Alvin Plantinga is a famous philosopher who is widely respected and seems to be able to publish in all the right places. He is a theist (Calvinist) and for a long time he was at the University of Notre Dame in Indiana (USA). Since his retirement from there, he has taken a position at Calvin College.
Plantinga has long advocated the accommodationist position from the perspective of Christian apologetics. I bought his latest book, Where the Conflict Really Lies, because I'm interested in the conflict between science and religion.
I've been struggling for weeks with how to explain Plantinga's case. My problem was that I found the whole book quite ridiculous and it seemed to me that Plantina's idea of logic and rationality was much closer to kindergarten philosophy than to something one might expect from a distinguished scholar. I hesitated to say that out loud because it sounds very condescending coming from a scientist.
I had to be missing something. There must be some sophisticated philosophy in there somewhere and I just wasn't getting it. I couldn't post.
As I'm sure you can imagine, the Intelligent Design Creationists are delighted with the ENCODE publicity. This is a case where some expert scientists support one of their pet beliefs; namely, that there's no such thing as junk DNA. The IDiots tend not to talk about other expert evolutionary biologists who disagree with them—those experts are biased Darwinists or are part of a vast conspiracy to mislead the public.
You might think that distinguishing between these two types of expert scientists would be a real challenge and you would be right. Let's watch how David Klinghoffer manoeuvres through this logical minefield at: ENCODE Results Separate Science Advocates from Propagandists. He begins with ....
"I must say," observes an email correspondent of ours, who is also a biologist, "I'm getting a kick out of watching evolutionary biologists attack molecular biologists for 'hyping' the ENCODE results."
True, and equally enjoyable -- in the sense of confirming something you strongly suspected already -- is seeing the way the ENCODE news has drawn a bright line between voices in the science world that care about science and those that are more focussed on the politics of science, even as they profess otherwise.
It's no secret that I'm a big fan of Stephen Jay Gould. I'm also a big fan of Sydney Brenner. Here's Gould writing in The Structure of Evolutionary Theory (pages 1269-1270). This is long and complicated but if you want to understand junk DNA and why it conflicts with Darwinism, then you've got to make the effort. I especially like the idea that Gould understands the difference between junk DNA, which can't be explained by any adaptive mechanism, and "selfish DNA," which isn't junk and has a Darwinian explanation. Many people don't get this.
Gould and Brenner are talking about repetitive DNA. This includes highly repetitive sequences of simple repeats and moderately repetitive sequences that include the transposons.
Some people have trouble understanding the difference between Darwinism and modern evolutionary theory.
In spite of the fact that he has been dead for a decade, Stephen Jay Gould remains the authority on challenges to classical Darwinism and the hardened version of the Modern Synthesis (sometimes referred to as Neo-Darwinism).
If you really want to understand this issue then you have to read The Structure of Evolutionary Theory. One of my criticism of those who would overthrow modern evolutionary theory is that they are often completely ignorant of the work done by Gould and his allies and they end up attacking a strawman version of modern evolutionary theory.
Gould described the essential features of Darwinism in many of his writings. The most important feature is an emphasis on natural selection as the mechanism of evolution. In much of his work Gould emphasizes the roles of contingency, constraints, and non-gradualistic evolution as extensions of Darwinism. However, he doesn't forget direct challenges to Darwinism in the form of nonadaptive mechanisms that don't, under any circumstances, fit within the Darwinian framework.
These are complicated issues and that partially explains why so many people have not been able to follow Gould's reasoning. He doesn't help by using a writing style that requires your full attention. The advantage of that style is that he doesn't dumb down the subject and he covers all the exceptions and qualifications.
Here's Gould explaining why some features could arise as one form of adaptation then shift to serve another adaptive role (functional shift) (page 1246-1247). These features are called exaptations since they did not originally arise as adaptation to their present role. (Think of a defective transposon that becomes a regulatory sequence.)
Nevertheless, also emphasized throughout, ... the basic concept of exaptation remains consistent with orthodox Darwinism (while expanding its purview and adding some structural clarification and sophistication) for an obvious reason: the principle of quirky functional shift does not challenge the control of evolution by natural selection as an adaptational process. Unpredictable shift of function may establish the ground of contingency, and may imply a rule for structural constraints upon phyletic pathways. But this principle does not undermine the functionalist basics of evolutionary change because features so effected remain adaptive throughout: they originate from one function (presumably by natural selection), and then undergo quirky shift to a different utility.
