After years of negotiation between the administration and the Faculty Association, the university has finally allowed full time lecturers to calls themselves "professors" [U of T introduces new teaching stream professorial ranks]. This brings my university into line with some other progressive universities that recognize the value of teaching.
Unfortunately, the news isn't all good. These new professors will have a qualifier attached to their titles. The new positions are: assistant professor (conditional), teaching stream; assistant professor, teaching stream; associate professor, teaching stream; and professor, teaching stream. Research and scholarly activity is an important component of these positions. The fact that the activity is in the field of pedagogy or the discipline in which they teach should not make a difference.
Meanwhile, current professors will not have qualifiers such as "professor: research," or "professor: administration," or "professor: physician," or "professor: mostly teaching."
The next step is to increase the status of these new professors by making searches more rigorous and more competitive, by keeping the salaries competitive with other professors in the university, and by insisting on high quality research and scholarly activity in the field of pedagogy. The new professors will have to establish an national and international reputation in their field just like other professors. They will have to publish in the pedagogical literature. They are not just lecturers. Almost all of them can do this if they are given the chance.
Some departments have to change the way they treat the new professors. The University of Toronto Faculty Association (UTFA) has published a guideline: Teaching Stream Workload. Here's the part on research and scholarly activity ....
In section 7.2, the WLPP offers the following definition of scholarship: “Scholarship refers to any combination of discipline-based scholarship in relation to or relevant to the field in which the faculty member teaches, the scholarship of teaching and learning, and creative/professional activities. Teaching stream faculty are entitled to reasonable time for pedagogical/professional development in determining workload.”
It is imperative that teaching stream faculty have enough time in their schedules, that is, enough “space” in their appointments, to allow for the “continued pedagogical/professional development” that the appointments policy (PPAA) calls for. Faculty teaching excessive numbers of courses or with excessive administrative loads will not have the time to engage in scholarly activity. Remember that UTFA fought an Association grievance to win the right for teaching stream faculty to “count” their discipline-based scholarship. That scholarship “counts” in both PTR review and review for promotion to senior lecturer.
And here's a rule that many departments disobey ...
Under 4.1, the WLPP reminds us of a Memorandum of Agreement workload protection: “faculty will not be required to teach in all three terms, nor shall they be pressured to volunteer to do so.” Any faculty member who must teach in all three terms should come to see UTFA.
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!
Intelligent Design Creationists often get upset when I refer to them as creationists. They think that the word "creationist" has only one meaning; namely, a person who believes in the literal truth of Genesis in the Judeo-Christian Bible. The fact that this definition applies to many (most?) intelligent design advocates is irrelevant to them since they like to point out that many ID proponents are not biblical literalists.
There's another definition of "creationist" that's quite different and just as common throughout the world. We've been describing this other definition to ID proponents for over two decades but they refuse to listen. We've been explaining why it's quite legitimate to refer to them as Intelligent Design Creationists but there's hardly any evidence that they are paying attention. This isn't really a surprise.
God Only Knows is one of my favorite pop songs.1 It's from the Pet Sounds album by the Beach Boys (1966).
Experts have admired Brian Wilson and the Beach Boys for decades but most people have forgotten (or never knew) about their best songs. (Good Vibrations was released as a single at the same time as Pet Sounds.)
I haven't yet seen the movie about Brian Wilson (Love & Mercy).
The first video is a BBC production from 2014 paying tribute to (and featuring) Brian Wilson. The second video is from 1966.
1. I will delete any snarky comments about God and atheism.
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.
Intelligent Design Creationists are committed to the idea that most of our genome is functional. They oppose the idea that a significant proportion is junk. It's easy to see why a junky genome is incompatible with intelligent design but there's something more to their opposition than that.
I think they've painted themselves into a corner. They are so opposed to evolution and modern science that they will take any opportunity to discredit it. They saw a chance to do so about twenty years ago when they became aware of the controversy surrounding junk DNA. This was their chance to (pretend to) rely on real science to back their position. By taking a stance against junk DNA they could seen to be supporting the latest evidence ... or so they thought.
