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.
I'm reading Eternal Ephemera by Niles Eldredge and learning about the early history of evolution and geology. Eldredge describes the work of James Hutton who is known as the father of modern geology. Here's the Wikipedia description of his work ...
He originated the theory of uniformitarianism—a fundamental principle of geology—which explains the features of the Earth's crust by means of natural processes over geologic time. Hutton's work established geology as a proper science, and thus he is often referred to as the "Father of Modern Geology".[2][3]
Through observation and carefully reasoned geological arguments, Hutton came to believe that the Earth was perpetually being formed; he recognised that the history of the Earth could be determined by understanding how processes such as erosion and sedimentation work in the present day. His theories of geology and geologic time,[4] also called deep time,[5] came to be included in theories which were called plutonism and uniformitarianism.
Vincent Torley was reading Darwin's Doubt when he came across a passage "that struck me as the best case I’ve ever seen for Intelligent Design, in 200 words or less" [A succinct case for Intelligent Design].
This is pretty interesting since there's always been a bit of confusion over what Intelligent Design Creationism actually means. It seems to me that the movement concentrates on criticizing evolution (and materialism) and doesn't really present much of a case for believing that the history of life was directed by gods.
Here's the passage that Torley admires. See for yourself ...
"This book has presented four separate scientific critiques demonstrating the inadequacy of the neo-Darwinian mechanism, the mechanism that Dawkins assumes can produce the appearance of design without intelligent guidance. It has shown that the neo-Darwinian mechanism fails to account for the origin of genetic information because: (1) it has no means of efficiently searching combinatorial sequence space for functional genes and proteins and, consequently, (2) it requires unrealistically long waiting times to generate even a single new gene or protein. It has also shown that the mechanism cannot produce new body plans because: (3) early acting mutations, the only kind capable of generating large-scale changes, are also invariably deleterious, and (4) genetic mutations cannot, in any case, generate the epigenetic information necessary to build a body plan." (pp. 410-411)
This passage merely affirms what we all know to be true; namely that there is no case for Intelligent Design Creationism. It's just a bunch of whining about the inadequacies of the IDiot version of evolution. That version assumes that all of evolution is due to natural selection acting on random mutations and this gives rise to the appearance of design.
I don't believe in that version of evolution and I don't think that most species look as though they were designed. Does that mean that I'm an Intelligent Design Creationist? Of course not. Meyers (and Torley) have fallen for the trap of the false dichotomy.
Even if all four of Stephen Meyer's critiques were correct1, he still isn't offering an alternative explanation and he still isn't showing us evidence for an intelligent designer—or any other kind of designer.
If this is the best case for Intelligent Design Creationism then it cannot survive. But we all know that this is all a bunch of lies. The "best" case for Intelligent Design Creationism is taught in the churches, not the classrooms.
Here's the May 13, 2015 version of Jesus and Mo. The barmaid is correct. There are lots of studies showing that you can't dispel major misconceptions by simply describing the scientifically correct view. For example, if you are teaching evolution to creationists you can describe the science until you are blue in the face but it's likely to have little impact on changing their minds.
The only way to correct misconceptions is to address them directly and show why they are wrong. That means you have to teach the reasons why a 6000-year-old Earth is a misconception and explain why irreducible complexity and the Cambrian explosion do not refute evolution.
The journal Genomics is a journal devoted to the study of genomes. It describes itself like this ...
Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation.
As a journal that has evolved with the field that carries its name, Genomics focuses on the development and application of cutting-edge methods, addressing fundamental questions with potential interest to a wide audience. Our aim is to publish the highest quality research and to provide authors with rapid, fair and accurate review and publication of manuscripts falling within our scope.
They claim that all submissiosn are subjected to rigorous peer review and only 25-30% of submissions are accepted for publication.
The composition of genomes is important so it's no surprise that the journal is interested in publishing articles that address the junk DNA debate. In fact, it is so interested that it is going to devote a special issue to the subject for publication in February 2016.
That's the good news. Now for the bad news ....
Special issue on the functionality of genomic DNAs
Guest Editors:
Prof. Shi Huang
State Key Laboratory of Medical Genetics
Central South University , China
huangshi@sklmg.edu.cn
Prof James Shapiro
Department of Biochemistry and Molecular Biology
University of Chicago
jsha@uchicago.edu
The field of genome evolution and population genetics has for the past half of a century assumed that genomic DNA can be divided into functional and non-functional (“junk”) regions. Experimental molecular science has found little evidence for this assumption. A majority of the noncoding parts of the human genome are transcribed, and numerous experimental researchers have now recognized an important functional role in the so called junk DNA regions, such as syn sites, lncRNA, psudogene transcripts, antisense transcripts, microRNA, and mobile elements. In fact, evidence for functional constraints on noncoding genome regions has long been recognized. New theoretical frameworks based on less arbitrary foundations have also appeared in recent years that can coherently account for the reality of far more functional DNAs, as well as all other major known facts of evolution and population genetics. Nonetheless, there still remains a large gap in opinions between bench scientists in experimental biology and those on the theory side in bioinformatics and population genetics. This special issue will aim to close that gap and provide a view of evidence from a perspective that all genome regions have (or can easily acquire) functionality.
