work on it. The differences between these editions are not trivial: they're part of a plan to transform the way we teach biochemistry. This is not unusual.

Churning editions is just a way for the publisher to suck more money out of a captive audience. It makes it difficult for students to sell off their used textbooks, it gives faculty the headache of having to constantly update their assignments, and if you allow your students to use older editions, it means we have to maintain multiple assignments. It's extraordinarily annoying, and to no good purpose at the university (to great purpose at the publisher, though).

This is simply not accurate. It's part of the urban myth about publishing. Everyone likes to blame someone else for the cost of textbooks.

I'm surprised that PZ would complain about having to update his assignments. You can't have it both ways, PZ. Either the new editions are trivial, in which case you don't have to change much, or they contain substantive changes, in which case your complaint about it being motivated to rip off students is unjustified. If you were using my textbook then be aware of the fact that my goal is to get you to change the way you've been teaching biochemistry. That's why I have new editions.

PZ, it sounds like you would never consider switching textbooks because it would be too much trouble for you to change your teaching. Is this a correct assumption?

On the plus side of their ledgers, though, I also urge the students to keep their textbooks once the course is over. These are valuable reference books that they may well find handy throughout their college careers and in their life afterwards. I've never quite understood the rush to dispose of those books the instant the semester ends — I kept my undergraduate biology and chemistry books until they fell apart (another gripe: the increasingly cheap bindings of these books), and I still have several of my old history texts on my shelves.

I'm with you on that one, PZ. I have all my old college textbooks. They are my friends. I never, ever, thought of selling them. They are full of notes in the margins and text highlights that reflect how I learned the material and what was important or controversial. I don't understand why students want to get rid of their textbooks when the course ends. Unless, of course, they never really cared about the subject in the first place and just needed a grade to graduate or get into medical school. But that's probably being too cynical.

Vote for your favorite BPR3 icon

 
Bloggers for Peer-Reviewed Research Reporting is a fledgling organization that's going to try and impose some standards on the reporting of peer-reviewed papers by bloggers. Here's their mission statement at [BPR3.org].

Bloggers for Peer-Reviewed Research Reporting strives to identify serious academic blog posts about peer-reviewed research by developing an icon and an aggregation site where others can look to find the best academic blogging on the Net.

The idea is to list all blog posts about peer-reviewed scientific literature on one site (with an RSS feed) and to identify all such blogs with a copyrighted icon. I've expressed some skepticism about this attempt to organize bloggers (sort of like herding cats) [Bloggers for Peer-Reviewed Research Reporting] but let's see how it works out.

Here are the three finalist in the icon contest from BPR3 website. Vote below.

Richard's Fleas

 
The image below is taken from The Fleas Are Multiplying! on RichardDawkins.net. It's pretty amazing when you think about it because, according to many accommodationists, Dawkins isn't having any impact on believers. Can you imagine how many fleas would have been produced in one year if Dawkins was having an impact?

AAAS Panel: Communicating Science in a Religious America

 
Matt Nisbet has organized a panel for the American Association for the Advancement of Science meetings in Boston next January. The title of the panel is Communicating Science in a Religious America. According to Nisbet's posting [AAAS Panel: Communicating Science in a Religious America], the panel will discuss framing. Here's the synopsis for the panel.

Over the coming decades, as society faces major collective choices on issues such as climate change, biomedical research, and nanotechnology, scientists and their organizations will need to work together with religious communities in order to formulate effective policies and to resolve disputes. A major challenge for scientists will be to craft communication efforts that are sensitive to how religiously diverse publics process messages, but also to the way science is portrayed across types of media. In these efforts, scientists must adopt a language that emphasizes shared values and has broad appeal, avoiding the pitfall of seeming to condescend to fellow citizens, or alienating them by attacking their religious beliefs.

Part of this process includes "framing" an issue in ways that remain true to the science, but that make the issue more personally meaningful, thereby potentially sparking greater interest or acceptance. With these themes in mind, the proposed panel combines the insights of scientists who have been successful at engaging religious publics with the findings of researchers on how media messages and opinion-leaders shape the perspectives of citizens. The panelists draw upon their experience working across the issues of evolution, climate change, stem cell research, and nanotechnology.

Who's on this panel, you might ask? It's some of the usual suspects and some others who I don't recognize.

