A recent article in Nature reminded me of the importance of definitions. The article discusses evolution and evolutionary algorithms in a special issue on machine learning (Eiben and Smith, 2015). I think we all know that "evolutionary" algorithms are based on natural selection and we all know that there's more to evolution than just adaptation. It's too late to change the name of these procedures in computer science but at the very least I expect computer scientists to be aware of the difference between their procedures and real evolution.
In this paper, there's a section on "how evolutionary computation compares with natural evolution." The authors consistently use "evolution" as a synonym for "selection" or "adaptation" and they seem to be unaware of any other mechanism of evolution.
In one sense, it's okay to conflate "evolution" and "adaptation" in computer science but if that error reflects and perpetuates a fundamental misunderstanding of the nature of real biological evolution then perhaps it's time to rename these algorithms "adpatation algorithms."
Eiben, A.E. and Smith, J. (2015) From evolutionary computation to the evolution of things. Nature 521: 476–482. [doi:10.1038/nature14544]
If students are going to learn critical thinking about evolution, they need to be exposed to controversial views and challenges concerning evolution, the history of life, and evolutionary theory. The Discovery Institute agrees with this strategy. It has published a handbook called The Educator's Briefing Packet that claims to outline what teachers should cover when they teach evolution.
As you might imagine, the Discovery Institute concentrates on showing that evolution is wrong rather than focusing on whether Intelligent Design Creationism is correct. That's partly because they don't want to advocate teaching Intelligent Design Creationism in schools.
They explain the strategy on page 7 ...
Teaching this subject objectively means presenting both the scientific evidence for and against neo-Darwinian evolution. This does not mean simply criticizing evolution or only presenting the case against the neo-Darwinian model. Rather, objective instruction means:
Fully teaching the evidence for neo-Darwinian evolution from the textbook.
Covering the entire required curriculum.
Helping students understand the scientific arguments in favor of neo-Darwinian evolution as well as the scientific criticisms as they are presented in the scientific literature.
This strategy implies that students are taught something called "Neo-Darwinism" in class. Here's how they define Neo-Darwinism.
Darwin argued that natural selection had the power to produce fundamentally new forms of life. Together, the ideas of universal common descent and natural selection form the core of Darwinian evolutionary theory. "Neo-Darwinian" evolution combines our knowledge of DNA and genetics to claim that mutations in DNA provide the variation upon which natural selection acts.
Right away we have a problem since many textbooks do not describe modern evolutionary theory in this manner. The handbook doesn't explain what teachers should do if they are teaching modern evolutionarytheory instead of Neo-Darwinism but I think it's pretty obvious what the Intelligent Design Creationists would recommend if they actually understood evolution. They would still recommend criticizing it.
In a real classroom run by competent teachers, the teachers would begin by pointing out that many creationist organizations have an incorrect and distorted view of evolution and they would pass out copies of the handbook. Then they would discuss why the Discovery Institute is promoting nonsense about evolution when they claim to be experts on the subject. The class could analyze the difference between the DI version of evolution that only covers natural selection and the modern view that includes random genetic drift and population genetics. This would be a highly effective way of teaching critical thinking and exposing students to one of the most common misconceptions about evolution.
In the right hands, this could lead to a discussion about why creationists seem to resist being educated about evolution even though the correct information is readily available on the internet. The class could learn about confirmation bias, begging the question, false dichotomy, and the strawman fallacy using examples from the handbook.
The Educator's Briefing Packet contains lots of other myths and misrepresentations that are commonly found in creationist literature. Debunking and correcting these examples can also be used to foster critical thinking and teach the truth about evolution. I'd like to thank the Discovery Institute for putting them all in one place. I'd love to spend a few days in a senior high school class showing the students why these are myths and/or misconceptions.
Here's the list1 ...
Genetics:Mutations Tend to Cause Harm and Do Not Build Complexity. Darwinian evolution relies on random mutations which are acted on by natural selection, a blind and unguided process that has no goals. Such a random and undirected process tends to harm organisms. They do not seem capable of improving organisms or building new complex systems.