However, the principle of functional shift, ... implies a disarmingly simple and logical extension that does challenge the role of Darwinian mechanics and functionalist control over evolutionary change. Ironically, the very simplicity of the argument has often led to its dismissal as too obvious to hold any theoretical importance—a "feeling" that I shall try to refute in this section, and whose disproof represents an important step in the central logic of this book.
The deeper challenge posed to orthodox Darwinism by the principle of functional shift flows from the implication that, if current utility does not reveal the reasons for hisorical origin, then these initial reasons need not be adaptational or functional at all—for features with current adoptive status may have originated from nonadaptive reasons in an ancestral form. In other words, and in the terminology of table 11-1, when certain aptations rack rank as exaptations rather than adaptations, the coopted source will be identifiable as an ancestral structure with either adaptive origins (for a different function) or nonadaptive origins (for no function at all). ...
The general conclusion may be stated in a simple manner, but I believe that the resulting implications for evolutionary theory are both profound and curiously underappreciated: If many features that operate as adaptations under present regimes of natural selection were exapted from ancestral features with nonadaptive origins—and were not built as adaptations for their current use (or exapted from ancestral features with adaptive origins for different functions)—then we cannot explain all the pathways of evolutionary change under functionalist mechanics of the theory of natural selection. Instead, we must allow that many important (and currently adaptive) traits originated for nonadaptive reasons that cannot be attributed to the direct action of natural selection at all and, moreover, cannot be inferred from the exaptive utility of the trait in living species. Because the subject of evolutionary biology must engage many critical questions about the origins of features, and cannot be confined to the study of current utilities and selective regimes, nonadaptationist themes therefore assume an important role in a full account of life's history and the mechanisms of evolutionary change.
In other words, lots of things can't be explained by Darwinism even if they look adaptive today.
Last week's molecules were the four common nuleosides in DNA [Monday's Molecule #185]. The winner was Matt Talarico.
This week I'm asking you to identify a complex structure made up of eight different components (top) plus one other (bottom). Name the structure making sure to be as specific as possible, Name the none components.
Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post 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 comment.)
One of the good things to come out of this ENCODE/junk DNA fiasco is that I've discovered a number of excellent scientists who aren't afraid to speak out on behalf of science. One of them is Mike White, a systems biologist at the Center for Genome Sciences and Systems Biology, Washington Univ. School of Medicine, St. Louis (USA). He blogs at The Finch & Pea.
Mike published an impressive article on the Huffington Post a few days ago. This is a must-read for anyone interested in the controversy over junk DNA: A Genome-Sized Media Failure. Here's part of what he says ...
If you read anything that emerged from the ENCODE media blitz, you were probably told some version of the "junk DNA is debunked" story. It goes like this: When scientists realized that classical, protein-encoding genes make up less than 2% of the human genome, they simply assumed, in a fit of hubris, that the rest of our DNA was useless junk. (You might have also heard this from your high school or college teacher. Your teacher was wrong.) Along came the ENCODE consortium, which found that, far from being useless, junk DNA is packed with functionality. And so everything scientists thought they knew about the genome was wrong, wrong wrong.
The Washington Post headline read, "'Junk DNA' concept debunked by new analysis of human genome." The New York Times wrote that "The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as 'junk' but that turn out to play critical roles in controlling how cells, organs and other tissues behave." Influenced by misleading press releases and statements by scientists, story after story suggested that debunking junk DNA was the main result of the ENCODE studies. These stories failed us all in three major ways: they distorted the science done before ENCODE, they obscured the real significance of the ENCODE project, and most crucially, they mislead the public on how science really works.
What you should really know about the concept of junk DNA is that, first, it was not based on what scientists didn't know, but rather on what they did know about the genome; and second, that concept has held up quite well, even in light of the ENCODE results.
Way to go, Mike!
In the past week, lot's of scientists have demonstrated that they don't know what they're talking about when they make statements about junk DNA. I don't expect any of those scientists to apologize for misleading the public. After all, their statements were born of ignorance and that same ignorance prevents them from learning the truth, even now.
However, I do expect lots of science journalists to write follow-up articles correcting the misinformation that they have propagated. That's their job.