The special issue on the functionality of genome will focus on the following tentative topics:
Theoretical foundation for all genome regions to be functional. It will cover both the theory and all major features of genome evolution.
Functional studies on junk DNA regions, including lncRNA sequences, viral DNAs and mobile elements
Functionalities associated with genome spatial organization in the nucleus
Isocores and compositional constraints on genomes
Genetic basis of complex traits and diseases focusing on the collective effects of normal genetic variations
Cancer genomics
Roles of repetitive DNA elements in major evolutionary transitions
Correlations of genome composition and organismal complexity
Epigenetics
Evo Devo and extended synthesis
Important dates:
First submission date: July 1, 2015
Deadline for paper submissions: October 1, 2015
Deadline for final revised version: December 1, 2015
Expected publication: February 2016
Some of you will recognize the names of the guest editors. Jim Shapiro is one of the poster boys of Intelligent Design Creationism because he attacks evolutionary theory. He's one of the founders of the "The Third Way."
You may be less familiar with Shi Huang. He is also part of the Third Way movement but we've recently learned a lot more about him because he posts comments under the name "gnomon." You can see some of his comments in this thread: Ford Doolittle talks about transposons, junk DNA, ENCODE, and how science should work. Shi Huang appears to have a great deal of difficulty expressing himself in a rational manner.
Those guest editors will publish papers that "... provide a view of evidence from a perspective that all genome regions have (or can easily acquire) functionality." In other words, skeptics need not apply.
The controversy is over the amount of junk DNA in genomes. There are two sides in this controversy. Many scientists think there is abundant and convincing evidence that most of our genome is junk. Other scientists think that most of our genome is functional. It looks like Genomics is only interested in hearing from the second group of scientists. That's why they appointed guest editors with an obvious bias. Those guest editors also happen to be skating very close to the edge of kookdom.
This is not how a credible science journal is supposed to behave.
Gitschier: I want to close with what you describe as your “latest rant.” How did you get on function?
Doolittle: Well, I’ve always been on that.
Back in 1980, people were talking about transposable elements as if their function was to speed evolution; that they exist because of their future utility. And I’ve never liked that kind of idea. I didn’t like it in terms of introns. And Dawkins had just published The Selfish Gene in 1978.
Carmen Sapienza, a student of mine who now works on eukaryotic imprinting, and I wrote a paper which was rejected by Science after seven referees. But we heard that Leslie Orgel and Francis Crick were working on something like this, so we sent it to them. They said, “If you submit it to Nature, we will tell Nature not to publish ours without publishing yours, and to publish yours first,” etc., which was very nice.
That paper, seemingly now very simplistic, said you don’t need to suppose that transposable elements are there for the purpose of speeding evolution. These are selfish things, and natural selection will favor such elements that can make copies of themselves in genomes and then spread horizontally to other genomes within the species. These are basically parasites. I think many people would now accept this, but it was radical at the time.
People don’t like to think that the human genome has junk in it. This came back when the ENCODE papers came out a few years ago and were touted as spelling the “demise of junk DNA.” That got my dander up.
I wrote a perspective in PNAS, and Dan Graur had a much more vituperative thing in Genome Biology and Evolution. I don’t think the ENCODE people have given up; they had a kind of semi-apology in PNAS, which wasn’t really an apology.
It is the same as the tree of life issue, but until we actually have some agreement about what we mean by words we are going to get into these arguments, and in my mind, there are two devastating things you can say about the ENCODE people.
One is that they completely ignored all that history about junk DNA and selfish DNA. There was a huge body of evidence that excess DNA might serve some structural role in the chromosomes, but not informational. They also ignored what philosophers of biology have spent a lot of time asking: what do you mean by “function?” And you can mean one of two things: we might mean either what natural selection favored, which is what I think most biologists mean, or we might mean what it does. Some people might say, “Well the function of this gene is in the development of cancer,” but they don’t really mean that natural selection put it there so that it would cause cancer. These are not-so-subtle differences.