Biochemistry:Unguided and Random Processes Cannot Produce Cellular Complexity.Cells contain incredible complexity, similar to machine technology but dwarfing anything produced by humans. Cells use circuits, miniature motors, feedback loops, encoded language, and even error-checking machinery which decodes and repairs our DNA. Many scientists have claimed that Darwinian evolution does not appear capable of building this type of integrated complexity.
Paleontology:The Fossil Record Lacks Intermediate Fossils. The fossil record’s overall pattern is one of abrupt explosions of new biological forms and possible candidates for evolutionary transitions are the exception, not the rule. For example, the Cambrian Explosion is an event in life’s history over 500 million years ago where nearly all the major body plans of animals appear in a geological instant without any apparent evolutionary precursors.
Taxonomy:Biologists Have Failed to Construct Darwin’s Tree of Life. Biologists hoped that DNA evidence would reveal a grand tree of life where all organisms are clearly related. Yet trees describing the alleged ancestral relationships between organisms based upon one gene or biological characteristic commonly conflict with trees based upon a different gene or characteristic. This implies a challenge to universal common descent, the hypothesis that all organisms share a single common ancestor.
Chemistry:The Chemical Origin of Life Remains an Unsolved Mystery. The mystery of the origin of life is unsolved, and all existing theories of chemical evolution face major problems. Basic deficiencies in chemical evolution include a lack of explanation for how a primordial soup could arise on the early earth’s hostile environment, or how the information required for life could be generated by blind chemical reactions.
In all theses cases we have situations where the Discovery Institute is challenging the views of the vast majority of scientists who have devoted careers to studying these issues. That's a good opportunity to teach students how they should go about deciding who to believe when faced with scientific questions. Should you believe doctors or movie actors when trying to decide whether to vaccinate your children? Should you believe climatologists or politicians about climate change? Should you believe evolutionary biologists or religious leaders when trying to decide if evolution is true?
However, I'm not sure if we could ever have much of a discussion about these issues because the latest "ID the Future" podcast features a discussion between Nate Herbst and Casy Luskin about students who question evolution in class. As it turns out, many of those students have bad experiences because they end up feeling stupid when they challenge science in class. Luskin and Herbst recommend that they hide their beliefs in order to avoid such embarrassment [see Listen: Good Advice for Students Learning about Evolution]. Maybe that's not always a good idea, however, because Herbst and Luskin also have some stories about how they stumped the professors and caused them to change their minds about evolution and origins.
1. I wonder who they used as an authority on evolution in order to make up these questions?
Napoleon's Army of the North had crossed the Belgian frontier and was advancing toward Brussels. Napoleon had surprised the allied armies with his rapid advance and now they choose the risky strategy of a forward concentration in the face of an enemy attack. The Prussians had an easier task since they choose to concentrate their army at Ligny covering their supply lines to the East. The forward outposts fall back to Ligny under pressure from the French right under Grouchy. [see Battle of Waterloo]
On Thursday evening Wellington attended a ball given by the Duchess of Richmond in Brussels and it wasn't until the early hours of Friday the 16th that he gave orders to concentrate the Anglo-Dutch army at Quatre-Bras. Prince Orange was ordered to hold Quatre-Bras until the rest of the army arrived.
Wellington's strategy was to stay in contact with the Prussians at Ligny where the combined armies could defeat Napoleon. Napoleon's goal was to prevent the allied armies from supporting each other and crush one of them with overwhelming superiority of numbers. As it turned out, neither strategy succeeded on Friday, June 16th.
Ney held the Anglo-Dutch troops at bay around Quatre-Bras in a tough battle with heavy losses. He eventually took the crossroads at Quatre-Bras only to be driven back when Wellington arrived with fresh troops. Meanwhile, Napoloeon attacked the Prussians at Ligny with Grouchy's corps and the reserve that had been under his personal command. The Prussians were defeated but not destroyed [Battle of Ligny].
