David Raup died last month. He was 82 years old. Raup was a paleontologist at the University of Chicago, where he studied the big picture of the history of life, concentrating on mass extinctions. Here's an excerpt from the University of Chicago website [David Raup, paleontologist who transformed his discipline, 1933-2015].
Raup’s former students and colleagues uniformly praised his unique creativity along with his astute capabilities as an academic adviser, senior colleague and paleontological statesman. They remember him for the sweeping scope of the questions he asked, his analytical and quantitative rigor, and his skepticism and humility.
“David Raup ushered in a renaissance in paleontology,” said Raup’s former student and colleague Charles Marshall, SM’86, PhD’89, director of the University of California’s Museum of Paleontology and professor of integrative biology at UC Berkeley. “Before Dave, much of the discipline was centered on describing what was. Dave taught the discipline to think about the processes that might have generated the past record.”
Raup introduced statistical concepts to paleontology that treated the fossil record as an outcome of yet-to-be-discovered processes. Raup was widely known for the new approaches he brought repeatedly to paleontology, such as extensive computation, modern evolutionary biology, theoretical ecology and mathematical modeling.
As Marshall put it, Raup created new intellectual space for paleontology. “That was, in my opinion, his greatest contribution. It is not that Dave just transformed the discipline, but his students, and their students, continue to fill and expand that space,” Marshall said.
Another former student and colleague, Michael Foote, expressed similar sentiments.
“By any conception of what it means to be influential, Dave was one of the most influential paleontologists active during the second half of the 20th century,” said Foote, SM’88, PhD’89, a professor in geophysical sciences at UChicago. “In the areas he chose to touch, nobody, in my view, surpassed him.”
Raup hung out with the likes of John Sepkoski, Steven Stanley, and Stephen Jay Gould and they shared many of the same views on evolution. He was very good at describing those views in books for the general public and that's why I rate him as one of the best scientists who are also science writers [Good Science Writers: David Raup]. His book, Extinction: Bad Genes or Bad Luck? (1991), is one of my top five books on evolution [Top Five Books on Evolution]. Here's a quotation from the introduction to that book ...
I have taken the title of this book from a research article I published in Spain some years ago. I was concerned then with the failure of trilobites in the Paleozoic era. Starting about 570 million years ago, these complex, crab-like organisms dominated life on ocean bottoms—at least they dominated the fossil assemblages of that age. But through the 325 million years of the Paleozoic era, trilobites dwindled in numbers and variety, finally disappearing completely in the mass extinction that ended the era, about 245 million years ago.
My question in Spain is the one I still ask: Why? Did the trilobites do something wrong? Were they fundamentally inferior organisms? Were they stupid? Or did they just have the bad luck to be in the wrong place at the wrong time? The first alternative, bad genes, could be manifested by things like susceptibility to disease, lack of good sensory perception, or poor reproductive capacity. The second, bad luck, could be a freak catastrophe that eliminated all life in areas where tilobites happened to be living. The question is basically one of nature versus nurture. Is proneness to extinction an inherent property of a species—a weakness—or does it depend on vagaries of chance in a risk-ridden world?
Of course, the problem is more complex than I have presented it, just as the nature-nurture question in human behavior is complex. But in both situations, nature (Genetics) and nurture (environment) operate to some degree, and the challenge is to find out which process dominates and whether the imbalance varies in time and space. (pp. 5-6)
If you don't already own a copy of that book, you should buy one right now and read it. They may not be easy to get in the future and your life will be poorer if you don't learn about the difference between bad genes and bad luck.
Raup is famous for the Field of Bullets analogy to explain why extinction is as much bad luck as bad genes. He made a strong case for his belief that chance plays an important role in the history of life. He was not alone in making this claim but it doesn't seem to be popular these days for reasons that confound me. It's part of what I call Evolution by Accident. It means that if you replay the tape of life, things will come out very differently and there's no guarantee that sentient beings like ourselves will evolve [see Café Scientifique: Replaying the tape of life]. You don't have to agree with Raup, Gould, and other experts but if you want to participate in discussions of evolution you have to be familiar with this important concept.