... the panel features Brown University biologist Ken Miller, Vatican astronomer Brother Guy Consolmagno, William & Mary anthropologist Barbara King, Kansas science standards chair Steve Case, and University of Wisconsin communication researcher Dietram Scheufele. The panel is moderated by David Goldston, former chief of staff for the House science committee, now a lecturer at Princeton's Woodrow Wilson School and a columnist for Nature magazine.

As part of the panel, I will be presenting on the topic of "The New Atheism and the Public Image of Science," a first paper based on a research project I am currently working on here at American University with the help of two graduate students.

I have sent the following letter to Professor Goldston, the panel moderator.

Professor Goldston,

I have just read Matt Nisbet's blog article on the upcoming AAAS meeting in Boston.

As I'm sure you know, Nisbet has some very strong views on this issue and he is known to be a vocal opponent of athiests like Richard Dawkins, Christopher Hitchens, and Sam Harris. He has attacked the positions of many atheist scientist bloggers such as PZ Myers, Jason Rosenhouse, and me. He refers to this group as the "New Atheists," a term that is widely perceived as misleading at best, and offensive at worst.

Nisbet believes that scientists should spin their scientific messages in a way that avoids upsetting religious people and religious groups. That point of view has been hotly contested in the blogosphere. Many of us believe that this is a fundamentally dishonest way for scientists to behave. We believe that science should not be deliberately "framed" by the personal beliefs of scientists whether they are atheists - as are the majority of scientists - or Christians, or whatever.

We believe that science should be presented as uncompromised pure science and that it is wrong for scientists to consciously alter their message in order to appease religious citizens who might be offended by hearing the scientific truth. It is not the business of scientists to second guess what the religious public wants to hear, or not hear. Furthermore, it is not the business of scientists to tailor their message to the citizens of a particular country as the title of the panel implies. Is it realistic to expect scientists to communicate science one way in America, and another in Saudi Arabia, China, or France?

We all know there are scientists who have strong opinions about religion. Richard Dawkins is a vocal atheist, for example, and Ken Miller is a vocal Roman Catholic. Both of them have written books putting forth their points of view on religion. They are free to do so as long as they do not distort or misrepresent science.

But this is not what Nisbet is talking about when he refers to the public presentation of science - at least it's not what he should be talking about. Both Dawkins and Miller are perfectly capable of communicating scientific information without referring to religion, and they do so quite capably in many forums. Nisbet strongly implies that the Ken Millers of this world should be given preference over Richard Dawkins and other atheists when it comes to science education. This a form of censorship that should not be tolerated by AAAS.

I don't object to Nisbet presenting his point of view at a AAAS meeting but my respect for AAAS and your panel would be greatly diminished if the other side did not get a chance to make its case. Surely you do not want to give the impression that AAAS will only support scientists who agree with Nisbet? Surely you do not want to have a panel where the so-called "New Atheist" perspective is excluded and only religious scientists, or their close allies, are allowed to speak? Is that fair?

Please make sure that you have appropriate balance on your panel. Please make sure you don't give the impression that AAAS endorses Nisbet and his ideas about framing. The other side needs to be heard.


Laurence (Larry ) A. Moran
Professor of Biochemistry
University of Toronto

UPDATE: Jason Rosenhouse and Mike Dunford have also suggested that the panel might be biased.

Who Is David Tyler?

 
In an earlier posting, I quoted David Tyler's views about evolution and the peppered moth story [Peppered Moths and the Confused IDiots]. I didn't know who David Tyler was but he's obviously considered to be an authority (i.e., prominent IDiot) by Denyse O'Leary, among others.

Since posting that article, I've become more informed about this man. I thought I'd share this information so that everyone will know who's considered to be a leading IDiot on evolution.

David Tyler is a Young Earth Creationist who belongs to The Biblical Creation Society. Tyler believes in the literal truth of Genesis. It's no wonder that he has some doubts since there's nothing in Genesis about peppered moths.

Tyler has a day job. He is a Senior Lecturer (Professor, in North American terms) in the Department of Clothing Design and Technology, Hollings Faculty of Food, Clothing & Hospitality Management, Manchester Metropolitan University [Homepage for David J. Tyler]. He has a Ph.D. in physical sciences and his current interests focus on the textile industry, according to the Manchester Metropolitan University [Dr. David Tyere].