The map (left) shows the positions on Friday evening as the Prussian center collapses. It also shows the wandering of D'Erlon's corps that never got into either battle. It it had attacked the flank of the Prussian army Napoleon might have gained a decisive victory and if it had supported Ney it could have prevented Wellington's army from using the crossroads at Quatre-Bras. [see Waterloo: Myth and Reality]
Now comes one of the decisive moments of the Waterloo campaign. Blücher's Prussians retreated in orderly fashion on Wavre where he could remain in touch with Wellington who was forced to fall back to Wavre after the position at Quatre-Bras became untenable. Grouchy was ordered to pursue Blücher and prevent the Prussians from supporting the Anglo-Dutch army. Grouchy failed to do this because his corps did not move quickly and was confused about the direction of the Prussian retreat. As we shall see, Grouchy's failure is blamed for the defeat at Waterloo two days later.
Meanwhile, Wellington was able to fall back to a defensive position at Waterloo where he waited for the French army.
"Ligny by Ernest Crofts (1875). This representation of the battle shows Napoleon surrounded by his staff surveying the battlefield while columns of infantry advance to the front. The windmill at Brye on a hill, north west from Ligny, was a good vantage point and Blücher made it his headquarters during the battle, hence in this context it is an iconic symbol of Napoleon's victory." [Battle of Ligny]
Summoned to Waterloo: Brussels, dawn of June 16, 1815 by Robert Alexander Hillingford. Officers leaving the Duchess of Richmond's ball.
Quatre Bras (Black Watch at Bay) by William Barnes Wollen
Michael Behe first proposed the idea of "irreducible complexity" in Darwin's Black Box back in 1996. He defines it as ...
By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.
That's interesting. Let's look at the paper to see what it says. The reference is Muskhelishvili, G. and Travers, A. (2015) and the relevant passage is on page 4556.
Thus, the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organisational complexity of the genetic regulation system of any cell. Put another way, this implies that the structural dynamics of the chromosome must be fully convertible into its genetic expression and vice versa. Since the DNA is an essential carrier of genetic information, the fundamental question is how this self-referential organisation is encoded in the sequence of the DNA polymer.
What they are saying is that proper gene regulation requires both transcription factors AND a particular organization of the chromosome that facilitates transcription. It also requires input from metabolic pathways. If any one of these three things are missing then the cell cannot regulate gene expression in the same manner as cells where all three are present.
The authors then go on to discuss how this system could have evolved. Look at Figure 3 of their paper (below) where they clearly show the relationships between transcription, supercoiling, and small regulatory molecules. The paper describes their belief that this "irreducible organisational complexity" arose by evolution from these three existing features.
So, these authors are using "irreducible complexity" to describe a system that's clearly possible according to their understanding of evolution. Uncommon Descent states that this is exactly the same sense in which the term is used by Michael Behe. In fact, it quotes a physicist named David Snoke who says,
Three comments: 1) the authors are “serious” scientists, not fringe people. 2) They are using “irreducible complexity” in the same sense as Behe. This is not a case of accidental use of the same phrase to mean something different. Their term “holistic” is another way of saying the same thing, that the system requires all of its parts to work. 3) This “holistic” approach is one that is becoming common in systems biology. I have a paper coming out on that, in the works.
We've been telling Intelligent Design Creationists for years that irreducibly complex systems can easily arise by naturalistic processes (i.e. evolution). I'm really glad that they have finally seen the light.
That should be the end of any more posts saying that irreducibly complex systems can't evolve.
(Not holding my breath.)
Muskhelishvili, G. and Travers, A. (2015) Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information. Cell. Molec. Life Sci. 70:4555-4567. [Abstract]
It was 200 years ago today that Napoleon's army crossed the Belgian border at Charleroi and advanced on Quatre-Bras in order to split the Prussian and British armies. By occupying the central position, Napoleon hoped to defeat each army separately and occupy Brussels and the channel ports.
Neither Blücher nor Wellington were expecting such a rapid advance so Napoleon gained the element of surprise in the opening days of the campaign [Battle of Waterloo].