Intelligent Design Creationists claim that they "predicted" that most our genome would be functional. They claim that "Darwinists" predicted junk DNA. The second part isn't true since evolutionary theory is silent on whether some genomes could become bloated with junk DNA or not. However, the ID proponents are sticking to their guns in spite of the growing consensus that most of our genome is junk.
It's Sunday. I assume that most of you are at church but here's something for the rest of you. It's a sermon by William Lane Craig on The Moral Argument for the Existence of Gods. I found the link on Evolution News & Views (sic) a blog that's devoted to the "science" of Intelligent Design Creationism [Watch: Three from William Lane Craig]. I'm not sure what this has to do with evolution except that the word is mentioned a few times in the videos.
I'm also not sure what this has to do with intelligent design since, as we all know, the "science" of intelligent design has nothing to do with gods.
The National Academies of Sciences (USA) formed a committee to look into scientific integrity. A summary of the report was published in the June 26th issue of Science (Alberts et al., 2015)
I'd like to highlight two paragraphs of that report.
Like all human endeavors, science is imperfect. However, as Robert Merton noted more than half a century ago "the activities of scientists are subject to rigorous policing, to a degree perhaps unparalleled in any other field of activity." As a result, as Popper argued, "science is one of the very few human activities—perhaps the only one—in which errors are systematically criticized and fairly often, in time, corrected." Instances in which scientists detect and address flaws in work constitute evidence of success, not failure, because they demonstrate the underlying protective mechanisms of science at work.
All scientists know this, but some of us still get upset when other scientists correct our mistakes. We have learned to deal with such criticism—and dish it out ourselves—because we know that's how knowledge advances. Our standards are high.
I've just read Conceptual Breakthroughs in Evolutionary Genetics by John Avise. Avise is a Distinguished Professor of Ecology & Evolutionary Biology in the School of Biological Sciences at the University of Califonia at Davis (Davis, California, USA). He has written a number of excellent books including, Inside the Human Genome: A Case for Non-Intelligent Design.
His latest book consists of 70 idiosyncratic "breakthroughs" that have changed the way we think about biology. Each one is introduced with a short paragraph outlining "The Standard Paradigm" followed by another paragraph on "The Conceptual Revolution." There are 70 chapters, one for each "breakthrough," and all of them are two pages in length.
Chapter 42 is entitled: "1970 The Flow of Information."
Here's the "standard paradigm" according to John Avise.
In biochemical genetics, the molecular direction of information flow is invariably from DNA → RNA → protein. In other words, DNA is first transcribed into RNA, which then may be translated into polypeptides that make up proteins. This view was so ensconced in the field that it had become known as the "central dogma" (Crick, 1970) of molecular biology.
It's true that the Watson version of the Central Dogma was "ensconced" by 1970 and it's true that the incorrect Watson version is still "ensconced" in the textbooks.
... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. (F.H.C. Crick, 1970)
The version that John Avise refers to is the incorrect version promoted by Jim Watson.
I understand that many biologists have been taught an incorrect version of the Central Dogma but if you are going to write about it you are wise to read the original papers. In this case, Avise quotes the correct paper but he clearly has not read it.
Now let's look at the "conceptual revolution" according to John Avise.
Researchers showed that biochemical information could also flow from RNA → DNA. The key discovery came when Howard Temin and David Baltimore, working independently and on different viral systems, identified an enzyme (reverse transcriptase) that catalyzes the conversion of RNA into DNA, thus enabling the passage of genetic information in a direction contrary to the central dogma.
How do I know that John Avise has not read Crick's 1970 paper? Because here's what Crick says in that paper ...
"The central dogma, enunciated by Crick in 1958 and the keystone of molecular biology ever since, is likely to prove a considerable over-simplification."