After joining the Department of Clothing Design and Technology at Manchester Metropolitan University, he has pursued a number of research interests related to responsive manufacturing and systems modelling. Earlier work was concerned with flow line systems and management strategies to optimise performance. Research interests over the past decade relate to teamworking in new product development and its relation to operational practices, and the optimisation of performance of textile/apparel supply chains. Since March 2000, he has managed the North West Advanced Apparel Systems Centre, a European-funded initiative to support clothing and textile companies in NW England.

This is an example of the sort of expert the IDiots think is a good spokesman for Intelligent Design Creationism: a Young Earth Creationist (YEC) with no obvious background in biology.

I really don't understand people like Denyse O'Leary and some of her friends. Denyse is Roman Catholic. She is not a Young Earth Creationist. How can she put any faith in the credibility of a man who thinks that science is compatible with a 6000-year-old Earth?

Parsing John Pieret

 
John Pieret has posted an intersting article in which he criticizes Mary Jordan for writing something silly about atheists in the Washington Post [Harebrained Hairpins]. I agree with John that she went way overboard.

However, I'm more interested in John's opening paragraph where he repeats a position he has long mantained.

I'm not overly sympathetic to the complaints of the "New Atheists" that they are unfairly being told to mute their criticism of religion lest they drive religious people further away from science in particular and rationalism in general. In my opinion, science is definitely not coextensive with atheism. And atheism, far from having a lock on rationalism, is, in fundamental ways arational, at least, if not outright irrational at times. And, it seems to me, if a dialogue is what you intend in which you hope to convince the religious to become atheists, starting off calling them delusional may be a tad counterproductive.

This is a bit confusing. Let's see if we can parse the sentences to get at the essence of John's problem. If I understand him correctly, he is saying ...

It is fair to tell atheists to mute their criticism of religion because it might be driving religious people away from science.

How, exactly, does this work, John? What is the ethical reasoning that justifies telling someone to keep quiet because you don't like their message? There is none. It's pefectly okay to disagree with us—something you do quite often—but it's a whole different thing to tell us to shut up, and maintain that it's fair to do so. It's not fair. It's unfair, ... and reprehensible.

If there's a rational argument there, then it has to be something like the following. You believe that religious people are going to embrace science—a good thing—but they won't do it if we atheists start telling them that there's no such thing as God or miracles. Hmmm ... very interesting. Does it also apply to other groups? Will astrologers embrace science as long as we stop telling them that astrology is a bunch of superstitious nonsense?

I interpret John to be saying.

It is fair to tell atheists to mute their criticism of religion because it might be driving them away from rationalism.

John, Aren't you making an unwarranted assumption here? Aren't you assuming that the average religious person already embraces rationalism? Otherwise, how could they be driven away?

What exactly are you saying? Are you saying that by criticizing religion we are making religious people abandon rationalism? And if we stop the criticism they will become rational? What arguments do you use to support that claim?

In my opinion, science is definitely not coextensive with atheism.

I agree. "Science" and the lack of belief in supernatural beings are two different things. It is possible to avoid believing in supernatural beings and be opposed to science. There are many examples. In addition, there are some people who fully accept all the fundamentals of science, and its implications, while still being religious. Deists are one example. Buddhists are another.

And atheism, far from having a lock on rationalism, is, in fundamental ways arational, at least, if not outright irrational at times.

The atheists are saying that they don't buy into the superstitious belief in the existence of supernatural beings. They don't accept most of the basic tenets of the major religions because they are not based on evidence. How in the world is this "irrational"?

And, it seems to me, if a dialogue is what you intend in which you hope to convince the religious to become atheists, starting off calling them delusional may be a tad counterproductive.

The evidence so far is against you. We've never had so much dialogue between atheists and religious leaders as we've had since the publication of The God Delusion. It is no longer possible for religious people get away with making the unchallenged assumption that there is a God. Millions of people are hearing for the first time that their core belief is being questioned. Not only that, it's being questioned in a particularly forceful way. That makes you sit up and take notice.

I'm sick and tired of this phony argument. It is completely irrational.

Casey Luskin Lies about Dawkins

 
I know, I know, so what else is new?

But this lie is so outrageous that it just has to be exposed. Over on the Discovery Institute website, Casey Luskin gloats over the famous video where Richard Dawkins pauses for 11 seconds when asked to give an example of an evolutionary process that increases information in the genome [Richard Dawkins on the Origin of Genetic Information].