The Prussian outposts were quickly overrun and the army was ordered to assemble at Ligny. Napoleon's right, under Marshal Grouchy, pursued the retreating Prussians while the left, under Marshal Ney, marched on Quatre Bras in order to prevent the British army from uniting with the Prussians.
It's particularly important to note that just presenting correct scientific facts isn't enough to correct myths and misinformation. You need to discuss the misinformation and show why it is wrong. This method is supported by numerous studies.
What it means is that if you want to correct misinformation about evolution, you have to address the false beliefs of your audience. You can't correct the beliefs of evolution deniers without bringing up the various forms of creationism and showing why they are wrong. In other words, teach the controversy.
Some of my American friends tell me that this is legally impossible in American schools. If they are right, then creationism wins. Ironically, by using the courts to keep all mention of creationism out of the public schools, these friends are playing right into the hands of the anti-evolution crowd and making it impossible to debunk their myths and misconceptions.
The meeting is on Sunday evening at 7:00 pm at The Franklin House, 263 Queen St. in Sreetsville. This is a relatively new Café Scientifique so new people are more than welcome. The talk is very informal (no slides or powerpoint) and there will be lots of time for discussion and debate. I'm told that various "refreshments" will be available to help make the evening more enjoyable.
Stephen Jay Gould wrote a book about the role of chance in evolution. He called it "Wonderful Life." On the surface it's a book about the Burgess Shale and the Cambrian explosion but there's a powerful message as well. Gould is interested in why some species survive while others go extinct. Are the survivors better adapted than the losers of is it a matter of luck? We could answer this question if we could carry out an experiment.
I call this experiment "replaying life's tape." You press the rewind button and, making sure you thoroughly erase everything that actually happens, go back to any time and place in the past—say, to the seas of the Burgess Shale. Then let the tape run again and see if the repetition looks at all like the original. If each replay strongly resembles life's actual pathway, then we must conclude that what really happened pretty much had to occur. But suppose that the experimental versions all yield sensible results strikingly different from the actual history of life? What could we then say about the predictability of self-conscious intelligence? or of mammals? or of vertebrates? or of life on land? or simply of multicellular persistence for 600 million years?
Stephen Jay Gould (1989) pp. 48-50
Here's a YouTube video of a talk by Michael Lynch from February 2015. He was talking at Darwin Week at the National Institute for Mathematical and Biological Synthesis at the University of Tennessee (USA).
The talk begins with a warning that evolution has gone beyond Darwinism. Lynch emphasizes, "Mutation, drift, and the origin of subcellular features." If you haven't been able to follow the discussion on the perils of adaptationism, then watch this lecture to get a sense of what it's all about.
I'm a big fan of Michael Lynch and I hope you will also be a fan after you learn more about his views.
Peggy Whitson is a biochemist. She did her Ph.D. with Kathleen Mathews at Rice University in Houston, Texas, USA. I frequently refer to her work on the lac repressor and its interaction with lac operator sequences [see Repression of the lac Operon]. Here are some of her papers. Once you understand this stuff, you are in a better position to judge the ENCODE results and the role of spurious binding sites.
Hsieh, W.T., Whitson, P.A., Matthews, K.S., and Wells, R.D. (1987) Influence of sequence and distance between two operators on interaction with the lac repressor. Journal of Biological Chemistry, 262: 14583-14591.
The influence of additional operator or pseudooperator sequences on the lactose repressor-operator interaction has been investigated. Results of kinetic and equilibrium binding measurements suggest an important in vivo role for the Z-gene pseudooperator in repressor-operator binding; the formation of a ternary, looped complex is indicated by the influence of secondary operator sites on binding parameters. Although the binding affinity of the Z-gene pseudooperator [Oz] is only approximately 1/30 that observed for the primary operator [O], the binding affinity to DNA containing both Oz and O is significantly higher than either sequence alone or the sum of the two. This synergistic effect is enhanced further by replacing the pseudooperator sequence [Oz] with the primary operator sequence and results in an even stronger ternary complex in plasmids with duplicate primary sites. The distance between the center of the two primary operators affects the formation of a ternary complex in the linear DNA molecules. Decreased dissociation rate constants were observed with spacing of operator-like sequences between 300 and 500 base pairs (bp). Minimal influence of the second operator on repressor binding is observed when the operators are separated by approximately 4000 or approximately 100 bp. The significant influence of distance on kinetic and equilibrium parameters was demonstrated by measurements on plasmid pRW1511 [Oi-O-PL-Oz] cleaved with restriction enzymes either in the polylinker region to place Oi-O and Oz on opposite ends of the linear plasmid or outside this region to maintain the sites within 500 bp. These results are consistent with the formation of operator-repressor-pseudooperator ternary complex to generate a looped DNA structure.
