Günther Witzany is one of those people who think the Modern Synthesis needs to be overthrown but he missed the real revolution that took place in the late 1960s. He's part of The Third Way crowd that includes Denis Noble and Jim Shapiro [see Physiologists fall for the Third Way and The Third Fourth Way].
Susan Mazur interviews him for the Huffington Post [Günther Witzany: Modern Synthesis "Must Be Replaced," Communication Key to Evolution]. Recall that Susan Mazur is fixated on the Altenburg 16 and their attempts to radically revise evolutionary theory without understanding anything about Neutral Theory and random genetic drift. Günther Witzany is a philosopher. He was not one of the Altenberg 16 but he clearly wants to be part of the outer circle. It's not clear why anyone should consider him an expert on evolutionary biology.
Susan Mazur did us a great favor when she asked him if he would like to make a final point. His answer shows us why we can ignore him.
The older concepts we have now for a half century cannot sufficiently explain the complex tendency of the genetic code. They can't explain the functions of mobile genetic elements and the endogenous retroviruses and non-coding RNAs. Also, the central dogma of molecular biology has been falsified -- that is, the way is always from DNA to RNA to proteins to anything else, or the other "dogmas," e.g., replication errors drive evolutionary genetic variation, that one gene codes for one protein and that non-coding DNA is junk. All these concepts that dominated science for half a century are falsified now. ...
Thank-you Susan. Keep up the good work. Fools need to be exposed.
William ("Will") Provine is an emeritus professor of history and of evolution at Cornell University (Ithaca, New YOrk, USA). He is no friend of creationism. Here's what Wikipedia has to say about him ...
Provine is an atheist, philosopher, and critic of intelligent design. He has engaged in prominent debates with theist philosophers and scientists about the existence of God and the viability of intelligent design. He has debated the founder of the intelligent design movement Phillip E. Johnson and the two have a friendly relationship. Provine has stated that he starts his course on evolutionary biology by having his students read Johnson's book "Darwin on Trial."
Provine is a determinist in biology, but not a determinist in physics or chemistry, thus rejecting the idea of free will in humans. Provine believes that there is no evidence for God, there is no life after death, there is no absolute foundation for right and wrong, there is no ultimate meaning for life, and that humans don't have free will.
When someone likes that publishes a book with the title, The 'Random Genetic Drift' Fallacy, I pay attention.
Of the Five Things You Should Know if You Want to Participate in the Junk DNA Debate, the most difficult to explain is "Modern Evolutionary Theory." Most scientists think they understand evolution well enough to engage in the debate about junk DNA. However, sooner or later they will mention that junk DNA should have been deleted by selection if it ever existed. You can see that their worldview leads them to believe that everything in biology has an adaptive function.
It's been a few years since I posted Michael Lynch's scathing comments on panadaptationism and how it applies to understanding genomes [Michael Lynch on Adaptationism and A New View of Evolution]. You're in for a treat today.
Here's what you need to know about evolution in order to discuss junk DNA. The first quotation is from the preface to The Origins of Genome Architecture (pages xiii-xiv). The second quotations are from the last chapter (page 366 and pages 368-369.
Contrary to popular belief, evolution is not driven by natural selection alone. Many aspects of evolutionary change are indeed facilitated by natural selection, but all populations are influenced by nonadaptive forces of mutation, recombination, and random genetic drift. These additional forces are not simple embellishments around a primary axis of selection, but are quite the opposite—they dictate what natural selection can and cannot do. Although this basic principle has been known for a long time, it is quite remarkable that most biologists continue to interpret nearly aspect of biodiversity as an outcome of adaptive processes. This blind acceptance of natural selection as the only force relevant to evolution has led to a lot of sloppy thinking, and is probably the primary reason why evolution is viewed as a soft science by much of society.
A central point to be explained in this book is that most aspects of evolution at the genome level cannot be fully explained in adaptive terms, and moreover, that many features could not have emerged without a near-complete disengagement of the power of natural selection. This contention is supported by a wide array of comparative data, as well as by well-established principles of population genetics. However, even if such support did not exist, there is an important reason for pursuing nonadaptive (neutral) models of evolution. If one wants to confidently invoke a specific adaptive scenario to explain an observed pattern of comparative data, then an ability to reject a hypothesis based entirely on the nonadaptive forces of evolution is critical.