I think many molecular biologists and genomicists, in particular, think that each and every nucleotide is there for a reason, that we are perfect organisms. It is almost as if we were still theists thinking God doesn’t make junk; we just now think natural selection doesn’t make junk. I think there is a deep issue about the extent to which we are noisy creatures and the extent to which we are finely honed machines. I think the latter view informs much of genomics, and I think it is false.
ENCODE wouldn’t have got funded had they said 80% of the human genome is just junk, transposable elements.
Gitschier: It is justifying itself, post hoc. They are the big players with a lot of money. It’s like a machine—“We can do it, so let’s just do it!”
Doolittle: It’s a juggernaut is what you are saying.
My other objection is that it is false ontology. I think all of our science suffers not only from the big science motivation, but from what I call “positivism.”
A couple of times we submitted papers saying, “Everybody’s doing something this way, and it doesn’t work, and it is wrong to do it this way.” And Nature would write back, “We’re not interested in negative reports like this. What does work?” And we say, “We don’t give a damn what does work, it is important to know that what people are doing now is not working.”
There is no critique in science, very little. You can’t actually say, “This doesn’t mean what people say it means.” You’ve got to be “positive;” you’ve got to be moving the program forward all the time. I don’t think that is right.
Now, and down the road, we’re going to tackle directly relevant questions, like what is the meaning of function in the concept of genomics? There are legitimate evolutionary constructs in which you can address transposable elements, and people have not really explored that. Questions about the tree of life, again, and some of the questions we’ve been through are things that continue to interest me and which have a strong philosophical component as well as a data-related component. That’s what I’m interested in pursuing.
Ford has lots of things to say about the origin of introns, the tree of life, transpsosons, ENCODE, and the meaning of "function." Here's the bit about the tree of life.
I'm gradually starting to work on my book about evolution by accident. The first chapter is "Darwin Died in 1882." The point I'm making is that evolutionary biology is a 21st century discipline not one that's stuck in the nineteenth century.
I was re-reading an old article from the 2006 issue of Skeptical Inquirer with the title1 I picked for this blog post. The author is W.G. Weyant, an historian at the University of Calgary (Calgary, Alberta, Canada). He says,
Why, then, did they bury Darwin in Westminster Abbey? The brief answer is "because he was dead," but that, while true, clearly is not the whole story."
The whole story is interesting because it reflects the attitudes of late Victorian society in England. This was a time when scientists were honored even if, or especially because, their ideas were upsetting. It appears to be an age when smart, rational, people were admired.
I don't know if this is still true in Europe but it's not true in Canada and it's certainly not true in the USA. Actors and singers are admired, but not intellectuals. I wonder what late Victorian society would have thought on seeing the memorial services for Francis Crick and Michael Jackson? I wonder what they would have thought of Ted Cruz?
Weyant also writes,
Approximately a decade after publication of the "Origin of Species" in 1859, most educated Englishmen, including many of the clergy, had accepted the fact of evolution. More that a few of them were uneasy about where the evidence and their reason were taking them, but they went nevertheless.
That's an interesting way of putting it. Today, we see many people who are faced with the same uneasiness but the response is quite different. When the choice is faith or facts, they choose not to follow the path of reason.
I think we're finally beginning to realize that science and religion are not compatible, confirming the worst fears of educated Victorians back in 1882. Jerry Coyne's new book is likely going to start a serious debate, one that has been largely ignored in the interests of accommodationism.
The American Society for Biochemistry and Molecular Biology (ASBMB) has recommended that biochemistry courses concentrate on core concepts rather than details. It has defined five categories of core concepts that are essential in understanding biochemistry and molecular biology [see ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function].
Theme
Better BiochemistryI strongly support the concept of teaching core concepts even though I disagree with many of the actual concepts that are proposed. Here are the five core concepts with links to my discussions.
Here's the final exam in my course. Students have to answer the first two questions and three of the next five questions. How would you do?
Choose a subtopic from your essay and explain it better than you did in your essay and/or rebut the comments and criticisms made by the marker/grader.
Michael Lynch says in The Origins of Genome Architecture ....
Nothing in Evolution Makes Sense Except in the Light of Population Genetics Evolution is a population genetic process governed by four fundamental forces, which jointly dictate the relative abilities of genotype variants to expand through a species. Darwin articulated a clear but informal description of one of those forces, selection (including natural and sexual selection), whose central role in the evolution of complex phenotypic traits is universally accepted, and for which an elaborate formal theory in terms of changing genotype frequencies now exists. The remaining three evolutionary forces, however, are non-adaptive in the sense that they are not the function of the fitness properties of individuals: mutation (broadly including insertions, deletions, and duplications) is the fundamental source of variation on which natural selection acts; recombination (including crossing-over and gene conversion) assorts variation within and among chromosomes; and random genetic drift insures that gene frequencies deviate a bit from generation to generation independently of other forces. Given the century of theoretical and empirical work devoted to the study of evolution, the only logical conclusion is that these four broad classes of mechanisms are, in fact, the only fundamental forces of evolution. Their relative intensity, directionality, and variation over time define the way in which evolution proceeds in a particular context.
