This post is about a paper recently published in Science (Dec. 13, 2013) by John Stamatoyannopoulos and his collaborators at the University of Washington in Seattle, Washington, USA.
Stergachis, A.B., Haugen, E., Shafer, A., Fu, W., Vernot, B., Reynolds, A., Raubitschek, A., Ziegler, S., LeProust, E.M., Akey, J.M. and Stamatoyannopoulos, J.A. (2013) Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution. Science 342:1367-1372. [doi: 10.1126/science.1243490] [Abstract] [PDF]
Stamatoyannopoulos is one of the ENCODE workers. He recently gave a talk at the University of Toronto where he defended the idea that pervasive transcription and pervasive transcription factor binding are evidence of widespread function in the human genome. This paper looks at transcription factor binding sites in exon sequences (coding sequences) and finds lots of them. What this means is that stretches of coding region contain codons AND transcription factor binding sites (duh!).
Glenn Branch of NCSE alerted me to this book: 1001 Ideas the Changed the Way We Think. He wrote some of the articles [see Creationism and Evolution in 1001 Ideas].
The last great idea that changed the way we think (#1001) is written by Simon Adams, a "historian and writer living and working in London." Simon Adams thinks that the discovery that most of our genome is not junk counts as a big idea. To his credit, Glenn Branch realizes that this is somewhat controversial.
That's putting it mildly. Knowledgeable scientists agree that most (~90%) of our DNA is junk in spite of what the ENCODE publicity campaign might have said back in September 2012. I'm reproducing the article that Simon Adams wrote to show you just how successful that publicity campaign was and how difficult it is for the corrections and rebuttals to make an impact on a gullible public. With apologies to Glenn, whose articles are probably accurate, you should not buy a book that makes such a serious mistake by allowing an amateur to write about genomes, a subject he knows nothing about.
NOT-JUNK DNA
Far more of the human genome has vital functions than was first realized
The ribbons of DNA (deoxyribonucleic acid) in our cells carry instructions for building proteins and thus continuing life, but it was long believed that stretches of them are useless. The idea of "junk DNA" was first formulated by the Japanese-American geneticist Susumu Ohno (1928-2000), writing in the Brookhaven Symposium in Biology in 1972. He argued that the human genome can only sustain a very limited number of genes and that, for the rest, "the importance of doing nothing" was crucial. In effect, he dismissed 98 percent of the total genetic sequence that lies between the 20,000 or so protein-coding genes.
Yet scientists always thought that such junk must have a purpose. And indeed, a breakthrough in 2012 revealed that this junk is in fact crucial to the way our human genome, that is the complete set of genetic information in our cells, actually works.
After mapping of the entire human genome was completed in 2003, scientists focused on the so-called junk DNA. Nine years later, in 2012, the international ENCODE (Encyclopedia of DNA Elements) project published the largest single genome update in Nature and other journals. It found that, far from useless, the so-called junk contained 10,000 genes—around 18% of the total—that help control how the protein-coding genes work. Also found were 4 million regulatory switches that turn genes on and off (it is the failure of these switches that leads to diseases such as type 2 diabetes and Crohn's disease). In total, ENCODE predicted that up to 80 percent of our DNA has some sort of biochemical function.
The discovery of these functioning genes will help scientists to understand common diseases and also to explain why diseases affect some people and not others. If that can be achieved, drugs can be devised to treat those diseases. Much work still needs to be done, but the breakthrough has been made.
The editor of this book is Robert Arp, a philosopher specializing in the philosophy of biology and evolutionary psychology. I assume that he approved of the article by Simon Adams, which means that even philosophers of biology were duped by the ENCODE leaders.1
The book was published on Oct. 29, 2013. That means there was plenty of time to read the critiques of the ENCODE publicity campaign and even the scientific articles that were published last winter and early spring. There's really no excuse for making such a mistake.
We're in Washington D.C. for a wedding. Our hotel is the Ritz-Carleton in Arlington, Virginia, right next door to the Pentagon City Mall.
This is a photo of the food court in the mall. I was here with my children 20 years ago (August 1993) when I discovered "Panda Express" and orange chicken for the very first time. Of course I had to celebrate this anniversary by having some more. (I just finished.) I think that orange chicken is my number one fast food dish. I'm pretty sure that my daughter likes it too since she eats it at least once a week.
