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.
None of these problems are discussed in the book.
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.
Vincent Torely writes at: Bad math: Why Larry Moran’s “I’m not a Darwinian” isn’t a valid reply to Meyer’s argument.
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.
1. They aren't.
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.
Here's more from the interview with Ford Doolittle [The Philosophical Approach: An Interview with Ford Doolittle].
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.
There's an interview with Ford Doolittle in PLoS Genetics [The Philosophical Approach: An Interview with Ford Doolittle].
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.
1. I wasn't the first to do this; see Why did they bury Darwin in Westminster Abbey?
Save this date: June 10, 20015.
Jerry Coyne is coming to Toronto to talk about his book. He'll be arriving from Vancouver and Imagine No Religion 2015. I'll see him there but I'm not sure I'll be back in Toronto in time. [Centre for Inquiry Canada: Jerry Coyne]
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?
Read it at" Genetics: We are the 98%. Here's the important bit ...
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.