Do you agree with Lynch that “Nothing in Evolution Makes Sense Except in the Light of Population Genetics”? If so, why isn’t population genetics taught in introductory biology courses? If not, why not?
Imagine that identical female twins were born to a woman in 1000 AD. Imagine that you could find a direct descendant of each twin in 2015. If you sequence the complete genomes of the descendants, approximately how many differences would you expect to find? How do these compare to the differences between any two randomly selected individuals from the same part of the world? Explain your reasoning and describe any assumptions you make. Think carefully before you answer. The second question is the most important one. (Human mutation rate = 130 mutations per generation. Haploid genome size = 3.2 × 109 bp.)
Why do some scientists think that there is no unique tree of life?
Many people believe that recombination evolved because it increases genetic variation in a population and this provided a selective advantage over species that didn’t have recombination. Do you agree with this explanation for the evolution of recombination? Why, or why not? What are the other possibilities?
What is “evolvability ”and why could it be important in evolution? Why are some scientists skeptical of this claim?
Richard Dawkins once wrote,
Even the most ardent neutralist is quite happy to agree that natural selection is responsible for all adaptation. All he is saying is that most evolutionary change is not adaptation. He may well be right, although one school of geneticists would not agree. From the sidelines, my own hope is that the neutralists will win, because this will make it so much easier to work out evolutionary relationships and rates of evolution. Everybody on both sides agrees that neutral evolution cannot lead to adaptive improvement, for the simple reason that neutral evolution is, by definition, random, and adaptive improvement is, by definition, non-random. Once again, we have failed to find any alternative to Darwinian selection, as an explanation for the feature of life that distinguishes it from non-life, namely adaptive complexity.
Richard Dawkins (1986) The Blind Watchmaker. p. 304
Can you describe situations in Richard Lenski’s ongoing evolution experiment where neutral or deleterious alleles were essential for adaptive change?
Finally, Junk DNA, like the genome, is crammed with repetitious elements and superfluous text. Bite-sized chapters parade gee-whizz moments of genomics. Carey's The Epigenetics Revolution (Columbia University Press, 2012) offered lucid science writing and vivid imagery. Here the metaphors have been deregulated: they metastasize through an otherwise knowledgeable survey of non-coding DNA. At one point, the reader must run a gauntlet of baseball bats, iron discs, Velcro and “pretty fabric flowers” to understand “what happens when women make eggs”. The genome seems to provoke overheated prose, unbridled speculation and Panglossian optimism. Junk DNA produces a lot of DNA junk.
The idea that the many functions of non-coding DNA make the concept of junk DNA obsolete oversells a body of research that is exciting enough. ENCODE's claim of 80% functionality strikes many in the genome community as better marketing than science.
Nessa Carey is a science writer with a Ph.D. in virology and she is a former Senior Lecturer in Molecular Biology at Imperial College, London.
She has written a book on junk DNA but it's not available yet (in Canada). Judging by her background, she should be able to sort through the controversy and make a valuable contribution to informing the public but, as we've already noted Nessa Carey and New Scientist don't understand the junk DNA debate.
Casey Luskin has a copy of the book so he wrote a blog post on Evolution News & Views. He's thrilled to find someone else who dismisses junk DNA and "confirms" the predictions of Intelligent Design Creationism. I hope Nessa Carey is happy that the IDiots are pleased with her book [New Book on "Junk DNA" Surveys the Functions of Non-Coding DNA].
There's some controversy over the rate of mutations in humans. The latest summary comes from science journalist Ewen Callaway, a Senior Reporter for Nature, writing on March 10, 2015: DNA mutation clock proves tough to set.
-definition
-mutation types
-mutation rates
-phylogeny
-controversies Let's review what we know. The first thing we have to do is define "mutation" [What Is a Mutation?]. A mutation is any alteration of the nucleotide sequence of a genome. It includes substitutions, insertions, and deletions.
The mutation rate can be described and defined in many ways. For most purposes, we can assume that it's equivalent to the error rate of DNA replication since that accounts for the vast majority of substitutions. Substitutions are far more numerous than most insertions and deletions. (But see, Arlin Stoltzfus on The range of rates for different genetic types of mutations).
The first video was posted to YouTube on April 23, 2005 [see YouTube]. I took this photo (right) a few years ago near my daughter's place in Playa Vista, California. It's a production facility, YouTube Space LA, on the site of the former Howard Hughes airport.