The blind worship of natural selection is not evolutionary biology. It is arguably not even science.
Michael Lynch
Despite the tremendous theoretical and physical resources now available, the field of evolutionary biology continues to be widely perceived as a soft science. Here I am referring not to the problems associated with those pushing the view that life was created by an intelligent designer, but to a more significant internal issue: a subset of academics who consider themselves strong advocates of evolution but who see no compelling reason to probe the substantial knowledge base of the field. Although this is a heavy charge, it is easy to document. For example, in his 2001 presidential address to the Society for the Study of Evolution, Nick Barton presented a survey that demonstrated that about half of the recent literature devoted to evolutionary issues is far removed from mainstream evolutionary biology.
With the possible exception of behavior, evolutionary biology is treated unlike any other science. Philosophers, sociologists, and ethicists expound on the central role of evolutionary theory in understanding our place in the world. Physicists excited about biocomplexity and computer scientists enamored with genetic algorithms promise a bold new understanding of evolution, and similar claims are made in the emerging field of evolutionary psychology (and its derivatives in political science, economics, and even the humanities). Numerous popularizers of evolution, some with careers focused on defending the teaching of evolution in public schools, are entirely satisfied that a blind adherence to the Darwinian concept of natural selection is a license for such activities. A commonality among all these groups is the near-absence of an appreciation of the most fundamental principles of evolution. Unfortunately, this list extends deep within the life sciences.
....
... the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer (without any direct evidence). True, we have actually seen natural selection in action in a number of well-documented cases of phenotypic evolution (Endler 1986; Kingsolver et al. 2001), but it is a leap to assume that selection accounts for all evolutionary change, particularly at the molecular and cellular levels. The blind worship of natural selection is not evolutionary biology. It is arguably not even science. Natural selection is just one of several evolutionary mechanisms, and the failure to realize this is probably the most significant impediment to a fruitful integration of evolutionary theory with molecular, cellular, and developmental biology.
Natural selection is just one of several evolutionary mechanisms, and the failure to realize this is probably the most significant impediment to a fruitful integration of evolutionary theory with molecular, cellular, and developmental biology.It should be emphasized here that the sins of panselectionism are by no means restricted to developmental biology, but simply follow the tradition embraced by many areas of evolutionary biology itself, including paleontology and evolutionary ecology (as cogently articulated by Gould and Lewontin in 1979). The vast majority of evolutionary biologists studying morphological, physiological, and or behavioral traits almost always interpret the results in terms of adaptive mechanisms, and they are so convinced of the validity of this approach that virtually no attention is given to the null hypothesis of neutral evolution, despite the availability of methods to do so (Lande 1976; Lynch and Hill 1986; Lynch 1994). For example, in a substantial series of books addressed to the general public, Dawkins (e,g., 1976, 1986, 1996, 2004) has deftly explained a bewildering array of observations in terms of hypothetical selection scenarios. Dawkins's effort to spread the gospel of the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms, and because more people have probably read Dawkins than Darwin, his words have in some ways been profoundly misleading. To his credit, Gould, who is also widely read by the general public, frequently railed against adaptive storytelling, but it can be difficult to understand what alternative mechanisms of evolution Gould had in mind.
I often observe that in discussions of evolution, both evolution skeptics and those who embrace neo-Darwinian evolution are prone to make one of two significant mistakes. Both stem from a failure to distinguish between microevolution and macroevolution.
The book was necessary because there has been so much criticism of the original Stephen Meyer's book Darwin's Doubt. David Klinghoffer has an interesting way of turning this defeat into a victory because he declares,
... the new book is important because it puts to rest a Darwinian myth, an icon of the evolution debate, namely...that there is no debate, about evolution or intelligent design!
Opponents of junk DNA usually emphasize the point that they were surprised when the draft human genome sequence was published in 2001. They expected about 100,000 genes but the initial results suggested less than 30,000 (the final number is about 25,0001. The reason they were surprised was because they had not kept up with the literature on the subject and they had not been paying attention when the sequence of chromosome 22 was published in 1999 [see Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome].