The explanation for this pause is well-known. Dawkins had just realized that he had been duped into giving an interview in his house by creationists from Australia. The pause was to collect his thoughts after realizing the dishonesty of the interviewers. He then asked that the cameras be turned off and he asked them to leave. You can see the video and read the essay Dawkins wrote on dozens of websites [see Creationist Delusions about Transitional Fossils and Information].

Casey must know about this. He can't be that stupid. Therefore, he is lying.

Peppered Moths and the Confused IDiots

I'm teaching part of a course on Popular Scientific Misconceptions. In my section we'll be talking about the evolution/creationism controversy and part of the discussion involves analysis of the techniques used by Jonathan Wells to denigrate evolution in his book Icons of Evolution. One of the chapters is Peppered Moths.

Creationists used to love the peppered moth story because they thought the evidence had been refuted by modern science. They were wrong, and most creationists will admit it. Not Jonathan Wells. He says,

Industrial melanism in peppered moths shows that the relative proportions of two pre-existing varieties can change dramatically. This change may be due to natural selection, as most biologists familiar with the story believe. But Kettlewell's evidence for natural selection is flawed., and the actual causes of the change remain hypothetical. As a scientific demonstration of natural selection—as "darwin's missing evidence"—industrial mealanism in peppered moths is no better than alchemy.

Open almost any biology textbook dealing with evolution, however, and you'll find the peppered moth presented as a classical demonstration of natural selection in action—complete with faked photos of moths on tree trunks. This is not science by myth-making.

Unfortunately for poor old Jonathan, the original work of Kettlewell has been replicated and natural selection is the explanation. The creationists were recently dealt a serious blow when Michael Majerus reported the results of his observations on peppered moths to the European Society for Evolutionary Biology. So what do they do now?

Denyse O'Leary thinks there's still propaganda to be made from the peppered moth story so she links to an article from last week that shows the new strategy. Denyse's link is here [Evolution in the light of intelligent design encyclopedia - new entries]. The article by David Tyler is The Peppered Moth: when will Darwinians admit that mistakes have been made?.

I'm going to quote part of David Tyler's article. I swear I'm not making this up.

The concluding words of Majerus' lecture are these: "If the rise and fall of the peppered moth is one of the most visually impacting and easily understood examples of Darwinian evolution in action, it should be taught. It provides after all: The Proof of Evolution." This quote explains why the issue is still important: Darwinists have always sought to use the peppered moth story as a proof of Darwinian evolution. This is a burden that cannot be carried by the evidence. Even with Majerus' new improved methodology, we have an example of natural selection within the peppered moth population with differential predation being the causal mechanism. It is an extraordinary mental leap to go from this to the origin of novelty, complexity and new body plans - which remain the central challenges for any theory of evolutionary transformation.

Okay, let's take this slowly so that even IDiots like David Tyer and Denyse O'Leary can understand.

It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I’d rather not consider that).

Richard DawkinsWhen people like Majerus talk about evolution they're talking about the process of evolution. In this case he's referring to the process of evolution by natural selection within populations. He is perfectly correct in saying that the peppered moth date is proof that evolution occurs. It's proof of Darwinian evolution.

The problem with the IDiots is that they don't even understand what evolution is. Evolution does not require the creation of new body plans and the peppered moth example does not pretend to account for such things directly. All it does is show that evolution by natural selection is an observable fact.

Is it scientifically defensible to find an example of natural selection within a population of an animal, and then use this as an evidence for evolutionary transformation from the first single cell to the extraordinary diversity of life that we find in the biosphere?

No.

When this simple question is answered with a negative, then we can have a more constructive dialogue.

David, or Denyse, I'm ready whenever you are. To start with, do you understand the minimal definition of evolution [What Is Evolution?]. Get back to me when you do.

---

[Photo Credit: The photographs are from bill.srnr.arizona. The original source is unknown.]

Extra Credit

 
On Adventures in Ethics and Science they're having a little debate about something called "extra credit" [Question of the day: Is extra credit fair?]. The debate seemed kind of interesting but I really didn't have a clue what they were talking about, so I asked.

Nobody answered. I gather the concept of "extra credit" for a course is so widespread in American schools that they must have thought I was joking. After a bit of internet searching I think I'm beginning to understand what this "extra credit" is all about. There seem to be universities that permit students to raise their grades by doing extra work. For example, they might get a grade of 75/100 on all the exams and tests but they could add another 5 marks to bring their final mark up to 80% if they do some project that is not required of all students in the class.