Once again, a group of scientists want to extend and revise the Modern Synthesis version of evolutionary theory in order to bring their pet projects into the mainstream. Once again, these scientists seem to have missed the real revolution that took place 45 years ago so they are attacking a strawman. And, once again, they seem to think that the core principles of evolutionary theory can be defined by how complex animals evolve, ignoring bacteria and single-cell eukaryotes that have been at the heart of the history of life for 3.5 billion years.
But the fact that some geniuses were laughed at does not imply that all who are laughed at are geniuses. They laughed at Columbus, they laughed at Fulton, they laughed at the Wright Brothers. But they also laughed at Bozo the Clown.
                     Carl SaganThe paper by Laland et al. (2015) was published in Proceedings of the Royal Society (UK) Series B just this month (August, 2015). The usual suspects are included in the author list including three of the Altenberg 16: Eva Jablonka, Gerd B. Müller, and John Odling-Smee. This is the same group that defended the "yes" side when Nature posed the question, "Does evolutionary theory need a rethink?" back in October, 2014 [see Rethinking evolutionary theory ].
I've been doing a bit of research on the human genome in preparation for a book. This led me to an article published in 2003 by Francis Collins, former head of the Human Genome Consortium (Collins, 2003). It's mostly about how he deals with science and religion but there was an interesting description of what he learned from completing the human genome sequence.
Here's what he said ....
We discovered some pretty surprising things in reading out the human genome sequence. Here are four highlights.
1. Humans have fewer genes than expected. My definition of a gene here—because different people use different terminology—is a stretch of DNA that codes for a particular protein. There are probably stretches of DNA that code for RNAs that do not go on to make proteins. That understanding is only now beginning to emerge and may be fairly complicated. But the standard definition of “a segment of DNA that codes for a protein” gives one a surprisingly small number of about 30,000 for the number of human genes. Considering that we’ve been talking about 100,000 genes for the last fifteen years (that’s what most of the textbooks still say), this was a bit of a shock. In fact, some people took it quite personally. I think they were particularly distressed because the gene count for some other simpler organisms had been previously determined. After all, a roundworm has 19,000 genes, and mustard weed has 25,000 genes, and we only have 30,000? Does that seem fair? Even worse, when they decoded the genome of the rice, it looks as if rice has about 55,000 genes. So you need to have more respect for dinner tonight! What does that mean? Surely, an alien coming from outer space looking at a human being and looking at a rice plant would say the human being is biologically more complex. I don’t think there’s much doubt about that. So gene count must not be the whole story. So what is going on?
2. Human genes make more proteins than those of other critters. One of the things going on is that we begin to realize that one gene does not just make one protein in humans and other mammals. On the average, it makes about three, using the phenomenon of alternative splicing to create proteins with different architectures. One is beginning to recover some sense of pride here in our genome, which was briefly under attack, because now we can say, “Well, we don’t have very many genes but boy are they clever genes. Look what they can do!”
3. The male mutation rate is twice that of females. We also discovered that simply by looking at the Y chromosome and comparing it to the rest of the genome—of course, the Y chromosome only passes from fathers to sons, so it only travels through males—you can get a fix on the mutation rate in males compared to females. This was not particularly good news for the boys in this project because it seems that we make mistakes about twice as often as the women do in passing our DNA to the next generation. That means, guys, we have to take responsibility for the majority of genetic disease. It has to start somewhere; the majority of the time, it starts in us. If you are feeling depressed about that, let me also point out we can take credit for the majority of evolutionary progress, which after all is the same phenomenon.