The experts were expecting about 30,000 genes and that's what the genome sequence showed. Normally this wouldn't be such a big deal. Those who were expecting a large number of genes would just admit that they were wrong and they hadn't kept up with the literature over the past 30 years. They should have realized that discoveries in other species and advances in developmental biology had reinforced the idea that mammals only needed about the same number of genes as other multicellular organisms. Most of the differences are due to regulation. There was no good reason to expect that humans would need a huge number of extra genes.
That's not what happened. Instead, opponents of junk DNA insist that the complexity of the human genome cannot be explained by such a low number of genes. There must be some other explanation to account for the the missing genes. This sets the stage for at least seven different hypotheses that might resolve The Deflated Ego Problem. One of them is the idea that the human genome contains thousands and thousands of nonconserved genes for various regulatory RNAs. These are the missing genes and they account for a lot of the "dark matter" of the genome—sequences that were thought to be junk.
Here's how John Parrington describes it on page 91 of his book.
The study [ENCODE] also found that 80 per cent of the genome was generating RNA transcripts having importance, many were found only in specific cellular compartments, indicating that they have fixed addresses where they operate. Surely there could hardly be a greater divergence from Crick's central dogma than this demonstration that RNAs were produced in far greater numbers across the genome than could be expected if they were simply intermediates between DNA and protein. Indeed, some ENCODE researchers argued that the basic unit of transcription should now be considered as the transcript. So Stamatoyannopoulos claimed that 'the project has played an important role in changing our concept of the gene.'
This passage illustrates my difficulty in coming to grips with Parrington's logic in The Deeper genome. Just about every page contains statements that are either wrong or misleading and when he strings them together they lead to a fundamentally flawed conclusion. In order to critique the main point, you have to correct each of the so-called "facts" that he gets wrong. This is very tedious.
I've already explained why Parrington is wrong about the Central Dogma of Molecular Biology [John Avise doesn't understand the Central Dogma of Molecular Biology]. His readers don't know that he's wrong so they think that the discovery of noncoding RNAs is a revolution in our understanding of biochemisty—a revolution led by the likes of John A. Stamatoyannopoulos in 2012.
The reference in the book to the statement by Stamatoyannopoulos is from the infamous Elizabeth Pennisi article on ENCODE Project Writes Eulogy for Junk DNA (Pennisi, 2012). Here's what she said in that article ...
As a result of ENCODE, Gingeras and others argue that the fundamental unit of the genome and the basic unit of heredity should be the transcript—the piece of RNA decoded from DNA—and not the gene. “The project has played an important role in changing our concept of the gene,” Stamatoyannopoulos says.
I'm not sure what concept of a gene these people had before 2012. It appears that John Parrington is under the impression that genes are units that encode proteins and maybe that's what Pennisi and Stamatoyannopoulos thought as well.
If so, then perhaps the publicity surrounding ENCODE really did change their concept of a gene but all that proves is that they were remarkably uniformed before 2012. Intelligent biochemists have known for decades that the best definition of a gene is "a DNA sequence that is transcribed to produce a functional product."2 In other words, we have been defining a gene in terms of transcripts for 45 years [What Is a Gene?].
This is just another example of wrong and misleading statements that will confuse readers. If I were writing a book I would say, "The human genome sequence confirmed the predictions of the experts that there would be no more than 30,000 genes. There's nothing in the genome sequence or the ENCODE results that has any bearing on the correct understanding of the Central Dogma and there's nothing that changes the correct definition of a gene."
You can see where John Parrington's thinking is headed. Apparently, Parrington is one of those scientists who were completely unaware of the fact that genes could specify functional RNAs and completely unaware of the fact that Crick knew this back in 1970 when he tried to correct people like Parrington. Thus, Parrington and his colleagues were shocked to learn that the human genome only had only 25,000 genes and many of them didn't encode proteins. Instead of realizing that his view was wrong, he thinks that the ENCODE results overthrew those old definitions and changed the way we think about genes. He tries to convince his readers that there was a revolution in 2012.