Here's an example from an introductory biology course at the University of Illinois at Urbana-Champaign [Integrative Biology 101].

During the semester you have an opportunity to earn up to 6% worth of extra credit points to be added to your course grade at the end of the semester. You may earn any number of extra credit points up to the maximum of 6 points. To earn the whole 6% you must start early and sustain your extra credit work throughout the semester. There is also an option for one additional bonus point if you complete one of the two "Bonus" projects in addition to the maximum number of projects determined by the date you start your extra credit work.

Extra Credit projects require that you engage in some independent learning in areas of biology that interest you, write a brief report or review and then read the work of your classmates and interact with them via the Web Crossing computer conferencing system to share and discuss what you and your classmates have learned.

Extra credit projects are due at three specific times during the semester - before each of the hour exams and at the end of the semester. You may earn two extra credit points at each of these due dates.

For most extra credit projects, one extra credit point can be earned by writing one project review and completing two interactions (dialog entries) by reading and replying to two classmate's extra credit projects. While you must write at least one dialog entry to a classmate for each extra credit point, you may count another student's dialog entry to your project as your second dialog entry. If no one writes to you, you must then write a second dialog entry to another student.

I'm dumbfounded. How widespread is this practice?

Does this mean that when we're evaluating transcripts from the University of Illinois we have to consider the possibility that, while a student may have an "A" on the transcript, they may have only gotten a "B" when it comes to understanding the required material in the course?

There may be a logical reason for giving out extra credits but the logic escapes me. Can someone explain it?

Non-Religious Weddings and Funerals

 
An article on EurekAlert reports that in the UK Funerals without religion set for huge increase.

The number of people in the UK who opt for non-religious funeral services is set to rise dramatically over the coming years, according to a presenter at the Death, dying & disposal conference organised by the University of Bath today (Friday 14 September).

Around two per cent of UK funerals are currently non-religious, but according to 2001 census figures 27 per cent of the population consider themselves to be non-religious.

This, says Simon Allen, a Humanist Officiant, suggests that the current growth in secular funerals is just the beginning of an immense and rapid change in funeral practice.

I want to make sure that everyone in the Toronto area knows that non-religious weddings and funerals have been available for 10 years through the Humanist Association [Humanist Association of Toronto: Ceremonies].

The website lists Humanist officiants who are legally registered to perform marriages—they will also do funerals and childnaming ceremonies. We recently engaged one of these officiants, Kathryn Cook, for our daughter's wedding in June. I highly recommend her. There's no reason that one should be forced to hire a religious person for any of these ceremonies.

What Is DMCA and Why Should We Care?

 
YouTube is taking down a number of anti-religious videos on the grounds that they violate copyright. The accusations are being organized by Creationist groups, especially those associated with Kent Hovind, who is currently in prison for tax evasion [Hovind’s Goons use Fraud to Remove Critical YouTube Videos].

The Rational Response Squad is the latest group to lose their YouTube account [We're ready to help sue Creation Science Evangelism Ministries].

The legal tool that's being used is the Digital Millennium Copyright Act. This is an American law that imposes stiff penalties for copyright infringement on the internet. The problem is that the law encourages websites to take down material whenever a "charge" of copyright infringement is made. By doing this the websites avoid the threatened legal action.

Here's how the Wikipedia article describes the problem,

The DMCA has been criticized for making it too easy for copyright owners to encourage website owners to take down infringing content and links when it may not in fact be infringing. When website owners receive a takedown notice it is in their interest not to challenge it, even if it is not clear if infringement is taking place, because if the potentially infringing content is taken down the website will not be held liable. The Electronic Frontier Foundation senior IP attorney Fred von Lohmann has said this is one of the problems with the DMCA.[2]

Many sites are receiving DMCA notices and taking down links to infringing material as a result. Because the links are taken down it is rarely challenged in court resulting in link liability being a grey area of the law, although based on previous legal cases it leans in favor of copyright owners.[3] Stephan Ott of LinksandLaw.com states that "linking to infringing content is unlawful and that is also what most of the courts say."

I'm constantly amazed at how easy it is to use legal trickery to curtail basic freedoms such as free speech. In this case, the freedom/anarchy of the internet seems to be too much to stomach for those people who want to control peoples' thoughts. I suppose we should have seen this coming. After all, the other kinds of media are also highly censured in America.