4. “Junk” DNA may not be junk after all. I have been troubled for a long time about the way in which we dismissed about 95% of the genome as being junk because we didn’t know what its function was. We did not think it had one because we had not discovered one yet. I found it quite gratifying to discover that when you have the whole genome in front of you, it is pretty clear that a lot of the stuff we call “junk” has the fingerprints of being a DNA sequence that is actually doing something, at least, judging by the way evolution has treated it. So I think we should probably remove the term “junk” from the genome. At least most of it looks like it may very well have some kind of function.
The folks at Evolution News & Views (sic) can serve a very useful purpose. They are constantly scanning the scientific literature for any hint of evidence to support their claim about junk DNA. Recall that Intelligent Design Creationists have declared that if most of our genome is junk then intelligent design is falsified since one of the main predictions of intelligent design is that most of our genome will be functional.
THEME
Genomes & Junk DNA They must be getting worried because their most recent posts sounds quite desperate. The last one is: The Un-Junk Industry. It quotes a popular press report on a paper published recently in Procedings of the National Academy of Sciences (USA). The creationists concede that the paper itself doesn't even mention junk DNA but the article in EurekAlert does.
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.
I find it very frustrating to read reports about RNA these days because the writers almost always misrepresent the history of the field and exaggerate the significance of recent discoveries. An article in the July 23, 2015 issue of Nature illustrates the problem. The article is written by Elie Dolgin (@ElieDolgin), a freelance science journalist based in Massachusetts (USA). He graduated from McGill University (Montreal, Quebec, Canada) with a degree in biology and obtained a Ph.D. in genetics and evolution from the University of Edinburgh (Edinburgh, Scotland, UK).
At 8:15 AM on August 6, 1945 an atomic bomb was detonated over Hiroshima, Japan. Approximately 78,000 civilians were killed on that day. Six months later the death toll had risen to about 140,000 people.
There are many arguments in favor of dropping the bomb, just as there are many arguments against it. What's clear is that in the context of 2015 we are not in a good position to judge the actions of countries that had been at war for many years.
The most important lesson of Hiroshima is that war is hell and many innocent people die. It's all very well to enter into a war with the best of intentions—as the Japanese did on December 7, 1941—but it's foolish to pretend that when you start a war there won't be any suffering. When you do that, you can really say that the victims of Hiroshima will have died in vain.
The killing and maiming of civilians is an inevitable outcome of war, no matter how hard you might try to restrict your targets to military objectives. Before going to war you need to take the consequences into account and decide whether the cost is worth it.
Hiroshima was not a glorious victory. It was ugly, heartbreaking, and avoidable. War is not an end in itself, it is the failure of peace. War is not an instrument of foreign policy—it is an admission that you don't have a foreign policy.
[The top photograph shows the mushroom cloud over Hiroshima on the morning of August 6, 1945 (Photo from Encyclopedia Britanica: Hiroshima: mushroom cloud over Hiroshima, 1945. [Photograph]. Retrieved August 7, 2007, from Encyclopædia Britannica Online.
The bottom image is taken from a Japanese postcard (Horoshima and Nagassaki 1945). It shows victims of the attack on Hiroshima.]
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.
From an academic pedagogical perspective, there’s nothing wrong with a course that has a reading list emphasizing quack medicine. This is the view that people outside of the university don’t understand. They appear to want to prevent students from ever learning about, or discussing, the anti-vax movement and how to deal with it.
Those of you who read the articles and have seen talks by supporters of science-based medicine like Steve Novella and myself will recognize this for the straw man that it is. We never say anything like this, that we want to prevent students from learning about or discussing the antivaccine movement. That is an assertion that is unsupported and, quite frankly, downright risible. So you should understand that I was more than a little pissed off when I read this part of Moran’s post. We never say that we don’t want alternative medicine to be taught or antivaccine views taught. (Indeed, I really wish that pediatrics residency programs, for instance, would do a better job of teaching antivaccine views, so that they don’t catch pediatricians by surprise when parents start expressing them.) What we complain about is the uncritical teaching of these topics, the teaching, for example, of alternative medicine modalities as though they had scientific merit. This is a massive problem in medical academia. I’ve lost track of how many times I’ve reiterated this very point going back at least a decade.