David Klinghoffer showed up in the comments on James Shapiro Claims Credit for Predicting That Junk DNA Is Actually Part of a "highly sophisticated information storage organelle" to ask about creationism.
He didn't like the fact that I define "creationism" as belief in a creator and anyone who believes in a creator is a creationist. I identified several flavors of creationism including Young Earth Creationism, Intelligent Design Creationism, and Theistic Evolution Creationism. This is exactly the same sort of definition used by many people and it's the one described in the Wikipedia article on creationism. (It has even more flavors.)
David Klinghoffer didn't like that so he decided to make an issue of it by posting on Evolution News & Views: What Is a "Creationist"? Let's take a look at what he says in order to learn a little more about the creationist mindset.
Lots of people don't understand the Central Dogma of Molecular Biology and that's probably why there are so many articles announcing its death. The article and book by James Shapiro is just one example [Revisiting the Central Dogma in the 21st Century].
The correct version of the Central Dogma of Molecular Biology is .... [see Basic Concepts: The Central Dogma of Molecular Biology]
... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)
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. (F.H.C. Crick, 1970)
Eugene Koonin has an article in Biology Direct entitled Does the central dogma still stand (Koonin, 2012).
The IDiots (e.g. Tom Bethell) over at Evolution News & Views are gloating about a comment made on The Wall Street Journal website [Why ENCODE Is a Significant Defeat for Darwinism].
The WSJ article is: Groupthink Science And That 'Junk DNA'.
Anyone with even the slightest understanding of the evolutionary process knows that evolution is too relentlessly efficient to have allowed most, or even large sections, of DNA to be "junk" ("'Junk DNA' Theory Debunked," U.S. News, Sept. 6). Any intelligent scientist would have simply said, "I don't know."
Unfortunately, this says something important about the quality of contemporary Ph.Ds. Groupthink has become pervasive in part because of how research is now financed: grants. The disillusioning sociological aspects of scientific research that Thomas Kuhn identified more than four decades ago have become more pronounced, not less.
Tom Shillock
Portland, Ore.
This is exactly backwards, in my opinion. The real problem is that many scientists think, incorrectly, that natural selection would have removed all junk DNA so they are looking for reasons why it isn't junk. If they can't find evidence then they just make up a story or re-define the word "function." They don't have even the slightest understanding of evolution, just like Tom Shillock.
UPDATE: Shapiro and Sternberg Anticipated the Fall of Junk DNA.
Do you remember James Shaprio? He's the University of Chicago scientist who claims to have discovered a new theory of evolution in his book evolution: A View from the 21st Century [see my review in NCSE Reports]. The book criticizes the old hardened version of the Modern Synthesis and never mentions things like random genetic drift or Nearly-Neutral Theory. It's difficult to imagine how someone could criticize evolutionary theory without understanding population genetics but he managed to pull it off.
You might also recall that he's the scientist who criticized the Central Dogma of Molecular Biology when he clearly didn't understand it [Revisiting the Central Dogma in the 21st Century]. I was shocked to learn that he had published a paper with the title "Revisiting the Central Dogma in the 21st Century" without ever bothering to read the literature to find out how Francis Crick actually defined the Central Dogma. (In fact, Shapiro misrepresented Crick's view.) It goes to show you how silly you look when you criticize something you don't understand.
Casey Luskin has devoted an entire post to discussing my views on junk DNA. I'm flattered. Read it at: What an Evolution Advocate's Response to the ENCODE Project Tells Us about the Evolution Debate.
Let's look at how the IDiots are responding to this publicity fiasco. Casey Luskin begins with ...
University of Toronto biochemistry professor Larry Moran is not happy with the results of the ENCODE project, which report evidence of "biochemical functions for 80% of the genome." Other evolution-defenders are trying to dismiss this paper as mere "hype".
Yes that's right -- we're supposed to ignore the intentionally unambiguous abstract of an 18-page Nature paper, the lead out of 30 other simultaneous papers from this project, co-authored by literally hundreds of leading scientists worldwide, because it's "hype." (Read the last two or so pages of the main Nature paper to see the uncommonly long list of international scientists who were involved with this project, and co-authored this paper.) Larry Moran and other vocal Internet evolution-activists are welcome to disagree and protest these conclusions, but it's clear that the consensus of molecular biologists -- people who actually study how the genome works -- now believe that the idea of "junk DNA" is essentially wrong.
