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Friday, April 22, 2016

Don't call it "The Theory of Evolution"

By now, we all know that a "theory" in science is much more than idle speculation, a point that has been made repeatedly over the past century. With respect to evolution, the most famous essay is by Stephen Jay Gould: "Evolution as Fact and Theory" and the latest explanation is an article in the New York Times by Carl Zimmer: In Science, It’s Never ‘Just a Theory’.

Unfortunately, it's not that simple and there are many scientists who use "theory" in the sense of hypothesis or speculation [see Facts and theories of evolution according to Dawkins and Coyne]. That's not what I want to talk about today.

What do scientists really mean when they refer to "The Theory of Evolution"? There is no single theory of evolution that covers all the mechanisms of evolution. There's the Theory of Natural Selection, and Neutral Theory, and the Theory of Random Genetic Drift, and a lot of theoretical population genetics. Sometimes you can lump them all together by referring to the Modern Synthesis or Neo-Darwinism. These terms are much more accurate than simply saying "The Theory of Evolution" as long as we all understand what those theories mean.

The problem with "The Theory of Evolution" is not only that it's ambiguous but it's misleading. It implies that there's only one theory to explain evolution. Another problem is that it sounds too much like we're talking about the history of life and saying that it's a "theory" that can be explained by evolution.

Instead of using the phrase "The Theory of Evolution," I think we should be referring to "evolutionary theory," which may come in different flavors. The term "evolutionary theory" encompasses a bunch of different ideas about the mechanisms of evolution and conveys a much more accurate description of the theoretical basis behind evolution. Douglas Futuyma prefers "evolutionary theory" in his textbook Evolution and I think he's right. It allows him to devote individual chapters to "The Theory of Random Genetic Drift" and "The Theory Natural Selection."

Here's how Futuyma explains the concept of theory in his book Evolution 2nd ed. p. 613.
So is evolution a fact or a theory? In light of these definitions, evolution is a scientific fact. That is, descent of all species, with modification, from common ancestors is a hypothesis that in the past 150 years or so has been supported by so much evidence, and so successfully resisted all challenges, that it has become a fact. But this history of evolutionary change is explained by evolutionary theory, the body of statements (about mutation, selection, genetic drift, developmental constraints, and so forth) that together account for the various changes that organisms have undergone. [my emphasis ... LAM]
He makes the same point in the opening pages of his book where he uses both terms when discussing the history of evolutionary theory. (Note that when Darwin used the word "theory" to describe natural selection he was not using it in the same sense as Gould and Zimmer to describe a modern scientific theory. That's why Futuyma uses "hypothesis" in the quote below.)
We now know that Darwin's hypothesis of natural selection on hereditary variation was correct, but we also know that there are more causes of evolution than Darwin realized, and that natural selection and hereditary variation themselves are more complex than he imagined. A body of ideas about the causes of evolution, including mutation, recombination, gene flow, isolation, random genetic drift, the many forms of natural selection, and other factors, constitute our current theory of evolution, or "evolutionary theory." Like all theories in science, it is a work in progress, for we do not yet know the causes of all of evolution, or all the biological phenomena that evolutionary biology will have to explain. Indeed, some details may turn out to be wrong. But the main tenets of the theory, as far as it goes, are so well supported that most biologists confidently accept evolutionary theory as the foundation of the science of life. p. 14 [my emphasis ... LAM]
When you're talking about the mechanisms of evolution, please use "evolutionary theory" instead of "the theory of evolution."

I wish the proponents of the Extended Evolutionary Synthesis would agree that the version of evolutionary theory they wish to extend is the one described by Douglas Futuyma. This would make it easier for them to explain what's wrong with that version and why their proposals are an improvement [see Templeton gives $8 million to prove that there's more to evolution than natural selection].

Templeton gives $8 million to prove that there's more to evolution than natural selection

The Templeton Foundation will fund a group of researchers who promote something called "The Extended Evolutionary Synthesis" (EES). The grant is for $8 million (US). The project is headed by Kevin N, Laland of the University of St. Andrews (Scotland, UK) and Tobias Uller of Lund University in Sweden. You can read all about it at: Putting the Extended Evolutionary Synthesis to the Test.

There are two problems with this funding. The first is the source of the funds. I agree with Jerry Coyne and many others that Templeton Fund money is tainted because the clear purpose of the fund is to lend credence to religion [Templeton keeps up the woo]. Templeton will only fund projects that advance that objective.