We agree. I wasn't referring to people like Orac who understand how universities should work. I was referring to those people outside of the university community who really do want to ban any mention of alternative medicine at universities. I guess I didn't make that clear.
I'm pretty sure that Orac knows about this crowd. They are totally opposed to the idea of teaching the controversy. They have some very strong views on what's right and what's wrong and they firmly believe that the only views that should ever be expressed in university classes are the ones they agree with.
In the end, my little fit of pique over Prof. Moran’s condescending and dismissive attitude towards those of us who were so outraged by this course being offered by U. of T. aside, we actually (mostly agree). Moran supports “teaching the controversy” with respect to evolution and with respect to alternative medicine. So do I. Where we disagree is over what “teaching the controversy” actually entails. Can Prof. Moran can honestly say that he wouldn’t be the least bit upset if his own department were to offer an entire course on “controversies in evolution” taught by Ken Ham, Casey Luskin, and a Discovery Institute fellow to be named later? That he would approve of such a class as a great way to “teach the controversy”? If he can, I’d say there’s a problem. If he can’t say that, I congratulate him. That’s the correct reaction. In that case, I also point out that he has no business being so contemptuous of our anger over a homeopath teaching a course in alternative medicine as a way of “teaching the controversy.”
As I said in my earlier post, the problem wasn't that an anti-vaccine point of view was being discussed in a university course. The problem was that the course was being taught by someone who wasn't qualified to offer a university course that encouraged critical thinking. That situation has been rectified.
I would love to invite Casey Luskin to come and give a few lectures on Intelligent Design Creationism to my students. It would be far better for them to hear the other side directly from the horse's mouth than filtered through me.
There's been a recent kerfluffle about a course called "Alternative Health: Practive and Theory" taught as part of a program in Health Studies at the University of Toronto's Scarborough campus (Toronto, Ontario, Canada).
Most of the readings in the course emphasized non-evidence-based medicine and health. The instructor was Beth Landau-Halpern, a homeopath who warns her patients about the dangers of vaccines [see Beth Landau-Halpern]. She's also the wife of Rick Halpern, the Dean and Vice-Principle of University of Toronto, Scarborough (UTSC). Ms. Landau-Halpern will no longer be teaching and the Dean has resigned [Rick Halpern Resigns].
This is the game my son, Gordon Moran, and his friends at IronOak Games are developing. Please send him lots of money when Kickstarter is activated in September.
I'm buying a university and a professor character for the game. The professor will battle the forces of evil and superstition. Ms. Sandwalk is contributing enough for a medieval faire with lots of games where you can win prizes.
The draft sequence of the human genome was published in 2001. The "finished" version was published a few years later but annotation continues.
A massive amount of data on complex genomes has been published, especially on the human genome. The next step is to decide what this data means. Here are the most important questions from my perspective.
I don't think scientific journals or scientific organizations should take a position on the conflict between science and religion but that doesn't mean they should stay away from the subject altogether. The journal Nature has just (July 28, 2015) published a defense of accomodationism written by David M. Lodge [Faith and science can find common ground]. Lodge describes himself as a "Protestant ecologist embedded for 30 years in a Roman Catholic university." The Catholic University is Notre Dame [see David M. Lodge].
His main argument is that the current Pope understands the science of the environment and has spoken out in favor of protecting the environment. David Lodge thinks this represents an accomomodation between science and religion.
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.
Interviewed by The New Yorker earlier this year, the great novelist and journalist Tom Wolfe acknowledged that he's writing a book about evolution -- actually, "a history of the theory of evolution from the nineteenth century to the present." No indication of what his overall thesis might be, but he "invokes the Spanish Inquisition when discussing how academics have cast out proponents of intelligent design for 'not believing in evolution the right way.'"