Whitson, P.A., Hsieh, W.T., Wells, R.D., and Matthews, K.S. (1987) Supercoiling facilitates lac operator-repressor-pseudooperator interactions. Journal of Biological Chemistry, 262:4943-4946.
The binding affinity of the Escherichia coli lactose repressor to operator-containing plasmids was increased by negative supercoiling of the DNA. The increased affinities observed were dependent on the sequence context of the DNA as well as the degree of supercoiling. Dissociation rate constants for plasmids containing a single operator site decreased as a function of the negative supercoil density. However, the presence of pseudooperators in the plasmid DNA in addition to the primary operator sequence resulted in a significant decrease in the operator-plasmid dissociation rate at higher negative supercoil densities. Approximately eight ionic interactions were determined for both the supercoiled plasmids and the linear DNAs examined. These results suggest that the stabilization provided by the topology of supercoiled DNA affects the nonionic component of the protein-DNA interaction. The ability to form a ternary complex of protein with two DNA segments is increased by the presence of multiple operator-like sites on the DNA. Furthermore, supercoiling DNA with multiple operator-like sequences profoundly diminishes the dissociation rate and results in a remarkably stable ternary, presumably looped complex (t1/2 approximately 28 h). These data suggest a critical role in vivo for DNA topology and pseudooperator(s) in transcriptional regulation of the lac operon.
Whitson, P.A., Hsieh, W.T., Wells, R.D., and Matthews, K.S. (1987) Influence of supercoiling and sequence context on operator DNA binding with lac repressor. Journal of Biological Chemistry, 262(30), 14592-14599.
The dissociation of the repressor-operator complex from a series of negatively supercoiled plasmid DNAs was examined as a function of the sequence context, orientation, and spacing. The plasmids were grouped into four classes, each with common sequence context. The highest dissociation rate constants were observed for the plasmids containing only a single operator (or pseudooperator) sequence, while approximately 10-fold lower rate constants were measured for plasmids with the I gene pseudooperator in conjunction with either the Z gene pseudooperator or the primary operator. Comparison of the behavior of these two classes of plasmids demonstrated the importance of two operator sequences and supported a model of DNA loop formation to stabilize the repressor-operator complex (Whitson, P. A., and Matthews, K. S. (1986) Biochemistry 25, 3845-3852; Whitson, P. A., Olson, J. S., and Matthews, K. S. (1986) Biochemistry 25, 3852-3858; Whitson, P. A., Hsieh, W. T., Wells, R. D., and Matthews, K. S. (1987) J. Biol. Chem. 262, 4943-4946; Krämer, H., Niemöller, M., Amouyal, M., Revet, B., von Wilcken-Bergmann, B., and Müller-Hill, B. (1987) EMBO J. 6, 1481-1491). The third class, with intermediate dissociation rate constants, was comprised of plasmids which contained the primary operator and the higher affinity pseudooperator normally located in the Z gene. Neither the additional presence of the I gene pseudooperator nor the orientation of the primary operator relative to the Z gene pseudooperator significantly affected the dissociation rate constants. The binding characteristics of this group of plasmids demonstrated the essential role of the Z gene pseudooperator in the formation of intramolecular ternary complex and suggested an in vivo function for this pseudooperator. Plasmids containing two primary operator sequences were the class with lowest dissociation rate constants from lac repressor, and minimal effects of salt or spacing on dissociation of this class were observed. These data are consistent with formation of an intramolecular complex with a looped DNA segment stabilized by the combination of increased local concentration of binding sites and torsional stresses on the DNA which favor binding in supercoiled DNA.