The second problem is the science. The advocates of EES promote things like "developmental plasticity," "niche construction," "evo-devo," and "epigenetics"—all of these phenomena are supposed to play a major role in evolutionary theory, a role that is not covered by the Modern Synthesis.

I think that all of these processes may play a role in explaining the history of life on Earth1 but so do plate tectonics, asteroid impacts, and endosymbiosis. The problem is that there's a difference between explaining the events behind the history of life and evolutionary theory. They are not the same thing.

The real question is whether any of these things need to be incorporated into modern evolutionary theory and whether they extend the Modern Synthesis. Personally, I don't think any of them make a significant contribution to evolutionary theory.

But my real beef is with the outdated view of evolution held by EES proponents. To a large extent they are fighting a strawman version of evolution. They think that the "Modern Synthesis" or "Neo-Darwinism" is the current view of evolutionary theory. They are attacking the old-fashioned view of evolutionary theory that was common in the 1960s but was greatly modified by the incorporation of Neutral Theory and increased emphasis on random genetic drift. The EES proponents all seem to have been asleep when the real revolution occurred.

When you listen to them, you get the distinct impression they have never read The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. I have no confidence in biologists who want to overthrow a view of evolutionary theory that's already been dead for half a century. I have no confidence in biologists who aren't at ease talking about non-adaptive evolution. This is the 21st century.2

Elizabeth Pennisi is all over this. She wrote an article for the April 22 (2016) edition of Science: Templeton grant funds evolution rethink. The opening sentence is very revealing ....
For many evolutionary biologists, nothing gets their dander up faster than proposing that evolution is anything other than the process of natural selection, acting on random mutations.
Damn right! I'm not an evolutionary biologist but my dander gets up whenever scientists make such a ridiculous claim.

Help is one the way, according to Elizabeth Pennisi because the Templeton Foundation is funding research to show that there's more to evolution than natural selection. Unfortunately, the "extended" version doesn't include random genetic drift and modern population genetics.
No wonder some evolutionary biologists are uneasy with an $8.7 million grant to U.K., Swedish, and U.S. researchers for experimental and theoretical work intended to put a revisionist view of evolution, the so-called extended evolutionary synthesis, on a sounder footing. Using a variety of plants, animals, and microbes, the researchers will study the possibility that organisms can influence their own evolution and that inheritance can take place through routes other than the genetic material.
I don't object to work on those subjects. My beef is with the idea that they pose a problem for our current understanding of evolutionary theory. More importantly, my main complaint is that the biologists who will spend all this money missed the real revolution that took place 50 years ago.

Here's how Pennisi describes the extended evolutionary synthesis. Her description is pretty accurate.
The extended evolutionary synthesis is a term coined in 2007 to imply that the preeminent current evolutionary theory, the so-called modern synthesis, needed to broaden its focus because it concentrated too much on the role of genes in evolution and lacked adequate incorporation of new insights from development and other areas of biology. The idea has gradually gathered momentum since its advocates first met in Germany in 2008 (Science, 11 July 2008, p. 196). Later, Kevin Laland, an evolutionary biologist at the University of St. Andrews in the United Kingdom, and several colleagues took up the cause, arranging for a point-counterpoint discussion in Nature in 2014 and a comprehensive review last year in the Proceedings of the Royal Society B's annual Darwin Review.

Advocates stress that animals, plants, and even microbes modify their environments, exhibit plasticity in their physical traits, and behave differently depending on the conditions they face. Chemical modifications of the DNA that affect gene activity—so-called epigenetic changes—seem to explain some of this flexibility. These and other factors suggest to some biologists that an organism's development is not simply programmed by the genetic sequences it inherits. For them, such plasticity implies that parents can influence offspring not just through their DNA but by passing on the microorganisms they host or by transmitting epigenetic marks to subsequent generations. “Innovation may be a developmental response that becomes stabilized through genetic changes,” explains Armin Moczek, an evolutionary developmental biologist at Indiana University, Bloomington.

Nor is evolution controlled only by natural selection, the winnowing process by which the fittest survive and reproduce, Laland and others argue. Organisms, by transforming their environments and responding to environmental factors, help control its course, they contend. As such, the extended synthesis “represents a nascent alternative conceptual framework for evolutionary biology,” Laland and dozens of colleagues wrote in a funding proposal to the Templeton Foundation last year.
This is a profoundly adaptationist view of evolutionary theory. The "extended" version merely adds a few more mechanisms that might improve adaptation.