The main purpose of this post is to give me an excuse to post one of my granddaughter's favorite YouTube videos (below top). She's a big fan of YouTube and so is my two year old grandson—he likes videos of rocket launches (below bottom).
Razib Khan is an adaptationist and he's discovered a paper that gets him very excited: Selectionism Strikes Back!.
Here's the paper and the abstract.
Corbett-Detig, R.B., Hartl, D.L., Sackton, T.B. (2015) Natural Selection Constrains Neutral Diversity across A Wide Range of Species. PLoS Biology Published: April 10, 2015 doi: 10.1371/journal.pbio.1002112
The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.
It is impossible for someone like me to evaluate this paper. Can someone take a look to see if it's valid?
How many selective sweeps must there every 50,000 years in order to remove substantial amounts of neutral diversity from junk DNA?
Shortly after being elected last Fall, the new Mayor of Mississauga, Bonnie Crombie, decided that the City Council would continue to say a prayer before each council meeting. She voted in favor of continuing the practice even though she heard the arguments against it and even though she knew that the Ontario Court of Appeal (in 1999) had ruled it illegal [Mississauga council debates removing Lord’s Prayer from meetings].
Crombie, who is Catholic, said she doesn’t have a problem with the recitation of the prayer. But, she does want to touch base with the municipality’s 11 councillors to get their opinions.
She has already heard lot of different ideas from her peers, such as leaving the practice the way it is to replacing it with a non-denominational blessing to even rotating a prayer from a different faith before each meeting.
"I don’t think there’s anything wrong with (reciting the prayer)," said Crombie. "But, I am asking each councillor about it and there is a diversity of opinion."
...
Larry Moran, who described himself as an atheist, is also a University of Toronto professor and an advisory fellow with the Centre for Inquiry Canada, an organization he said strongly supports the separation of religion and government.
He wrote a blog post condemning the practice in Mississauga earlier this year and Moran estimates about 30 per cent of Canadians aren’t religious. He strongly believes the Lord’s Prayer before council should come to an end.
"There is no reason to invoke any of the gods at a public meeting of any government body," said Moran. "It sends the wrong message to … citizens who don’t believe in those gods or who believe in other gods. Nobody has been able to tell me why religion has to be mixed in with government business."
Now Bonnie Crombie says she will obey the law—no mention of fairness or of consideration for non-Christians in the community. Oh well, at least she's not going to fight it and cost the city lots of money.
The Toronto Star reports that the mayor of Oshawa plans to ignore the Supreme Court decision. I bet he backs down after talking to the city lawyers [Oshawa mayor plans to keep Lord’s Prayer].
Brampton Mayor Linda Jeffrey stopped the practice of reciting the Lord's Prayer before council meetings earlier in the year and today Mississauga Mayor Bonnie Crombie indicated her council will now do the same, after the Supreme Court decision. At the beginning of the year she supported keeping the Lord's Prayer in Mississauga council meetings.
"Today’s ruling sets a precedent and the City of Mississauga will abide by the Supreme Court’s ruling," Crombie said.
At the beginning of the year Crombie supported keeping the Lord's Prayer in Mississauga council meetings, after Councillor Carolyn Parrish had pushed to remove it from council meetings.
Austin Booth and Ford Doolittle have just published a paper that discusses the origin of eukaryotes (Austin and Doolittle, 2015). They point out that many of the stories about this event are not grounded in fact. Read the paper.
Writing for public audiences, and often even for themselves, biologists are not loath to make simplifying claims about uniqueness and importance that are rhetoric disguised as fact. Such generalizations serve purposes in the doing of science, but are often not themselves testable scientific claims and are subject to biases. Evolutionary biology may be especially vulnerable to hype, as suggested by the frequency with which revolutionary evolutionary claims in top-notch journals are debunked. Additionally, anthropocentrism, as it grades into "zoocentrism" and then "eukaryocentrism," surely remains a subtle distorter of objectivity.
Our aim here is to critique general claims about the uniqueness and special importance of eukaryogenesis, with an aim to making them more open to question and conceptual and empirical analysis. We ask (i) whether eukaryogenesis entailed such a "genuinely unlikely sequence of events" as to justify belief in its uniqueness as a process, (ii) if, as is often claimed, eukaryogenesis has a problematic or unique theoretical status in evolutionary biology, (iii) what intrinsic features might have conferred on eukaryotes their presumed "richer evolutionary potential," and (iv) if this greater potential might be just a presumption, an illusion reflecting eukaryocentric bias.