This quotation is taken from the beginning of an unsigned article headed "Central dogma reversed", recounting the very important work of Dr Howard Temin and others showing that an RNA tumor virus can use viral RNA as a template for DNA synthesis. This is not the first time that the idea of the central dogma has been misunderstood, in one way or another. In this article I explain why the term was originally introduced, its true meaning, and state why I think that, properly understood, it is still an idea of fundamental importance.
Crick tells us that the discovery of reverse transcriptase did NOT conflict with the central dogma. Thus, John Avise's conceptual revolution never happened. What happened instead, at least for some biologists, is that the discovery of reverse transcriptase taught them that their view of the central dogma was wrong. Most biologists still haven't experienced that particular conceptual revolution.
Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. XII:138-163.
Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227, 561-563. [PDF file]
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.
My copy of The Deeper Genome: Why there's more to the human genome than meets the eye has arrived and I've finished reading it. It's a huge disappointment. Parrington makes no attempt to describe what's in your genome in more than general hand-waving terms. His main theme is that the genome is really complicated and so are we. Gosh, golly, gee whiz! Re-write the textbooks!
You will look in vain for any hard numbers such as the total number of genes or the amount of the genome devoted to centromeres, regulatory sequences etc. etc. [see What's in your genome?]. Instead, you will find a wishy-washy defense of ENCODE results and tributes to the views of John Mattick.
John Parrington is an Associate Professor of Cellular & Molecular Pharmacology at the University of Oxford (Oxford, UK). He works on the physiology of calcium signalling in mammals. This should make him well-qualified to write a book about biochemistry, molecular biology, and genomes. Unfortunately, his writing leaves a great deal to be desired. He seems to be part of a younger generation of scientists who were poorly trained as graduate students (he got his Ph.D. in 1992). He exhibits the same kind of fuzzy thinking as many of the ENCODE leaders.
My copy of John Parrington's new book, The Deeper Genome: Why there is more to the human genome than meets the eye, is due to arrive in about three weeks. However, we already have a number of clues about what's in the book [see How the genome lost its junk according to John Parrington]. The excerpt on Amazon [How the genome lost its junk] tells us that Parrington is aware of the controversy surrounding the ENCODE project but comes down on the side of ENCODE.
That view is shared by science writer Claire Ainsworth who wrote a review in New Scientist: Its' so last century.1 Ainsworth is a freelance science writer with a Ph.D. in developmental genetics from Oxford (Oxford, UK). She is co-founder of SciConnect, a company that teaches science communication skills to scientists.
Here's what she says in her review ....
John Parrington is an associate professor in molecular and cellular pharmacology at the University of Oxford. In The Deeper Genome, he provides an elegant, accessible account of the profound and unexpected complexities of the human genome, and shows how many ideas developed in the 20th century are being overturned.
Take DNA. It's no simple linear code, but an intricately wound, 3D structure that coils and uncoils as its genes are read and spliced in myriad ways. Forget genes as discrete, protein-coding "beads on a string": only a tiny fraction of the genome codes for proteins, and anyway, no one knows exactly what a gene is any more.
A key driver of this new view is ENCODE, the Encyclopedia of DNA Elements, which is an ambitious international project to identify the functional parts of the human genome. In 2012, it revealed not only that the protein-coding elements of DNA can overlap, but that the 98 per cent of the genome that used to be labelled inactive "junk" is nothing of the sort. Some of it regulates gene activity, some churns out an array of different kinds of RNA molecules (RNAs for short), some tiny, some large, many of whose functions are hotly debated. Parrington quotes ENCODE scientist Ewan Birney as saying at the time, "It's a jungle in there. It's full of things doing stuff." And that is one of the most apt genome metaphors I've ever read.
People, including science writers, can have different opinions about the validity of the ENCODE results and whether most of our genome is junk. They can also have different opinions about whether many of the ideas developed in the 20th century are still valid. However, I think it's only fair to at least acknowledge that others may have different opinions.