Whitson, P.A., and Matthews, K.S. (1986) Dissociation of the lactose repressor-operator DNA complex: Effects of size and sequence context of operator-containing DNA. Biochemistry, 25:3845-3852.
The dissociation kinetics for repressor-32P-labeled operator DNA have been examined by adding unlabeled operator DNA to trap released repressor or by adding a small volume of concentrated salt solution to shift the Kd of repressor-operator interaction. The dissociation rate constant for pLA 322-8, an operator-containing derivative of pBR 322, was 2.4 × 10-3 s-1 in 0.15 M KCl. The dissociation rate constant at 0.15 M KC1 for both Xplac and pIQ, each of which contain two pseudooperator sequences, was ~6 × l0-4 s-1. Elimination of Elimination flanking nonspecific DNA sequences by use of a 40 base pair operator-containing DNA fragment yielded a dissociation rate constant of 9.3 × 10-3 s-l. The size and salt dependences of the rate constants suggest that dissociation occurs as a multistep process. The data for all the DNAs examined are consistent with a sliding mechanism of facilitated diffusion to/from the operator site. The ability to form a ternary complex of two operators per repressor, determined by stoichiometry measurements, and the diminished dissociation rates in the presence of intramolecular nonspecific and pseudooperator DNA sites suggest the formation of an intramolecular ternary complex. The salt dependence of the dissociation rate constant for pLA 322-8 at high salt concentrations converges with that for a 40 base pair operator. The similarity in dissociation rate constants for pLA 322-8 and a 40 base pair operator fragment under these conditions indicates a common dissociation mechanism from a primary operator site on the repressor.
There's an interesting discussion going on at Uncommon Descent. Barry Arrington is wondering who to believe when it comes to evolutionary theory and many of the ID regulars have chimed in [Authority in evolutionary theory]. Clearly, this is an important issue for them because they don't want to be accused of not understanding evolution. They want to protect their version of Darwinism.
They seemed to have reached a consensus. They say you can't be an authority on evolutionary theory unless you have published a scientific paper on the subject in the last decade or so. What this means is that they can dismiss the views of many evolution supporters because we don't meet the minimum qualification.1 Our view on what is, and isn't, proper evolutionary theory are just personal opinions so they don't count.
Unfortunately for them, this also eliminates Barry Arrington, Vincent Torley, Denyse O'Leary, Casey Luskin, Stephen Meyer, Jonathan Wells, Jonathan McLatchie, Michael Behe, Salvador Cordova, Jonathan Bartlet, Michael Egnor, Cornelius Hunter, Gordon Elliot Mullings, Ann Gauger and just about everyone else in the Intelligent Design Creationist camp. If they stick to their guns, it means that nothing posted on the ID blogs is anything more than a personal opinion by someone who is not an authority on evolutionary theory.
So, who are they going to believe now? My first thought is that this can only be good for the evolution side since people who publish scientific articles on evolutionary theory are not ID supporters. It means that the Intelligent Design Creationists are obligated to trust many prominent evolution biologists as authorities while dismissing most of their own crowd.
I don't think that's what they have in mind. What they have in mind is that people like Jim Shapiro and other critics of modern evolutionary theory are the real authorities because they have published in the scientific literature. I suppose it's part of a strategy to maintain the illusion that "Darwinism" is deeply flawed.
The one good thing that will come out of this discussion, I'm sure, is that the number of posts and comments on their blogs will be greatly reduced since the general consensus is that none of them are authorities on the subject of evolution. Lot's of people are going to have to shut up because they haven't published anything on evolutionary theory.2
Strange, but I will miss Barry Arrington and Denyse O'Leary's attacks on evolutionary theory. They will now be criticized by their own people as non-authorities whenever they post.