There are many useful ways of understanding evolution, and their articulations can be intellectually valuable and experimentally fruitful. We advocate a more self-conscious pluralism that would require not that we stop telling eukaryogenesis stories but that we do recognize them for what they are. We do not claim to know whether there is any best story, any theory by which the apparent differential success of eukaryotes can be objectively probed and causally rationalized. What we have questioned here is whether premises of existing theories have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was "special," any such notion has more than rhetorical value.
Booth, A. and Doolittle, W.F. (2015) Eukaryogenesis, how special really? Proc. Natl. Acad. Sci. (USA) Published online before print April 16, 2015 [doi: 10.1073/pnas.1421376112]
The state’s duty of religious neutrality results from an evolving interpretation of freedom of conscience and religion. The evolution of Canadian society has given rise to a concept of this neutrality according to which the state must not interfere in religion and beliefs. The state must instead remain neutral in this regard, which means that it must neither favour nor hinder any particular belief, and the same holds true for non‑belief. The pursuit of the ideal of a free and democratic society requires the state to encourage everyone to participate freely in public life regardless of their beliefs. A neutral public space free from coercion, pressure and judgment on the part of public authorities in matters of spirituality is intended to protect every person’s freedom and dignity, and it helps preserve and promote the multicultural nature of Canadian society. The state’s duty to protect every person’s freedom of conscience and religion means that it may not use its powers in such a way as to promote the participation of certain believers or non‑believers in public life to the detriment of others. If the state adheres to a form of religious expression under the guise of cultural or historical reality or heritage, it breaches its duty of neutrality. The Tribunal was therefore correct in holding that the state’s duty of neutrality means that a state authority cannot make use of its powers to promote or impose a religious belief. Contrary to what the Court of Appeal suggested, the state’s duty to remain neutral on questions relating to religion cannot be reconciled with a benevolence that would allow it to adhere to a religious belief.
This seems so obvious to most people that it's a wonder why anyone ever thought that reciting prayers at city council meetings was justified.
Now, let's see how long it takes for other cities to stop the practice.
I'm interested in science education in general and teaching biochemistry and molecular biology in particular. A recent publication in PLoS Biology caught my eye ...
Reindl, K.M., White, A. R., Johnson, C., Vender, B., Slator, B.M., and McClean, P. (2105) The Virtual Cell Animation Collection: Tools for Teaching Molecular and Cellular Biology. PLoS Biology 13(4): e1002118 DOI: 10.1371/journal.pbio.1002118
The paper focuses on the value of short animations for teaching biochemistry and molecular biology to advanced high school students and college students.
There's nothing in the paper about the scientific accuracy of the presentations or the pedagogical approach and this is unfortunate. The animations only show complex eukaryotic cells in spite of the fact that the American Society for Biochemistry and Molecular Biology recommends an evolutionary approach to teaching. The fact that the videos emphasize eukaryotes leads to some interesting descriptions of fundamental processes.
Look at the video on transcription regulation for example [Regulated Transcription]. The textbooks teach this using simple systems such as E. coli transcription then they move on to more complex prokarotic systems such as the lac operon. Then they cover the eukaryotic examples pointing out how they differ from the simple bacterial systems. This has always been a successful approach to teaching the basic concepts of transcription and transcription regulation. 1
Is the approach taken by the authors of The Virtual Cell Animation project better? I don't think so. What do you think? Does anyone out there teach transcription without introducing it first in bacteria?
Let's not forget my favorite example of biochemical misconceptions: the Citric Acid Cycle. Did you know that it's sometimes called the "tricarboxylic acid cycle" because three CO2 molecules are released for every pyruvate molecule? 2
The carboxylate groups on citrate, isocitrate etc. are shown as -COOH instead of COO- as in the textbooks. I don't know why they did this ... it leads to some extra protons being released in the reactions.
The authors make a very common mistake with succinate dehydrogenase. They show FADH2 as one of the products of the reaction whereas the IUBMB database shows that the real final product is QH2 [see Succinate Dehydrogenase]. I don't understand why biochemistry teachers can't check out a leading textbook (or the scientific literature) before producing a video.
Did you know that some of the reactions of glycolysis are irreversible? Check out the video on Glycolysis to find out which reactions have this interesting property. 3 There is no video on gluconeogenesis and that's surprising because the synthesis of glucose is far more important than glycolysis in most species.
I wonder if the editors of PLoS bothered to watch the videos or whether they just assumed that they were scientifically accurate and pedagogically sound? I'm guessing that they didn't see the need to review the videos and simply concentrated on whether all the words in the article were spelled correctly.
1. There's a separate video on the lac Operon. How many errors, flaws, or missed opportunities, can you spot?
2. Silly me. I always though it had something to do with the fact that two of the key intermediates (citrate and isocitrate) were tricarboxylic acids. Most of the others are dicarboxylic acids.