Now I suppose there's going to be a big legal fight and the courts will have to decide whether these YouTube videos violate the Digital Millennium Copyright Act. Oh well, it keeps the lawyers off the streets and gives all the amateur lawyers something to blog about.

Perhaps the experts could answer a question? If a company like YouTube were to relocate to another country would the act still apply? Could the act be used to censor foreign websites?

The Domino Theory

 
I watched President Bush on TV the other day. I was wondering where his buddy was hiding. Ahh, here he is ...

According to the Washington Post Vice President Dick Cheney has some words of advice on Iraq [Cheney: chaos if U.S. pulls out too soon from Iraq].

If U.S. and coalition forces left Iraq before Iraqis could defend themselves, moderates would be "crushed," extremists would push the country into "chaos," and competing factions including groups backed by Iran "would unloose an all-out war, with the violence unlikely to be contained within Iraq," Cheney said.

"The ensuing carnage would further destabilize the Middle East and magnify the threat to our friends throughout the region," he said.

Now, where have I heard that before. Google is my friend ....

Here it is. It's called the Domino Theory.

The domino theory was a mid-20th century foreign policy theory, promoted by the government of the United States, that speculated that if one land in a region came under the influence of communism, then the surrounding countries would follow in a domino effect. The domino effect suggests that some change, small in itself, will cause a similar change nearby, which then will cause another similar change, and so on in linear sequence, by analogy to a falling row of dominoes standing on end. The domino theory was used by successive United States administrations during the Cold War to justify American intervention around the world.

Referring to communism in America and Mexico, Eisenhower vocalized the theory:

"Finally, you have broader considerations that might follow what you would call the "falling domino" principle. You have a row of dominoes set up, you knock over the first one, and what will happen to the last one is the certainty that it will go over very quickly. So you could have a beginning of a disintegration that would have the most profound influences."

It worked before. Americans stayed in Viet Nam for years because of the Domino Theory. Eventually 58,000 soldiers died and another 350,000 were wounded. Between one and two million Vietnamese citizens died. And the dominos didn't fall when America pulled out.

But who cares about history?

Genome Size, Complexity, and the C-Value Paradox

Forty years ago it was thought that the amount of DNA in a genome correlated with the complexity of an organism. Back then, you often saw graphs like the one on the left. The idea was that the more complex the species the more genes it needed. Preliminary data seemed to confirm this idea.

In the late 1960's scientists started looking at the complexity of the genome itself. They soon discovered that large genomes were often composed of huge amounts of repetitive sequences. The amount of "unique sequence" DNA was only a few percent of the total DNA in these large genomes.¹ This gave rise to the concept of junk DNA and the recognition that genome size was not a reliable indicator of the number of genes. That, plus the growing collection of genome size data, soon called into question the simplistic diagrams like the one shown here from an article by John Mattick in Scientific American (Mattick, 2004). (There are many things wrong with the diagram. Can you identify all of them? See What's wrong with this figure? at Genomicron).

Today we know that there isn't a direct correlation between genome size and complexity. Recent data, such as that from Ryan Gregory's website (right) reveals that the range of DNA sizes in many groups can vary over several orders of magnitude [Animal Genome Size Database]. Mammals don't have any more DNA in their genome than most flowering plants (angiosperms). Or even gymnosperms, for that matter.

Many of us have been teaching this basic fact for twenty years. The bottom line is ....

Anyone who states or implies that there is a significant correlation between total haploid genome size and species complexity is either ignorant or lying.

It is notoriously difficult to define complexity. That's only one of the reasons why such claims are wrong. Ryan Gregory wants everyone to know that the figure showing genome sizes in different phylogenetic groups is not meant to imply a hierarchy of complexity from algae to mammals.

A recent paper by Taft et al. (2007) says complexity can be "broadly defined as the number and different types of cells, and the degree of cellular organization." We can quibble about the definition but there's nothing better that I know of. The real question is whether organism complexity is a useful scientific concept.

Here's the problem. Have some scientists already made up their minds that mammals in general, and humans in particular, are the most complex organisms? Do they construct a definition f complexity that's guaranteed to confer the title of "most complex" on humans? Or, is complexity a real scientific phenomenon that hasn't yet been defined satisfactorily?

I, for one, don't know whether humans are more complex than an owl, or an octopus, or an orchid. For all I know, humans may be less complex by many scientific measure of complexity. Plants can grow and thrive on nothing but water, some minerals, and sunlight. We humans can't even make all of our own amino acids. Does that make us less complex than plants? Certainly it does at the molecular level.