We have a nice view from our room of some big odd-shaped building.
It's always difficult to pin down an intelligent design creationist. They demand detailed "naturalistic" explanations of everything before they will accept them but, on the other hand, they won't ever give you their explanation. For example, we know they have doubts about the evolution of bacterial flagella but have you ever heard them describe their hypothesis? Like who made the first flagellum? When? Why?
It's also difficult to tell the difference between the various creationist cults. Clearly there are Young Earth Creationists who support the Intelligent Design Creationist movement but sometimes the IDiots say that YEC is inconsistent with Intelligent Design Creationism. Isn't that strange?
Most IDiots define their movement in very broad terms but they get really upset with Theistic Evolution Creationists. Apparently, you can't believe in theistic evolution and still be an IDiot. Who knew?
Now Granville Sewell comes to the rescue by describing what Intelligent Design Creationists actually believe [Granville Sewell: Intelligent design shouldn't be dismissed]. A link was posted on Uncommon Descent under the title "Introduction to ID."
Here's the important part of Sewell's article.
So what do ID proponents believe?
Perhaps the best way to answer this question is to state clearly what you have to believe to not believe in intelligent design. Peter Urone, in his 2001 physics text "College Physics" writes, "One of the most remarkable simplifications in physics is that only four distinct forces account for all known phenomena."
The prevailing view in science today is that physics explains all of chemistry, chemistry explains all of biology, and biology completely explains the human mind; thus physics alone explains the human mind and all it does. This is what you have to believe to not believe in intelligent design, that the origin and evolution of life, and the evolution of human consciousness and intelligence, are due entirely to a few unintelligent forces of physics.
Thus you must believe that a few unintelligent forces of physics alone could have rearranged the fundamental particles of physics into computers and science texts and jet airplanes.
Contrary to popular belief, to be an ID proponent you do not have to believe that all species were created simultaneously a few thousand years ago, or that humans are unrelated to earlier primates, or that natural selection cannot cause bacteria to develop a resistance to antibiotics.
If you believe that a few fundamental, unintelligent forces of physics alone could have rearranged the basic particles of physics into Apple iPhones, you are probably not an ID proponent, even if you believe in God. But if you believe there must have been more than unintelligent forces at work somewhere, somehow, in the whole process: congratulations, you are one of us after all!
This is a very broad definition. If you believe in God then you pretty much have to be an IDiot unless you are a strict deist. Every single religious person that I know believes that "there must have been more than unintelligent forces at work somewhere, somehow, in the whole process."1 Therefore, every Roman Catholic and every evangelical Christian is an IDiot, according to Granville Sewell. This includes Ken Miller and Francis Collins. In fact, it includes every religious scientist.
Not bad, eh?
For the record, I do not "believe" that " ... a few fundamental, unintelligent forces of physics alone could have rearranged the basic particles of physics into Apple iPhones." I think it's the most reasonable explanation. I don't know of any other explanation that is supported by evidence.
1. Yes, I know about atheist Buddhists. That doesn't count as a "religion" in my book.
We had a big ice storm in Southern Ontario last weekend. There are still thousands or people without power and many are unlikely to have power restored before Christmas (tomorrow).
We got off fairly lightly. We were never without power (underground wires) and the roads were cleared pretty quickly. However, lots of trees in our neighborhood suffered and some were almost completely destroyed by the weight of the ice. A large branch of the ash tree in our front yard cracked but did not fall. It was hanging over our driveway so we had to move our cars. We called Davey Tree on Sunday and they showed up yesterday to remove the broken branch.
It was quite a production. The woman in charge had to park this huge truck in our driveway and maneuver the cherry picker trough the branches. As you can imagine, it attracted an audience from the neighboring houses. When the job was done they swept up all the debris and turned it into sawdust in a wood chipper. There are more photos at: Uh Oh!. We have a daughter and a granddaughter who would love this job!
The Princeton Guide to Evolution is a collection of 107 articles on various aspect of evolution. The editors felt they should address the obvious conflict between evolution/science and religion. There are at least five different approaches they could have taken.
- An atheist perspective on the incompatibility of evolution/science and religion. Richard Dawkins or Jerry Coyne would be good choices.