1. I have never published a paper in the scientific literature on evolutionary theory.
Everybody loves Vij's. We were lucky. We arrived late at 5:20 for the first sitting when the restaurant opens at 5:30. The lineup was not as big as I've seen in the past and we were able to get seated when Vij opened up.
Left to right; Gordon Moran, Me, Chris Hogue, Jerry Coyne.
We talked about computer games. travel, India, Singapore, food, science, books, religion, evolution, politics, and solved most of the problems of the world. (Beer helps.) The food was delicious. Check out the entire meal, with photos, on Jerry's blog: Noms: Vij’s Indian restaurant in Vancouver.
My copy of Junk DNA by Nessa Carey has arrived and I'm working my way through it. It really is as bad as we imagined.
Here's an example (pp. 34-36). She describes a situation where an angry baboon might smash an expensive watch. If you hide the watch in large rolls of insulation, the baboon is less likely to cause damage.
And the insulation theory of junk DNA was built on the same premise. The genes that code for proteins are incredibly important. They have been subjected to high levels of evolutionary pressure, so that in any given organism, the individual protein sequence is as good as it's likely to get. A mutation in DNA—a change in a base pair—that changes the protein sequence is unlikely to make a protein more effective. It's more likely that a mutation will interfere with a protein's function or activity in a way that has negative consequences.
The problem is that our genome is constantly bombarded by potentially damaging stimuli in our environment. We sometimes think of this as a modern phenomenon, especially when we consider radiation from disasters such as those at the Chernobyl or Fukushima nuclear plants. But in reality this has been an issue throughout human existence. From ultraviolet radiation in sunlight to carcinogens in food, or emission of radon gas from granite rocks, we have always been assailed by potential threats to our genomic integrity. Sometimes these don't matter that much. If ultraviolet radiation causes a mutation in a skin cell, and the mutation results in the death of that cell, it's not a big deal. We have lots of skin cells; they die and are replaced all the time, and the loss of one extra is not a problem.
But if the mutation causes a cell to survive better than its neighbours, that's a step towards the development of a potential cancer, and the consequences of that can be a very big deal indeed. For example, over 75,000 new cases of melanoma are diagnosed every year in the United States, and there are nearly 10,000 deaths per year from the condition. Excessive exposure to ultraviolet radiation is a major risk factor. In evolutionary terms, mutations would be even worse if they occurred in eggs or sperm, as they may be passed on to offspring.
If we think of our genome as constantly under assault, the insulation theory of junk DNA has definite attractions. If only one in 50 or our bases is important for protein sequence because the other 49 base pairs are simply junk, then there's only a one in 50 chance that a damaging stimulus that hits a DNA molecule will actually strike an important region.
There are two obvious difficulties with the insulation theory of junk DNA. The first is that Nessa Carey believes that a lot of noncoding DNA is functional. If she's correct, that requires a great deal of insulating DNA if it's going to protect the functional parts. You can't have it both ways.
The second problem is that it doesn't pass the Onion Test. (I don't think the Onion Test is mentioned in the book but I haven't finished it yet.)
I'm sure you can come up with other objections.
Here's how I like to think of this explanation using the field of bullets analogy popularized by David Raup in his book Extinction: Bad Genes or Bad Luck.
Imagine an automatic machine gun in a pillbox firing 10 rounds a second. It swivels from left to right spraying bullets at random across a field. The enemy has only one grenade and in order to silence the machine gun, some soldier has to run across the field avoiding the bullets until he gets within throwing distance of the pillbox.
Will the soldier's chances be increased if he lines up side-by-side with 99 other soldiers (no grenades) and they all charge together? No.
What if all 100 soldiers line up in single file with the man holding the grenade at the back? That will work.
So, the only way that the insulation theory works is if the extra DNA forms a tight shield around the important functional DNA and physically protects it from cosmic rays or UV light. But this DNA is already "shielded" by a plasma membrane, a nuclear membrane, and various histones; not to mention all the other protein molecules, carbohydrates, and water molecules inside the cell. It's difficult to see what advantage DNA molecules have in direct shielding.