Most of the EES proponents are working on animals, many are physiologists. They share an evo-devo view of evolution that emphasizes the role of natural selection. I share Michael Lynch's view that we live in a post-Darwinian world and nothing in evolution makes sense except in the light of population genetics. I agree with him that most scientists think of evolution as a soft science and that includes many biologists. It includes most of the EES proponents who probably couldn't tell you anything about population genetics beyond the fact that it's too mathematical. That doesn't stop them from criticizing modern evolutionary theory.

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.

Michael Lynch
Here's a quote from Michael Lynch's book The Origins of Genome Architecture. In my view, it describes the group who were awarded $8 million to overthrow modern evolutionary theory.
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 real revolution was the incorporation of nonadaptive mechanisms into evolutionary theory and the overthrow of adaptationism. That revolution is not complete. There are still thousands of biologists who remain strict Darwinists even as they try to promote different ways of achieving adaptation. Those biologists still dominate the popular press (e.g. Elizabeth Pennisi) and they are largely responsible for skepticism about junk DNA. That has to change. Evo-devo types need to listen to Michael Lynch when he says ...
Unfortunately, the emerging field of evolutionary developmental biology is based almost entirely on a paradigm of natural selection, and the near-absence of the concept of nonadaptive processes from the lexicon of those concerned with cellular and developmental evolution does not follow from any formal demonstration of the negligible contribution of such mechanisms but simply reflects the failure to consider them. [my emphasis ... LAM] There is no fundamental reason why cellular and developmental features should be uniquely immune to nonadaptive evolutionary forces. One could even argue that the stringency of natural selection is reduced in complex organisms with behavioral and/or growth from flexibilities that allow individuals to match their phenotypic capabilities to the local environment.

1. Some of them are trivial and some are ineffective but that's been debated many times. I want to emphasize the fact that EES proponents don't understand modern evolutionary theory.

2. To be fair, some of these proponents do pay lip-service to non-adaptive evolution from time to time but it's clear that they don't really get it.

Monday, April 11, 2016

My DNA ancestry

I sent a DNA sample off to a few weeks ago and here are the results.

Ancestry has a peculiar way of identifying haplotypes. When they say "Ireland," they mean Ireland and Scotland.1 When they say Great Britain, they mean that they don't distinguish between England, most of Scotland, and most of Normandy.

The results look fairly accurate. My maternal grandmother is Irish—both her parents immigrated to Canada from Ireland in the late 1800s. They descend mostly from English settlers who moved to Ireland in the 1600s. That's why I'm not 25% Irish.

My maternal grandfather is a mixture of English, Scottish, French and Dutch ancestors. The dominant DNA markers should be Scottish and English.

My paternal grandfather is from Russia, near the Volga river north of Volgograd and south of Saratov. He was German ... descended from German immigrants brought in my Catherine the Great in the late 1700s. The German communities on the Volga did not mix genes with the local Russians so the haplotypes will be German. This is mostly why I'm almost 25% German.

My paternal grandmother is from Volhynia in northern Ukraine. Many of her ancestors were German having recently (1700s) settled in the regions from Germany and German-speaking parts of Poland. Those families mixed with the local populations of Poland, Lithuania (now Belarus), and northern Ukraine.

The trace Scandinavian haplotypes could come from either side of my family through Poland/Germany or through Scotland/Ireland. identifies all my DNA relatives who have had their DNA tested. There are 73 of them in all but none closer than 4th cousin. Fortunately, some of them seem to related to my paternal grandfather. That's the link I wanted to explore so I'll be getting in touch with them.

If you add in the other bits then I've got all of Europe covered except Italy. That doesn't explain why I like spaghetti & meatballs and pizza.

1. The DNA analysis is done in a lab in Ireland!

Sunday, March 27, 2016

Georgi Marinov reviews two books on junk DNA

The December issue of Evolution: Education and Outreach has a review of two books on junk DNA. The reviewer is Georgi Marinov, a name that's familiar to Sandwalk readers. He is currently working with Michael Lynch at Indiana University in Bloomington, Indiana, USA. You can read the review at: A deeper confusion.

The books are ...
The Deeper Genome: Why there is more to the human genome than meets the eye, by John Parrington, (Oxford, United Kingdom: Oxford University Press), 2015. ISBN:978-0-19-968873-9.