Parrington seems to be vaguely aware of the idea that most pervasive transcription is due to noise or junk RNA. However, he gives his readers no explanation of the reasoning behind such a claim. Spurious transcription is predicted because we understand the basic concept of transcription initiation. We know that promoter sequences and transcription binding sites are short sequences and we know that they HAVE to occur a high frequency in large genomes just by chance. This is not just speculation. [see The "duon" delusion and why transcription factors MUST bind non-functionally to exon sequences and How RNA Polymerase Binds to DNA]
If our understanding of transcription initiation is correct then all you need is a activator transcription factor binding site near something that's compatible with a promoter sequence. Any given cell type will contain a number of such factors and they must bind to a large number of nonfunctional sites in a large genome. Many of these will cause occasional transcription giving rise to low abundance junk RNA. (Most of the ENCODE transcripts are present at less than one copy per cell.)
Different tissues will have different transcription factors. Thus, the low abundance junk RNAs must exhibit tissue specificity if our prediction is correct. Parrington and the ENCODE workers seem to think that the cell specificity of these low abundance transcripts is evidence of function. It isn't—it's exactly what you expect of spurious transcription. Parrington and the ENCODE leaders don't understand the scientific literature on transription initiation and transcription factors binding sites.
It takes me an entire blog post to explain the flaws in just one paragraph of Parrington's book. The whole book is like this. The only thing it has going for it is that it's better than Nessa Carey's book [Nessa Carey doesn't understand junk DNA].
1. There are about 20,000 protein-encoding genes and an unknown number of genes specifying functional RNAs. I'm estimating that there are about 5,000 but some people think there are many more.
2. No definition is perfect. My point is that defining a gene as a DNA sequence that encodes a protein is something that should have been purged from textbooks decades ago. Any biochemist who ever thought seriously enough about the definition to bring it up in a scientific paper should be embarrassed to admit that they ever believed such a ridiculous definition.
Kirk Durston is a Canadian biophysicist with a Ph.D. from the University of Guelph (Guelph, Ontario, Canada). He's been attacking evolution for more than a decade using all the old tricks and sophistry that we've come to expect from creationists.
He begins by claiming that "Darwinian Theory" (what ever that is) makes an essential prediction. It predicts that information must increase over time.
In the neo-Darwinian scenario for the origin and diversity of life, the digital functional information for life would have had to begin at zero, increase over time to eventually encode the first simple life form, and continue to increase via natural processes to encode the digital information for the full diversity of life.
An essential, falsifiable prediction of Darwinian theory, therefore, is that functional information must, on average, increase over time.
This is ridiculous. I'm opposed to American politicians who meddle in science teaching and I'm opposed to British politicians who do the same even though I think creationism is bunk. Politicians should not be deciding what kind of science should, and should not, be taught in schools.
It's a matter of principle. It's as wrong as when American state governments banned the teaching of evolution.1
In addition, there are other reasons why this is a bad idea.
Where do you stop? Do there also need to be laws banning the teaching of astrology, climate change denial, homeopathy, and Thatcherism? Do they need laws defining the correct history of how the traitors in the Thirteen Colonies formed an alliance with the French in order to overthrow well-meaning British governments?
Why give creationists the ammunition to claim that they are being persecuted—especially when it's true?
What's wrong with showing that creationism is bad science and refuting it in the classroom? Is that forbidden? Evolution is true, it doesn't need legal protection.
Are the Brits so afraid of creationism that such a law is necessary in order to prevent creationist teachers from sneaking it into the classroom? If so, fix that problem by educating teachers.
Was this a serious enough problem to warrant giving creationism a huge publicity boost?
The government funding agreement notes that creationism "... should not be presented to pupils at the Academy as a scientific theory ..." Why not? I think that some parts of Intelligent Design Creationism really do count as valid scientific hypotheses, albeit bad ones. Why is the government taking a stand on the demarcation problem—especially an incorrect one?
1. I'm not exactly sure who made the decision in the UK. It could be the case that "government" is just a catch phrase for decisions made by a body of science teachers and science experts. Those decisions are just implemented by the "government."
Last night was my first visit to the Café Scientifique in Streetsville (Mississauga, Ontario, Canada). I had a great time discussing "Replaying the tape of life," Stephen Jay Gould, adaptationism, contingency, random genetic drift and lots of other things. This is a great group and I'll definitely be attending the next meeting.
The venue is perfect. We met in a room above a pub (The Franklin House) on the main street in Streetsville. There was plenty of good food and good beer.