3. Maybe I'm quibbling. In my textbook I describe these reactions as "metabolically irreversible" because the activities of the enzymes are regulated. That's not the same as saying that the reactions are irreversible.
Pseudogenes, a subclass of long noncoding RNA (lncRNA) that developed from the human genome’s 20,000 protein-coding genes but has lost the ability to produce proteins, have long been considered nothing more than genomic "junk."
Yet the retention of these 20,000 mysterious remnants during evolution suggests that they may in fact possess biological functions and contribute to the development of disease.
Now, a team led by investigators at Harvard Medical School and the Cancer Center at Beth Israel Deaconess Medical Center has provided some of the first evidence that one of these noncoding "evolutionary relics" actually has a role in causing cancer.
In a new study published in the journal Cell on April 2, the scientists report that, independent of any other mutations, abnormal amounts of the BRAF pseudogene led to the development of an aggressive lymphoma-like disease in a mouse model, a discovery suggesting that pseudogenes may play a primary role in a variety of diseases.
The new discovery also suggests that with the addition of this vast "dark matter" the functional genome could be tremendously larger than previously thought—three or four times its current known size.
There are many things wrong with that description but I'm not going to elaborate. If you don't know what's wrong you probably won't be interested in this post anyway.
I want to discuss two rules that should be enforced for every press release.
The press release must include the complete citation, including a link (doi). If This means delaying the press release for a day or two after the embargo is lifted then that's a small price to pay.
The press release should always include a notice from at least one author affirming, in writing, that the press release is a complete and accurate report of the results and conclusions that have been published in the peer reviewed literature.
This press release did not contain a citation. In this case, the paper has been published online but there's no volume number or page number because it hasn't appeared in the journal. Here's the citation ...
Florian A. Karreth, Markus Reschke, Anna Ruocco, Christopher Ng, Bjoern Chapuy, Valentine Léopold, Marcela Sjoberg, Thomas M. Keane, Akanksha Verma, Ugo Ala, Yvonne Tay, David Wu, Nina Seitzer, Martin Del Castillo Velasco-Herrera, Anne Bothmer, Jacqueline Fung, Fernanda Langellotto, Scott J. Rodig, Olivier Elemento, Margaret A. Shipp, David J. Adams, Roberto Chiarle, Pier Paolo Pandolfi (2015)The BRAF Pseudogene Functions as a Competitive Endogenous RNA and Induces Lymphoma In Vivo Cell published online April 2, 1015. [doi: 10.1016/j.cell.2015.02.043]
There. That wasn't so hard, was it?
I can't read the paper because it's behind a paywall but the abstract suggests that the authors really do think their work applies to most pseduogenes. The press release quotes the senior author, Pier Paolo Pandolfi, and while his views aren't nearly as idiotic as the beginning of the press release it does suggest that he isn't a fan of junk DNA.
In order to confirm that the views expressed by Bonnie Prescott are an accurate representation of the views in the peer-reviewed paper, it would be nice to see a note at the bottom of the press release signed by multiple authors. It would state that they stand by the press release and that the views in the press release represent those views that have passed peer review.
I call this "Author Responsibility" and I think it should be a requirement in all press releases.
James Lunney has quit the Conservative Party of Canada and decided not to run in the next federal election. He's upset because he doesn't believe in evolution and lots of people, including me, are pointing out the stupidity of his views. Because those views are based on religion, he interprets this to be an attack on his faith.
Maybe it’s because I am tired of seeing my faith community mocked and belittled. To not respond is to validate my accusers and worse yet, imply that I lack the courage of my convictions to stand–up for what I believe. This is not a legacy I wish to leave behind. Many of you colleagues represent constituencies beyond the ones who elected you; I hope that no member of any faith community in Canada is compelled to defend the beliefs of their community in the future.
Freedom of Religion and conscience are fundamental freedoms in Canada. Bigotry cloaked in defense of "science" is as intolerable and repugnant as bigotry from any other source.
It is contrary to our multi-racial, multicultural and multi-faith character and the tolerance for diversity that defines us as Canadians.
I know members on all sides of the house are concerned about bullying in general and cyber-bullying in particular. The government has brought in new legislative measures to address some aspects of this brutal phenomenon and there are many social actions like the pink shirt initiative that seek to shield the vulnerable.
We are living in an era where knowledge is increasing at an astounding pace; there are so many technical advances it is hard to keep up and what we refer to in general as "science" has been parsed into more and more diverse pursuits of knowledge.
I urge you to read the entire article that he posted on April 1st 2015. See if you think he deserves the respect he craves. He sounds like a kook to me.