Junk DNA: A Journey Through the Dark Matter of the Genome, by Nessa Carey, (New York, United States: Columbia University Press), 2015. ISBN:978-0-23-117084-0.
You really need to read the review for yourselves but here's a few teasers.
If taken uncritically, these texts can be expected to generate even more confusion in a field that already has a serious problem when it comes to communicating the best understanding of the science to the public.
Parrington claims that noncoding DNA was thought to be junk and Georgi replies,
However, no knowledgeable person has ever defended the position that 98 % of the human genome is useless. The 98 % figure corresponds to the fraction of it that lies outside of protein coding genes, but the existence of distal regulatory elements, as nicely narrated by the author himself, has been at this point in time known for four decades, and there have been numerous comparative genomics studies pointing to a several-fold larger than 2% fraction of the genome that is under selective constraint.
I agree. That's a position that I've been trying to advertise for several decades and it needs to be constantly reiterated since there are so many people who have fallen for the myth.

Georgi goes on to explain where Parringtons goes wrong about the ENCODE results. This critique is devastating, coming, as it does, from an author of the most relevant papers.1 My only complaint about the review is that George doesn't reveal his credentials. When he quotes from those papers—as he does many times—he should probably have mentioned that he is an author of those quotes.

Georgi goes on to explain four main arguments for junk DNA: genetic load, the C-value Paradox, transposons (selfish DNA), and modern evolutionary theory. I like this part since it's similar to the Five Things You Should Know if You Want to Participate in the Junk DNA Debate. The audience of this journal is teachers and this is important information that they need to know, and probably don't.

His critique of Nessa Carey's book is even more devastating. It begins with,
Still, despite a few unfortunate mistakes, The Deeper Genome is well written and gets many of its facts right, even if they are not interpreted properly. This is in stark contrast with Nessa Carey’s Junk DNA: A Journey Through the Dark Matter of the Genome. Nessa Carey has a PhD in virology and has in the past been a Senior Lecturer in Molecular Biology at Imperial College, London. However, Junk DNA is a book not written at an academic level but instead intended for very broad audience, with all the consequences that the danger of dumbing it down for such a purpose entails.
It gets worse. Nessa Carey claims that scientists used to think that all noncoding DNA was junk but recent discoveries have discredited that view. Georgi sets her straight with,
Of course, scientists have had a very good idea why so much of our DNA does not code for proteins, and they have had that understanding for decades, as outlined above. Only by completely ignoring all that knowledge could it have been possible to produce many of the chapters in the book. The following are referred to as junk DNA by Carey, with whole chapters dedicated to each of them (Table 3).

The inclusion of tRNAs and rRNAs in the list of “previously thought to be junk” DNA is particularly baffling given that they have featured prominently as critical components of the protein synthesis machinery in all sorts of basic high school biology textbooks for decades, not to mention the role that rRNAs and some of the other noncoding RNAs on that list play in many “RNA world” scenarios for the origin of life. How could something that has so often been postulated to predate the origin of DNA as the carrier of genetic information (Jeffares et al. 1998; Fox 2010) and that must have been of critical importance both before and after that be referred to as “junk”?
You would think that this is something that doesn't have to be explained to biology teachers but the evidence suggests otherwise. One of those teachers recently reviewed Nessa Carey's book very favorably in the journal The American Biology Teacher and another high school teacher reveals his confusion about the subject in the comments to my post [see Teaching about genomes using Nessa Carey's book: Junk DNA].

It's good that Georgi Marinov makes this point forcibly.

Now I'm going to leave you with an extended quote from Georgi Marinov's review. Coming from a young scientist, this is very potent and it needs to be widely disseminated. I agree 100%.
The reason why scientific results become so distorted on their way from scientists to the public can only be understood in the socioeconomic context in which science is done today. As almost everyone knows at this point, science has existed in a state of insufficient funding and ever increasing competition for limited resources (positions, funding, and the small number of publishing slots in top scientific journals) for a long time now. The best way to win that Darwinian race is to make a big, paradigm shifting finding. But such discoveries are hard to come by, and in many areas might actually never happen again—nothing guarantees that the fundamental discoveries in a given area have not already been made. ... This naturally leads to a publishing environment that pretty much mandates that findings are framed in the most favorable and exciting way, with important caveats and limitations hidden between the lines or missing completely. The author is too young to have directly experienced those times, but has read quite a few papers in top journals from the 1970s and earlier, and has been repeatedly struck by the difference between the open discussion one can find in many of those old articles and the currently dominant practices.

But that same problem is not limited to science itself, it seems to be now prevalent at all steps in the chain of transmission of findings, from the primary literature, through PR departments and press releases, and finally, in the hands of the science journalists and writers who report directly to the lay audience, and who operate under similar pressures to produce eye-catching headlines that can grab the fleeting attention of readers with ever decreasing ability to concentrate on complex and subtle issues. This leads to compound overhyping of results, of which The Deeper Genome is representative, and to truly surreal distortion of the science, such as what one finds in Nessa Carey’s Junk DNA.