A recent article in Nature reminded me of the importance of definitions. The article discusses evolution and evolutionary algorithms in a special issue on machine learning (Eiben and Smith, 2015). I think we all know that "evolutionary" algorithms are based on natural selection and we all know that there's more to evolution than just adaptation. It's too late to change the name of these procedures in computer science but at the very least I expect computer scientists to be aware of the difference between their procedures and real evolution.
In this paper, there's a section on "how evolutionary computation compares with natural evolution." The authors consistently use "evolution" as a synonym for "selection" or "adaptation" and they seem to be unaware of any other mechanism of evolution.
In one sense, it's okay to conflate "evolution" and "adaptation" in computer science but if that error reflects and perpetuates a fundamental misunderstanding of the nature of real biological evolution then perhaps it's time to rename these algorithms "adpatation algorithms."
Eiben, A.E. and Smith, J. (2015) From evolutionary computation to the evolution of things. Nature 521: 476–482. [doi:10.1038/nature14544]
If students are going to learn critical thinking about evolution, they need to be exposed to controversial views and challenges concerning evolution, the history of life, and evolutionary theory. The Discovery Institute agrees with this strategy. It has published a handbook called The Educator's Briefing Packet that claims to outline what teachers should cover when they teach evolution.
As you might imagine, the Discovery Institute concentrates on showing that evolution is wrong rather than focusing on whether Intelligent Design Creationism is correct. That's partly because they don't want to advocate teaching Intelligent Design Creationism in schools.
They explain the strategy on page 7 ...
Teaching this subject objectively means presenting both the scientific evidence for and against neo-Darwinian evolution. This does not mean simply criticizing evolution or only presenting the case against the neo-Darwinian model. Rather, objective instruction means:
Fully teaching the evidence for neo-Darwinian evolution from the textbook.
Covering the entire required curriculum.
Helping students understand the scientific arguments in favor of neo-Darwinian evolution as well as the scientific criticisms as they are presented in the scientific literature.
This strategy implies that students are taught something called "Neo-Darwinism" in class. Here's how they define Neo-Darwinism.
Darwin argued that natural selection had the power to produce fundamentally new forms of life. Together, the ideas of universal common descent and natural selection form the core of Darwinian evolutionary theory. "Neo-Darwinian" evolution combines our knowledge of DNA and genetics to claim that mutations in DNA provide the variation upon which natural selection acts.
Right away we have a problem since many textbooks do not describe modern evolutionary theory in this manner. The handbook doesn't explain what teachers should do if they are teaching modern evolutionarytheory instead of Neo-Darwinism but I think it's pretty obvious what the Intelligent Design Creationists would recommend if they actually understood evolution. They would still recommend criticizing it.
In a real classroom run by competent teachers, the teachers would begin by pointing out that many creationist organizations have an incorrect and distorted view of evolution and they would pass out copies of the handbook. Then they would discuss why the Discovery Institute is promoting nonsense about evolution when they claim to be experts on the subject. The class could analyze the difference between the DI version of evolution that only covers natural selection and the modern view that includes random genetic drift and population genetics. This would be a highly effective way of teaching critical thinking and exposing students to one of the most common misconceptions about evolution.
In the right hands, this could lead to a discussion about why creationists seem to resist being educated about evolution even though the correct information is readily available on the internet. The class could learn about confirmation bias, begging the question, false dichotomy, and the strawman fallacy using examples from the handbook.
The Educator's Briefing Packet contains lots of other myths and misrepresentations that are commonly found in creationist literature. Debunking and correcting these examples can also be used to foster critical thinking and teach the truth about evolution. I'd like to thank the Discovery Institute for putting them all in one place. I'd love to spend a few days in a senior high school class showing the students why these are myths and/or misconceptions.
Here's the list1 ...
Genetics:Mutations Tend to Cause Harm and Do Not Build Complexity. Darwinian evolution relies on random mutations which are acted on by natural selection, a blind and unguided process that has no goals. Such a random and undirected process tends to harm organisms. They do not seem capable of improving organisms or building new complex systems.
Biochemistry:Unguided and Random Processes Cannot Produce Cellular Complexity.Cells contain incredible complexity, similar to machine technology but dwarfing anything produced by humans. Cells use circuits, miniature motors, feedback loops, encoded language, and even error-checking machinery which decodes and repairs our DNA. Many scientists have claimed that Darwinian evolution does not appear capable of building this type of integrated complexity.