Ainsworth must be aware of the controversy over ENCODE's claim that most of our genome has a function. She could have pointed out that Parrington supports the function side but many prominent scientists support the junk DNA side. She could have noted that there have been several scientific papers published since 2012 that defend the concept of junk DNA—and defend it very well.
A good science journalist can express an opinion on a scientific controversy but good science journalists are obliged to point out to their readers that this is just an opinion and there are many expert scientists who disagree.
The readers of this New Scientist book review will think that ENCODE was the last word on the debate and that's not good science reporting.
1. The title of the online version is "DNA is life's blueprint? No, there's far more to it than that."
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."
I posted this photo on Facebook yesterday. It shows a large sign on the side of Princess Margaret Hospital (Toronto, Ontario, Canada) saying "WHY IS IN OUR DNA." (Click to embiggen.)
Similar signs are appearing all over Toronto, especially at bus stops and in the subway.
What the heck does it mean? The best response on Facebook was that they meant to say "Y is in our DNA" but I don't think that's what they meant. Maybe they are talking about genetic diseases? Maybe they're asking if 90% of our genome is junk? Are they questioning whether "it" is in our DNA (Why is it in our DNA?)? Are they talking about cancer? (The research wing of Princess Margaret Hospital studies cancer.)
As it turns out, none of the above. Here's the real story: Why is in Our DNA. It's straight from the The Princess Margaret Cancer Foundation press release.
As The Princess Margaret Cancer Foundation continues to raise funds for one of the top 5 cancer research centres in the world, we’re asked often: Why is The Princess Margaret a world leader? There are many reasons the centre has achieved a world-class reputation, but this spring, in our communications with donors and the public, we are focusing on one reason—our scientists and researchers never stop asking why…
Why is the body’s immune system not able to fight off all cancers? Why does cancer return in some patients? Why did a particular cancer drug work for one patient but not any of the others? Why did one patient’s tumour shrink dramatically with radiation, but another’s barely at all?
Starting in May, you’ll see on banners outside the cancer centre, the Princess Margaret Cancer Research Tower and in various media: WHY is in our DNA. This ‘Why gene’ that our team possesses in abundance has already helped to build The Princess Margaret’s rich history of discovery and innovation, ...
Now I get it. It's because scientists at PMH have a "why" gene.
I wonder what PR firm they hired and whether they thought this through? At the very least, this is a case where punctuation would help: "Why?" is in our DNA. Maybe they should have also put a disclaimer at the bottom: "But not in your DNA."
Intelligent Design Creationists like to pretend that their particular version of creationism is scientific. They claim they have evidence of an intelligent designer (gods), but 99% of their literature is an attack on evolution and not a defense of a new scientific theory. Those attacks take many forms but the worst ones are the attempts to smear Darwin and associate evolutionary biology with racism and the holocaust.
Of course, no one I've referred to endorses Dylann Roof's murderous rampage. I don't doubt that they are all sincerely mortified by the association, however unintended, with such unapologetic, undisguised evil.
I mention this at all not to blame them for Roof's crime, in any way, but simply to note -- because the mainstream media covers it up -- how certain ideas tend to hang together.
The racial elements in Charles Darwin's writing, the eugenicist implications, are often brushed aside as ugly but incidental, a mere byproduct of his time and place. Yet the myth of European superiority over inferior dark peoples continues to percolate in some evolutionary thinking, a century and more after the close of the Victorian era. It seems to have found an eager student in a disturbed young man named Dylann Roof.
I'm working my way through Jerry Coyne's new book. There's lots of good stuff in there but I was particularly interested in his comment about his former Ph.D. supervisor, Richard Lewontin. The issue is whether science is confined to methodological naturalism leaving religion as the only way to investigate supernatural claims.
We've been over this many times in the past few decades but it's still worth reminding people of the only rational response to such a claim. This is from pages 91 and 92 of Faith vs. Fact: Why Science and Religion Are Incompatible.