The field of functional genomics is especially vulnerable to these trends, as it exists in the hard-to-navigate context of very rapid technological changes, a potential for the generation of truly revolutionary medical technologies, and an often difficult interaction with evolutionary biology, a controversial for a significant portion of society topic. It is not a simple subject to understand and communicate given all these complexities while in the same time the potential and incentives to mislead and misinterpret are great, and the consequences of doing so dire. Failure to properly communicate genomic science can lead to a failure to support and develop the medical breakthroughs it promises to deliver, or what might be even worse, to implement them in such a way that some of the dystopian futures imagined by sci-fi authors become reality. In addition, lending support to anti-evolutionary forces in society by distorting the science in a way that makes it appear to undermine evolutionary theory has profound consequences that given the fundamental importance of evolution for the proper understanding of humanity’s place in nature go far beyond making life even more difficult for teachers and educators of even the general destruction of science education. Writing on these issues should exercise the needed care and make sure that facts and their best interpretations are accurately reported. Instead, books such as The Deeper Genome and Junk DNA are prime examples of the negative trends outlined above, and are guaranteed to only generate even deeper confusion.
It's not easy to explain these things to a general audience, especially an audience that has been inundated with false information and false ideas. I'm going to give it a try but it's taking a lot more effort than I imagined.

1. Georgi Marinov is an author on the original ENCODE paper that claimed 80% of our genome is functional (ENCODE Project Consortium, 2012) and the paper where the ENCODE leaders retreated from that claim (Kellis et al., 2014).

ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 48957-74. [doi: 10.1038/nature11247]

Kellis, M., Wold, B., Snyder, M.P., Bernstein, B.E., Kundaje, A., Marinov, G.K., Ward, L.D., Birney, E., Crawford, G.E., and Dekker, J. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. (USA) 111:6131-6138. [doi: 10.1073/pnas.1318948111]

When philosophers write about evolution

The latest issue of Evolution: Education and Outreach contains a review of two books about evolution written by philosophers. The author of the review is Egbert Giles Leigh Jr. You can read it for free at: Questions about NeoDarwinism: a review of two books.

The books are,
Mind and Cosmos: Why the Materialist NeoDarwinian Conception of Nature is Almost Certainly False by Thomas Nagel. New York: Oxford University Press, 2012. ISBN 978-0-19-991975-8.

Are You an Illusion? by Mary Midgley. New York, NY: Routledge. 2014. ISBN 978-1-84465-792-6.
Both of these books challenge the idea that random mutation and natural selection can explain the world we see around us today.

The reviewer responds with a defense of natural selection from an adaptationist perspective.

I think Nagel and Midgley are wrong but for different reasons. I think that the history of life is the culmination of many random and accidental events and it could easily have gone in different directions [see Replaying life's tape]. I also think that lots of modern features are epiphenomena and not adaptations. Consciousness, to the extent that it actually exists, is one of them.

Nevertheless, Leigh's review is interesting and informative and I urge you to read it if you are interested in knowing why philosophers attack evolution. It helps us understand, once again, where philosophy is going wrong.

Friday, March 25, 2016

Teaching about genomes using Nessa Carey's book: Junk DNA

Nessa Carey's book about junk DNA is an embarrassment to the scientific community [Nessa Carey doesn't understand junk DNA] [The "Insulation Theory of Junk DNA"].

Today, while searching for articles on junk DNA, I came across a review of Nessa Carey's book published in The American Biology Teacher: DNA. The review was written by teacher in Colorado and she liked the book very much. Here's the opening paragraph,
The term junk DNA has been used to describe DNA that does not code for proteins or polypeptides. Recent research has made this term obsolete, and Nessa Carey elaborates on a wide spectrum of examples of ways in which DNA contributes to cell function in addition to coding for proteins. As in her earlier book, The Epigenetics Revolution (reviewed by ABT in 2013), Carey uses analogies and diagrams to relate complicated information. Although she unavoidably uses some jargon, she provides the necessary background for the nonbiologist.
The author of the review does not question or challenge the opinions of Nessa Carey and, if you think about it, that's understandable. The average biology teacher will assume that a book written by a scientist must be basically correct or it wouldn't have been published.

That's not true, as most Sandwalk readers know. You would think that biology educators should know this and exercise a little skepticism when reviewing books. Ideally, the book reviews should be written by experts who can evaluate the material in the book.