Back in the olden days, when everyone was sure that humans were at the top of the complexity tree, the lack of correlation between genome size and complexity was called the C-value paradox where "C" stands for the haploid genome size. The term was popularized by Benjamin Lewin in his molecular biology textbooks. In Genes II (1983) he wrote.

The C value paradox takes its name from our inability to account for the content of the genome in terms of known function. One puzzling feature is the existence of huge variations in C values between species whose apparent complexity does not vary correspondingly. An extraordinary range of C values is found in amphibians where the smallest genomes are just below 10⁹bp while the largest are almost 10¹¹. It is hard to believe that this could reflect a 100-fold variation in the number of genes needed to specify different amphibians.

So, the paradox arises even if we don't know how to rank flowering plants and mammals of a complexity scale. It arises because there are so many examples of very similar species that have huge differences in the size of their genome. Onions, are another example—they are the reason why Ryan Gregory made up the Onion Test.

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

Imagine the following scenario. You are absolutely convinced that humans are the most complex species but total genome size doesn't reflect your conviction. The C-value paradox is a real paradox for you. Knowing that much of our genome is possibly junk DNA still leaves room for plenty of genes. You take comfort in the fact that under all that junky genome, humans still have way more genes than simple nematodes and flowering plants. You were one of those people who wanted there to be 100,000 genes in the human genome [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome].

But when the genomes of these species are published, it turns out that even this faint hope evaporates. Humans, Arabidopsis (wall cress, right), and nematodes all have about the same number of genes.

Oops. Now we have a G-value paradox, where "G" is the number of genes (Hahn and Wray, 2002). The only way out of this box—without abandoning your assumption about humans being the most complex animals—is to make up some stories about the function of so-called junk DNA. If it turns out that there are lots of hidden genes in that junk then maybe it will rescue your assumption. This is where we get some combination of the excuses listed in The Deflated Ego Problem.

On the other hand, maybe humans really aren't all that much more complex, in terms of number of genes, than wall cress. Maybe they should have the same number of genes. Maybe the other differences in genome size really are due to variable amounts of non-functional junk DNA.

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1. Thirty years ago we had to teach undergraduates about DNA reassociation kinetics and C_ot curves—the most difficult thing I've ever had to teach. I'm sure glad we don't have to do that today.

Hahn, M.W. and Wray, G.A. (2002) The g-value paradox. Evol. Dev. 4:73-75.

Mattick, J.S. (2004) The hidden genetic program of complex organisms. Sci Am. 291:60-67.

Taft, R.J., Pheasant, M. and Mattick, J.S. (2007) The relationship between non-protein-coding DNA and eukarotic complexity. BioEssays 29:288-200.

[Photo Credits: The first figure is taken from a course webite at the University of Miami (Molecular Genetics. The second figure is from Ryan Gregory's Animal Genome Size Database (Statistics).]

We're Number 2!!!

 
There is much wailing and gnashing of teeth in Toronto today as word has just been received that the Burj Dubai, under construction in the United Arab Emirates (UAR), has surpassed 553 metres. This makes it the tallest building in the world. The record has been held by the CN Tower in Toronto for over 30 years.

The bad news is reported in The Toronto Star [CN Tower no longer world's tallest].

"The accomplishment of being the world’s tallest free-standing structure is another defining moment for the multinational team of over 5,000 people who are using their collective intelligence to make this iconic structure a symbol of human achievement," said Mohamed Ali Alabbar, head of Emaar Properties, which owns the new tower. "This architectural and construction master-piece is truly an inspirational human achievement that celebrates the can-do mindset of Dubai."

CN Tower officials are playing it cool and, so far, the website still calls it "the world's tallest building." A short statement, sent out by email, said, "When the time comes and the building is complete, we will congratulate the Burj Dubai project on their unique achievement."

Okay, so we're not quite ready to officially concede just yet but the writing is clearly on the wall, so to speak.

A separate article in The Toronto Star attempts to console us by pointing out that we're #2 in a lot of things. It's nothing to be ashamed of [CN Tower topples to Number 2]. Some people wonder what all the fuss is about. An unidentified woman is prominently quoted in the print version of the story—the one that's being sold on the newsstands and delivered to suburban doors.

One woman, who didn't want to give her name, shrugged off the slight to Toronto as "such a guy thing."

"Who really cares? Trust me, length doesn't matter."