Paleontology:The Fossil Record Lacks Intermediate Fossils. The fossil record’s overall pattern is one of abrupt explosions of new biological forms and possible candidates for evolutionary transitions are the exception, not the rule. For example, the Cambrian Explosion is an event in life’s history over 500 million years ago where nearly all the major body plans of animals appear in a geological instant without any apparent evolutionary precursors.
Taxonomy:Biologists Have Failed to Construct Darwin’s Tree of Life. Biologists hoped that DNA evidence would reveal a grand tree of life where all organisms are clearly related. Yet trees describing the alleged ancestral relationships between organisms based upon one gene or biological characteristic commonly conflict with trees based upon a different gene or characteristic. This implies a challenge to universal common descent, the hypothesis that all organisms share a single common ancestor.
Chemistry:The Chemical Origin of Life Remains an Unsolved Mystery. The mystery of the origin of life is unsolved, and all existing theories of chemical evolution face major problems. Basic deficiencies in chemical evolution include a lack of explanation for how a primordial soup could arise on the early earth’s hostile environment, or how the information required for life could be generated by blind chemical reactions.
In all theses cases we have situations where the Discovery Institute is challenging the views of the vast majority of scientists who have devoted careers to studying these issues. That's a good opportunity to teach students how they should go about deciding who to believe when faced with scientific questions. Should you believe doctors or movie actors when trying to decide whether to vaccinate your children? Should you believe climatologists or politicians about climate change? Should you believe evolutionary biologists or religious leaders when trying to decide if evolution is true?
However, I'm not sure if we could ever have much of a discussion about these issues because the latest "ID the Future" podcast features a discussion between Nate Herbst and Casy Luskin about students who question evolution in class. As it turns out, many of those students have bad experiences because they end up feeling stupid when they challenge science in class. Luskin and Herbst recommend that they hide their beliefs in order to avoid such embarrassment [see Listen: Good Advice for Students Learning about Evolution]. Maybe that's not always a good idea, however, because Herbst and Luskin also have some stories about how they stumped the professors and caused them to change their minds about evolution and origins.
1. I wonder who they used as an authority on evolution in order to make up these questions?
Michael Behe first proposed the idea of "irreducible complexity" in Darwin's Black Box back in 1996. He defines it as ...
By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.
That's interesting. Let's look at the paper to see what it says. The reference is Muskhelishvili, G. and Travers, A. (2015) and the relevant passage is on page 4556.
Thus, the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organisational complexity of the genetic regulation system of any cell. Put another way, this implies that the structural dynamics of the chromosome must be fully convertible into its genetic expression and vice versa. Since the DNA is an essential carrier of genetic information, the fundamental question is how this self-referential organisation is encoded in the sequence of the DNA polymer.
What they are saying is that proper gene regulation requires both transcription factors AND a particular organization of the chromosome that facilitates transcription. It also requires input from metabolic pathways. If any one of these three things are missing then the cell cannot regulate gene expression in the same manner as cells where all three are present.
The authors then go on to discuss how this system could have evolved. Look at Figure 3 of their paper (below) where they clearly show the relationships between transcription, supercoiling, and small regulatory molecules. The paper describes their belief that this "irreducible organisational complexity" arose by evolution from these three existing features.
So, these authors are using "irreducible complexity" to describe a system that's clearly possible according to their understanding of evolution. Uncommon Descent states that this is exactly the same sense in which the term is used by Michael Behe. In fact, it quotes a physicist named David Snoke who says,
Three comments: 1) the authors are “serious” scientists, not fringe people. 2) They are using “irreducible complexity” in the same sense as Behe. This is not a case of accidental use of the same phrase to mean something different. Their term “holistic” is another way of saying the same thing, that the system requires all of its parts to work. 3) This “holistic” approach is one that is becoming common in systems biology. I have a paper coming out on that, in the works.
We've been telling Intelligent Design Creationists for years that irreducibly complex systems can easily arise by naturalistic processes (i.e. evolution). I'm really glad that they have finally seen the light.
That should be the end of any more posts saying that irreducibly complex systems can't evolve.
(Not holding my breath.)
Muskhelishvili, G. and Travers, A. (2015) Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information. Cell. Molec. Life Sci. 70:4555-4567. [Abstract]
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.
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.
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.
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.