Now we have a problem. The way to correct false information about genomes and junk DNA is to teach it correctly in high school and university courses. But that means we first have to teach the teachers. Here's a case where professional teachers have been bamboozled by a bad book and that's going of make it even more difficult to correct the problem.

The last paragraph of the review shows us what influence a bad book can have,
As a biology teacher who enjoys sharing with students some details that go beyond the textbook or that challenge dogma, I enthusiastically read multiple chapters at each sitting, making note of what I cannot wait to add to class discussions. “Junk DNA” may be a misnomer, but Junk DNA is an excellent way of finding out why.
Oh dear. It's going to be hard to re-educate those students once their misconceptions have been reinforced by a teacher they respect.

Tuesday, March 22, 2016

How do you characterize these scientists?

We've been having a discussion on another thread about ID proponents. Are some of them acting in good faith or are they all lying and deceiving their followers?

I have similar problems about many scientists. I've been reading up on pervasive transcription and the potential number of genes for noncoding, functional, RNAs in the human genome. As far as I can tell, there are only a few hundred examples that have any supporting evidence. There are good scientific reasons to believe that most of the detected transcripts are junk RNA produced as the result of accidental, spurious, transcription.

There are about 20,000 protein-coding genes in the human genome. I think it's unlikely that there are more than a few thousand genes for functional RNAs for a total of less than 25,000 genes.

Here's one of the papers I found.
Guil, S. and Esteller, M. (2015) RNA–RNA interactions in gene regulation: the coding and noncoding players. Trends in Biochemical Sciences 40:248-256. [doi: 10.1016/j.tibs.2015.03.001]
Trends in Biochemical Sciences is a good journal and this is a review of the field by supposed experts. The authors are from the Department of Physiological Sciences II at the University of Barcelona School of Medicine in Barcelona, Catalonia, Spain. The senior author, Manel Esteller, has a Wikipedia entry [Manel Esteller].

Here's the first paragraph of the introduction.
There are more genes encoding regulatory RNAs than encoding proteins. This evidence, obtained in recent years from the sum of numerous post-genomic deep-sequencing studies, give a good clue of the gigantic step we have taken from the years of the central dogma: one gene gives rise to one RNA to produce one protein.
The first sentence is not true by any stretch of the imagination. The best that could be said is that there "may" be more genes for regulatory RNAs (> 20,000) but there's no strong consensus yet. Since the first sentence is an untruth, it follows that it is incorrect to say that the evidence supports such a claim.

It's also untrue to distort the real meaning of the Central Dogma of Molecular Biology, which never said that all genes have to encode proteins. The authors don't understand the history of their field in spite of the fact they are writing a review of that field.

Here's the problem. Are these scientists acting in good faith when they say such nonsense? Does acting in "good faith" require healthy criticism and critical thinking or is "honesty" the only criterion? The authors are clearly deluded about the controversy since they assume that it has been resolved in favor of their personal biases but they aren't lying. Can we distinguish between competent science and bad science based on such statements? Can we say that these scientists are incompetent or is that too harsh?

Furthermore, what ever happened to peer review? Isn't the system supposed to prevent such mistakes?

Sunday, March 20, 2016

Another failure: "The Mysterious World of the Human Genome"

The Mysterious World of the Human Genome
by Frank Ryan
William Collins, an imprint of Harper Collins, London UK (2015)
ISBN 978-0-00-754906-1

This is just another "gosh, gee whiz" book on the amazing and revolutionary (not!) discoveries about the human genome. The title tells you what to expect: The Mysterious World of the Human Genome.

The author is Frank P. Ryan, a physician who was employed as an "Honorary Senior Lecturer" in the Department of Medical Education at the University of Sheffield (UK). He's a member of The Third Way group. You can read more about him at their website: Frank P. Ryan.

You need to understand biology if you are going to debate an Intelligent Design Creationist

Last night's debate between Lawrence Krauss, Stephen Meyer, and Denis Lamoureux was very entertaining. I finally got to meet Stephen Meyer in person. (My photographer wasn't very good at focusing.)

There were some interesting exchanges during the debate. I want to talk about one of them.

Krauss tried to hammer Meyer on the "ID is not science" issue using quotes from a judge based on things said by lawyers in the Dover trial.1 Krauss tried to dismiss ID by saying that it never makes predictions but Meyer countered effectively by pointing out that ID predicts that most of our genome is functional and claiming that the prediction was confirmed by the ENCODE study.