- An atheist perspective on the compatibility of science and religion (the accommodationist view). Michael Ruse or Nick Matzke are obvious choices.
- A theist view of the incompatibility of evolution and religion. Phillip Johnson could have explained this view but so could a number of other creationists.
- A theist explanation of the compatibility of evolution/science as long as they stick to their proper magisteria. Francis Collins, Ken Miller, and several other religious scientists could present their case.
- The editors could have published four articles representing the main viewpoints or commissioned a single article that would have covered all the angles.
The big advantage of an atheist perspective is that it fairly represents the views of a majority of evolutionary biologists. Having a theist write the article would not be as fair. I think we can all agree that option #5 is by far the best choice.
Before reading any further, take a minute to decide what you would do if you were the editors of The Princeton Guide to Evolution.
One of the problems in most debates and discussions in the problem of definitions. It's common for two opponents to end up talking past one another because they don't agree on what they are arguing about. That's why an important component of critical thinking is to define your terms so that everyone knows what you are defending (or attacking).
But there's more. If you are going to be a good critical thinker, then you have to be aware of other points of view. If there are other, equally valid, definitions out there then you MUST acknowledge them and incorporate them into your argument. You can't, for example, just make up your own definition of words like "noncoding," "junk," or "function," and declare that you are right. Since you know that there are other definitions out there, you are obliged to show why YOUR definition is the only correct one. That's a crucial part of the debate.
If you don't even know that there are other valid definitions then you are not an expert and you should not be pretending to be an authority on the subject. This is why I object to people who argue against the Central Dogma of Molecular Biology without understanding what Francis Crick actually said.
Let's look at a video of Elliott Sober lecturing on "Some Questions for Atheists to Think About." He begins by asking the members of his audience whether they are atheists or agnostics. Apparently, most members of the audience are atheists and ony a few are agnostics.
Next, he defines his terms ...
Theism = God exists
Atheism = God does not exist
Agnosticism = We don't know whether God exists
The lecture is about something called "evidentialism." Elliott Sober claims that the following proposition is true ...
For any proposition, you should believe it only if you have evidence that it is true and you should disbelieve it only if you have evidence that it is false.
He then goes on to show that we can never have evidence that God does not exist. Therefore, "If 'God exists' is untestable, you ought not to be an atheist. You should be an agnostic."
He suggests that all the atheists in the audience should become agnostics because of evidentialism. If I had been in the audience, I would have pointed out that MY definition of atheist is that an atheist is someone who doesn't believe in god(s). My definition is such a common definition that it's part of the Wikipedia article on Atheism. Since I do not need "evidence" to not believe in something, I'll remain an atheist, thank-you very much. My position is perfectly consistent with the proposition about evidentialism.
Here's the problem. Elliott Sober is a prominent philosopher. Doesn't he realize that his argument relies entirely on his definition of "atheism"? Doesn't he realize that his argument is completely useless if an atheist is simply someone who doesn't buy into the God delusion? This sort of thing makes me livid and it makes me wonder whether there's something seriously wrong with modern philosophy.1
1. I am not suggesting that Sober's definition is wrong. He should not be ignoring the fact that many members of his audience don't agree with his definition and that's why they are atheists.
A few days ago, I asked the following questions, Is the "Modern Synthesis" effectively dead?, and What do they mean when they say they want to extend the Modern Synthesis?. The point I was trying to make was that there are many different views on evolutionary theory and it's often difficult to figure out which version of evolutionary theory someone is defending.
For example, which version of evolutionary theory is compatible with the "selfish gene" as a metaphor for evolution? Or for adaptation? Which version of the "Modern Synthesis" is being attacked in the book edited by Massimo Pigliucci and Gerd Müller? Is it the version defended by Ernst Mayr? Does it incorporate Neutral Theory and random genetic drift?
Here are the questions on yesterday's exam for students in my course. Students will be graded on their explanations and not so much on the actual answer they give. The idea is to reward critical thinking and that includes the ability to see both sides of an issue and recognize problems with whatever side you choose to defend.
- Assuming that the technology is safe and effective, should we, or should we not, have laws forbidding the cloning of humans?
- What is the best definition of a "gene"? Explain why you choose that definition and give examples of possible "genes" that don’t fit your definition.