How many times have we heard this stuff before? And how many times have we seen this style of writing?
So is "Evolution Theory or Fact?
The late Stephen Jay Gould stated: "a fact is something that is proven to the extent that to not believe it is perverse"!
That translates to: a fact is something that my friends and I believe, AKA eminence-based science. There’s a lot of that in health-care, where it’s known as eminence-based medicine as opposed to evidence- based medicine. There are people in the medical world expressing concern about the immense influence of KOLs (Key Opinion Leaders) with influencing public policy and decision making in directing scientific inquiry
Darwin’s brilliant and convincing construct that defined a century and a half of scientific belief, is in crisis because of astounding advances in molecular biology and it’s all about THE CELL.
You have 80-100 trillion cells, 200 cell types, all reading the same genetic library, but as different as they are, working together in specialized communities to perform astonishing synchronized manufacturing, recycling, transport, packaging and delivery functions. Twenty-five thousand miles of blood vessels if you strung them end to end; that is a trip around the world at the surface.
Every cell is worlds within worlds of nanotechnology finely tuned and regulated.
Darwin’s elaborate construct is stalled at the cell; even the simplest prokaryotic cell is infinitely beyond the odds of ever coming together by random, undirected process.
Jame Lunney is attacking evolutionary biologists and their acceptance of the scientific evidence for evolution, which happens to be their area of expertise. It seems ironic that he accuses others of bigotry and bullying.
James Lunney is a chiropractor and he has a B.Sc. (science). He says, "I have a background in Science: my credentials modest as they are, are superior on this file to many in this chamber and most of my critics."
Some of you may recall James Lunney, Conservative Party Member of Parliament for Nanaimo-Alberni in British Columbia. He's a chiropractor who spoke out against evolution back in 2009 [James Lunney: Creationist, Chiropractor, Conservative].
More recently, he defended another MP who didn't believe in evolution. He was mocked and ridiculed in the popular press and now he has decided to resign from the Conservative Party and sit in the House of Commons as an Independent. That's not working out so well according to CBC News [James Lunney defends views on evolution in House of Commons].
One day after he announced he was leaving the Conservative caucus to better defend his religious beliefs, Nanaimo-Alberni MP James Lunney attempted to do just that from his new seat in the corner of the House of Commons reserved for independent MPs.
But despite his best efforts, he was unable to convince House of Commons Speaker Andrew Scheer that the "cyberbullying" and "crowd-shaming" that he claimed to have experienced after questioning the science behind evolution constituted a breach of his parliamentary privilege.
Imagine that! He was unable to convince Parliament that making fun of his silly beliefs is wrong! This is exactly how the Canadian public SHOULD deal with people who act like kooks.
Wanna hear about his beliefs? This is what he said in Parliament ....
Speaking to CBC News Power & Politics host Evan Solomon on Wednesday evening, Lunney said that he was tired of seeing his faith community bullied.
...
Lunney described evolution — or, as he calls it, "macro-evolution" is "a theory in crisis."
"Scientists are not able to speak their mind on that — at least half of them who feel this way, they're gagged by an old construct," he argued.
"There's a whole generation of kids being taught that what they're taught in Sunday School or in church is garbage, it's wrong, it's false, and it's simply a form of bullying that's no longer acceptable. It's not scientifically tenable, it's a disservice to science… it's not freedom of religion if your views are put down by your peers."
Freedom comes in several forms. If you live in a free society then you have to be prepared to accept criticism of your most cherished beliefs. You can't hide behind religion to protect you when you act like an IDiot. Pointing out the stupidity of a Member of Parliament is not bullying
As far as I'm concerned, this is exactly how freedom should work.
Edward Lanphier, Fyodor Urnov, Sarah Ehlen Haecker, Michael Werner and Joanna Smolenski have published a comment in Nature with a provocative headline "Don’t edit the human germ line. They are asking scientists to agree " not to modify the DNA of human reproductive cells." The idea is that editing the genome of sperm or egg cells produces changes that will be passed on to future generations and this poses certain dangers.
I looked forward to this "conversation" because I was already familiar with Denis Noble and his strange views of evolution [A physiologist thinks about evolution]. Noble reiterated his view of modern evolutionary theory at the meeting. He thinks that modern evolutionary theory (The Modern Synthesis or Neo-Darwinism) is all about random mutation and natural selection. He thinks it is based on the views of Richard Dawkins in The Selfish Gene. Neither he nor Michael Joyner (an anaethesiologist at the Mayo Clinic) have learned about random genetic drift or Neutral Theory and neither of them have much knowledge of population genetics. In other words, they are pretty ignorant about evolution even though they feel entitled to attack it.