The ID position is that Darwinists predicted that our genome would be full of junk while Intelligent Design Creationists predicted that most of our genome would be functional. ID was correct and Darwinism was wrong, according to this story.

Both Lawrence Krauss and Denis Lamoureux accepted the "fact" that ENCODE was right and most of the DNA in our genome has a function. Krauss was also hampered by his misunderstanding of evolution. It's obvious that he accepts the Richard Dawkins view of evolution so he tried to accommodate the ENCODE results by saying it's what you would expect of natural selection. This is the Richard Dawkins position.

Krauss tried to downplay the issue by saying that ID had not predicted what those functional parts of the genome would be doing but this was a weak rebuttal.

The facts are these ....
  • "Darwinists"—those who claim that natural selection is the only game in town—were opposed to the idea that most of our genome is junk. They still are.
  • Today, the majority of experts believe that most of our genome is junk in spite of the ENCODE publicity campaign from 2012.
  • The ENCODE Consortium has backed off it's original claim and now agrees that they misused the word "function." Some of them blame the media for distorting their position.
  • The ID "prediction" has been falsified.
A competent biologist would have known all this and could have challenged Meyer's statement. A biologist would have then demanded that Meyer explain how a genome that is 90% junk fits with Intelligent Design Creationism.

I talked to Denis Lamoureux after the debate to let him know that he was wrong about ENCODE and he was very gracious. I promised to send him more information. A genome full of junk DNA poses no threat to his version of Theistic Evolution.

Lawrence Krauss is an expert on cosmology but he's very weak on biology. I know it's common for physicists to think they are experts in everything but that's just not true. It was demonstrated in last night's debate.

1. This is a bad strategy. It's better to accept that ID proponents are doing science but just doing it very badly. Meyer ignored the issue of whether ID counted as science. He just presented the scientific case for ID and forced Krauss to respond to his "evidence."

Saturday, March 19, 2016

God, Science, and the Universe

Today's the day we find out "What's Behind It All?" The decision will be announced at the University of Toronto (Toronto, Ontario, Canada) by Lawrence Krauss when he educates the audience at Convocation Hall starting at 7 pm. Stephen Meyer (Intelligent Design Creationist) and Denis Lamoureux (Theistic Evolution Creationist) will also be there to learn the answer. (Spoiler Alert: the answer is "nothing.")
It's not too late to buy tickets. Email me if you want to join some of us for dinner before the event.

The event is being sponsored by Wycliffe College at the University of Toronto. This is an Anglican College that trains people to become Anglican Ministers (among other things). The college is the prime mover behind this series of events and it deserves a great deal of credit for the effort. Co-sponsors include the Centre for Inquiry, Canada and three Christian groups.

The event is being video-hosted at many locations around the world. See the list here. If you don't want to watch with others, you can see the live stream on YouTube at: Krauss, Meyer, Lamoureux: What’s Behind it all? God, Science and the Universe. It starts at 7 pm EST. (It's probably over already in Australia.)

The ID crowd is already anticipating defeat so they're preparing their audience by warning them that Lawrence Krauss will be nasty (i.e. refute their arguments) [see Watch Meyer Take on Krauss and Lamoureux, Streaming Live at Evolution News on March 19]. (Warning: check your irony meters before reading the first paragraph.)
Those on the Darwinist, materialist, atheist side of the debate that we follow here aren't normally very good at listening and responding to scientific perspectives at variance from their own. They are much more interested in condemning and ridiculing -- which has got to be a poor strategy for them if they want to persuade anyone.

With that as the background, as we noted already, it's refreshing that arch-atheist cosmologist Lawrence Krauss has agreed to participate in a public conversation with Discovery Institute's Stephen Meyer, joined by theistic evolutionist Denis Lamoureux. That will be March 19 at the University of Toronto's Convocation Hall. We're looking forward to it -- and here's the even better news. You won't have to be in Toronto to enjoy the discussion. The event will stream live here at Evolution News.

Monday, March 14, 2016

The best TED talk ever

I'm not a fan of TED talks. Comedian Will Stephen has figured them out and he gives a perfect example of everything that's wrong with a TED talk. Watch "How to sound smart in your TEDx Talk."