- Elliott Sober is a highly respected philosopher. He explains that theistic evolution is a reasonable hypothesis because God could easily cause mutations to occur in a way that scientists would not be able to detect. In other words, a specific, directed, mutation would be indistinguishable from a random mutation. Thus, it would appear that evolution was an entirely naturalistic process while, in fact, its direction was being guided by God. Do you think this is a reasonable argument in support of theistic evolution? Why or why not?
- In his book, The Myth of Junk DNA, Jonathan Wells writes.
According to intelligent design (ID), it is possible to infer from evidence in nature that some features of the world, and of living things, are better explained by an intelligent cause than by unguided natural processes.
What sorts of positive arguments do ID proponents use to support this inference from evidence in nature? Are they effective?
Today is the day of the final exam in my course on critical thinking and scientific misconceptions.
I thought my students would get a kick out of this photo.
I'm certain that all regular Sandwalk readers know what I'm talking about but just in case there's any new readers who don't get it, here's a short clip from the movie.1
1. Note to IDiots and other creationists ... Gandalf is a fictional character, he doesn't exist. There are many fictional characters who appear to be powerful and menacing but that's only in stories and myths.
Last week's molecule was the drug pantoprazole, a proton pump inhibitor used to treat excess stomach acid or acid reflux [Monday's Molecule #226 ]. The winner is Bill Gunn.
This week's molecule (left) is related to one from last April. That molecule, is one of the essential molecules in the human diet and today's molecule is the reason why. This is one of those molecules that everyone should recognize because it's a key metabolic precursor in a large number of species. This is one of those times when all you have to do is supply the common name (Merry Christmas!) and NOT the IUPAC systematic name that correctly identifies the exact molecule shown in the image. However, if anyone wants to supply the systemiac name, feel free to do so.
Email your answer to me at: Monday's Molecule #227. I'll hold off posting your answers for at least 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.)
As far as I'm concerned, the "Modern Synthesis" has been replaced by modern evolutionary theory that incorporates Nearly-Neutral Theory and random genetic drift as an important mechanism of evolution [see Is the "Modern Synthesis" effectively dead? ]. This extension, and replacement, of the 1940s version of evolutionary theory took place in mainly in the 1970s.
If I'm correct, then why all the fuss in the 21st century about extending the Modern Synthesis?
I think there are two things going on here. First, there are a bunch of biologists who want to incorporate their favorite fad into modern evolutionary theory. They think that their ideas are so revolutionary that this requires an extensive revision of evolutionary theory. Second, those biologists seem to have been asleep during the 1970s when the Modern Synthesis died so they are fighting a strawman.
The "Modern Synthesis," or modern evolutionary synthesis, refers to a framework of evolutionary theory developed and promoted by prominent biologists in the 1940s. The term comes from the subtitle of a 1942 book by Julian Huxley. The central theme was the integration of "classic" evolution with population genetics.
Although the original version was fairly broad, the later versions of the "Modern Synthesis" were much less so. The so-called "hardening" of the Modern Synthesis has been documented by many historians; notably, Stephen Jay Gould. By the time of the Darwin Centennial (1959) most biologists thought of the "Modern Synthesis" as a form of Darwinism + population genetics where natural selection was pretty much the only game in town.
Chris Mooney thinks that humans have certain innate tendencies that predispose them to believe in god(s) and reject evolution. That's why there's such a strong correlation between a fundamentalist religious belief and rejection of science, according to Mooney.
These innate tendencies are part of our evolutionary history thus providing an evolutionary excuse explanation of religion. It's interesting that these behaviors seem to tilt in favor of the Judeo-Christian gods and not Buddhist or Taoist philosophy. It's also quite interesting that million and millions of non-believers don't seem to have had any great difficulty "overcoming" their genetic predispositions.
You don't suppose that it could be religious brain-washing education that makes people think teleologically or adopt essentialist perspectives rather than the other way around? And what about dualism? Is that an innate belief or does religion teach you to think you have a soul? Nah, that would be too simple [Why don't people accept evolution?].
Here's Hemant Mehta explaining why people Americans have a natural inclination to believe in god(s) and not in evolution [7 Reasons Why People Believe in God and Don’t Accept Evolution].