With the publication of Jerry Coyne's new book, Fact vs Faith, you can expect a vigorous response from people of faith and from atheist accommodationists.
Believers will invariably respond with some version of The Courtier’s Reply so, if you don't know what that is, now is the time to read PZ Meyer's blog post from 2006. The argument will be that Jerry and his supporters (I am one) are attacking a strawman version of religion. They will claim that there is a secret, sophisticated version of religion, known only to a few experts, that will counter all of Jerry's arguments.
The fact that this "sophisticated" version of theology begins with the premise that god exists seems to escape them but it turns out that that's the whole point of their argument. They just can't seem to get their head around the real question, "Is the belief in a supernatural being compatible with science as a way of knowing?"
We don't really care if the Bible is viewed as literal truth, poetry, or metaphor. It's still a fairy tale because it describes beings that don't exist.
Now, it’s no skin off my nose if Professor Moran wants to call us creationists. Frankly, I couldn’t care less. But the Intelligent Design movement has never claimed to have scientific evidence that the history of life was “directed by gods.” What we claim is that certain highly specific, functional systems which are found in living things were designed by some intelligent agent or agents. By “intelligent,” I don’t mean “humanlike”; rather, what I mean is: capable of engaging in abstract reasoning, when selecting suitable means to achieve one’s goals. In the most clear-cut Intelligent Design cases, the agent has to engage in mathematical reasoning – whether it be about squares (in the case of the monolith on the Moon in the movie 2001, whose sides are in the ration 1:4:9) or about digital code (in the case of the DNA we find in living things), or about which complex geometrical arrangements of amino acid chains will prove to be capable of performing a biologically useful task (in the case of protein design).
When I speak of the agent’s “goals,” I don’t mean the agent’s personal motives for doing something, which we have no way of inferring from the products they design; rather, I simply mean the task that the agent was attempting to perform, or the problem that they were trying to solve. Beyond that, there is nothing more that we could possibly infer about the agent, unless we were acquainted with them or with other members of their species. For instance, we cannot infer that the designer of an artifact was a sentient being (since the ability to design doesn’t imply the ability to feel) , or a material being (whatever that vague term means), or a physical entity (since there’s no reason why a designer needs to exhibit law-governed behavior), or even a complex or composite entity. To be sure, all the agents that we are familiar with possess these characteristics, but we cannot infer them from the products designed by an agent. Finally, the fact that an agent is capable of performing a variety of functions does not necessarily imply that the agent is composed of multiple detachable parts. We simply don’t know that. In short: the scientific inferences we can make about non-human designers are extremely modest.
It's really just an amazing coincidence that all Intelligent Design Creationists believe in gods. There's not a single one who thinks that the universe was designed by a bunch of immaterial, nonsentient, mathematicians who were just fooling around after the bar closed.
Do you think anyone really believes this crap? Do they?
Here's an excerpt from the latest post about junk DNA on Uncommon Descent [Tossing Out the Junk]. The author is Eric Anderson1.
It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins. Even with the proliferation of functions for non-coding DNA, we still hear regular pronouncements from the purveyors of the materialist creation myth that “yes, there may be some function for non-coding DNA, but most of it is still junk.”
The whole idea of pervasive junk in our DNA is so naive and absurd as to boggle the mind. Thankfully, the trajectory of the evidence is clearly trending toward a more rational and complete assessment of DNA. Yes, hindsight is 20/20, and soon enough every biologist worth her salt will claim that she “always knew” that most DNA had function. But let us not forget that there were a few lone voices, including prominent ID proponents, long arguing for pervasive function — in the face of ridicule and the stifling, science-limiting attitude of the Darwin establishment about their beloved icon of “junk” DNA.
We need to preserve these comments for posterity just in case our genome actually turns out to be full of junk as most knowledgeable scientists believe. At that point, probably within a few years, the world will see that an important prediction of "prominent ID proponents" was falsified.
Meanwhile, let's hope they keep digging.
1. Nobody seems to know much about him. I'm guessing that he's an engineer.