Sunday, March 13, 2016

Paradigm shifting

I was reading up on non-coding RNAs and came across this recent paper.
Bhartiya, D., and Scaria, V. (2016) Genomic variations in non-coding RNAs: Structure, function and regulation. Genomics 107:59-68. [doi: 10.1016/j.ygeno.2016.01.005]

Abstract: The last decade has seen tremendous improvements in the understanding of human variations and their association with human traits and diseases. The availability of high-resolution map of the human transcriptome and the discovery of a large number of non-protein coding RNA genes has created a paradigm shift in the understanding of functional variations in non-coding RNAs. Several groups in recent years have reported functional variations and trait or disease associated variations mapping to non-coding RNAs including microRNAs, small nucleolar RNAs and long non-coding RNAs. The understanding of the functional consequences of variations in non-coding RNAs has been largely restricted by the limitations in understanding the functionalities of the non-coding RNAs. In this short review, we outline the current state-of-the-art of the field with emphasis on providing a conceptual outline as on how variations could modulate changes in the sequence, structure, and thereby the functionality of non-coding RNAs.
The concept of a scientific paradigm and a "paradigm shift" was promoted by Thomas Kuhn. His most popular work was The Structure of Scientific Revolutions, published in 1962.

Wednesday, March 09, 2016

University of Toronto post-doc shares lab notes

The University of Toronto publicity department is making a big deal of Rachel Harding. She's a post-doc in the Structural Genomics Consortium (SGC). She works on Huntington's disease.

Here's the link to the press release and the first few paragraphs [Researcher is an Open Book: First to Share Lab Notes in Real Time].

Faculty of Medicine researcher Rachel Harding will be the first known biomedical researcher to welcome the world to review her lab notes in real time. The post-doctoral fellow with U of T’s Structural Genomics Consortium (SGC) is also explaining her findings to the general public through her blog. She hopes her open approach will accelerate research into Huntington’s disease.

“This should drive the process faster than working alone,” Harding says. “By sharing my notes, I hope that other scientists will critique my work, collaborate and share data in the early stages of research.” Her research at SGC is funded by CHDI Foundation, a non-profit drug-development organization exclusively dedicated to Huntington’s disease. Both organizations aim to accelerate research by making it open and collaborative.

Her approach is intended to leverage the experience of a community of scientists. Individual researchers often still work in relative isolation and then publish only their positive discoveries, usually years after the experiments were actually done. Thus, scientists often pursue similar ideas in parallel and miss many opportunities to learn from each other’s mistakes.

She has started by publishing raw data and play-by-play details of her first effort on the CERN open digital repository Zenodo. She also posts regular updates on her blog Lab Scribbles, where she includes an experimental summary written in lay terms.

It's been over 35 years since I first starting thinking and talking about electronic (computerized) lab notes1 and it's been over twenty years since I first heard discussions about putting them online. I seriously doubt that Rachel Harding is the first biomedical researcher to put lab notes on the web. I'm also very skeptical about her keeping up the practice for very long.

Not only is it boring and tedious to write your lab notes in a word processing program but it's kinda embarrassing to post everything you do in the lab. At least it would have been for me. I made lots of mistakes and there are lots of R-rated words and phrases in my notes.

Let's keep an eye on this experiments to see how it goes. So far there are four items on the Zenodo website. The first is a Word document containing a few brief notes from Jan. 6, 7, 9, 11 and 25. There are brief notes posted on Feb. 6 and two on Feb. 11. I hope this isn't the extent of her lab notes.

The blog is Lab Scribbles. There are a few posts. It's interesting but I'm not sure anyone is going to read it even if you're interested in Huntington's.

Has anyone else experimented with open lab notes?

1. I still have a few floppy disks with those attempts from about 1981. Unfortunately, I don't have a machine that can read them.

A 2004 kerfuffle over pervasive transcription in the mouse genome

The first drafts of the human genome sequence were published in 2001. There was still work to do on "finishing" the sequence but a lot of the International Human Genome Project (IHGP) team shifted to work on the mouse genome. The FANTOM Consortium and the RIKEN Genome Exploration Groups (I and II) published an analysis of mouse transcripts in December 2002.
Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H. et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420:563-573. [doi: 10.1038/nature01266]

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 ‘transcriptional units’, contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense–antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Wednesday, March 02, 2016

When philosophers talk about genomes

Postgenomics is a compendium of twelve scholarly articles by philosophers and sociologists who write about the implication of the human genome sequence and subsequent work on interpreting the results. The volume is edited by Sarah Richardson, a professor in Social Sciences (History of Science) at Harvard University (Boston, Massachusetts, USA), and by Hallam Stevens, a professor of History at Nanyang Technology University in Singapore (Singapore).

The first essay is by Stevens and Richardson and it outlines the goal of the book.