... some scientists persist in claiming, wrongly, that naturalism is a set-in-stone rule of science. One of these is my Ph.D. advisor, Richard Lewontin. In a review of Carl Sagan's wonderful book The Demon Haunted World, Lewontin tried to explain the methods of science:
It is not that the methods and institutions of science somehow compel us to accept material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.
That quotation has been promulgated with delight by both creationists and theologians, for it seems to show the narrow-mindedness of scientists who refuse to even admit the possibility of the supernatural and immaterial. But Lewontin was mistaken. We can in principle allow a Divine Foot in the door; it's just that we've never seen the Foot. If, for example, supernatural phenomena like healing through prayer, accurate religious prophecies, and recollection of past lives surfaced with regularity and credibility, we might be forced to abandon our adherence to purely natural explanations. And in fact we've sometimes put naturalism aside by taking some of these claims seriously and trying to study them. Examples include ESP at other "paranormal phenomena" that lack any naturalistic explanation.
Sadly, arguments similar to Lewontin's—that naturalism is a unbreakable rule of science—are echoed by scientific organizations that want to avoid alienating religious people. Liberal believers can be useful allies fighting creationism, but accommodationists fear that those believers will be driven away by any claim that science can tackle the supernatural. Better to keep comity and pretend that science by definition can say nothing about the divine. This coddling of religious sentiments was demonstrated by Eugenie Scott, the former director of an otherwise admirable anti-creationist organization, the National Center for Science Education:
First, science is a limited way of knowing, in which practitioners attempt to explain the natural world using natural explanations. By definition, science cannot consider supernatural explanations: if there is an omnipotent deity, there is no way that a scientist can exclude or include it in a research design. This is especially clear in experimental research: an omnipotent deity cannot be "controlled" (as one wag commented, "you can't put God in a test tube, or keep them out of one"). So by definition, if an individual is attempting to explain some aspect of the natural world using science, he or she must act as if there were no supernatural forces operating on it. I think this methodological naturalism is well understood by evolutionists.
Note that Scott claims naturalism as part of the definition of science. But that's incorrect, for nothing in science prohibits us from considering supernatural explanations. Of course, if you define "supernatural" as "that which cannot be investigated by science," then Scott's claims become tautologically true. Otherwise, it's both glib and misleading to say that God is off-limits because he can't be "controlled" or "put in a test tube." Every study of spiritual healing or the efficacy of prayer (which, if done properly, includes controls) puts God into a test tube. It's the same for tests of non-divine supernatural phenomena like ESP, ghosts, and out-of-body experiences. If something is supposed to exist in a way that has tangible effects of the universe, it falls within the ambit of science. And supernatural beings and phenomena can have real-world effects.
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.
I do not agree with those who dismiss Intelligent Design Creationism because it is not science. I prefer to think of it as an approach that superficially resembles the scientific approach but fails in various ways. In this sense, it's not much different from lots of other bad examples of science.
Let's look at the way Intelligent Design Creationists describe their attempt to be scientific. This is from a recent post by that well-known scientist,1 Casy Luskin, on Eovlution News & Views (sic) [Does Intelligent Design Deserve Academic Freedom?]. In that post, Luskin lists four criteria proving that ID is a genuine scientific theory.
It's the first point on the list that I want to discuss. The link takes you to a brief description of how Intelligent Design Creationism uses the scientific method to prove that gods played a role in the history of life. Here's how it works ...
The diagram on the right shows the initial disposition of the Anglo-Dutch army under Wellington (red) and the French Army under Napoleon (blue). You can see how they got there by reading my earlier posts [Thursday, June 15, 1815 , Friday, June 16, 1815 , and Saturday, June 17, 1815 ].
There are many detailed descriptions of the battle online so I'm not going to bother with details. The French armies had to eliminate the fortified positions at Hougoumont, La Haye Sainte, and Papelotte. They succeeded at La Haye Saint and Papelotte but the British held on to Hougoumont. This is one of the decisive skirmishes of the battle. The French committed far too many troops to the attack on Hougomount and wasted far too much time.
The diagram on the left shows the situation late in the day when the Imperial Guard is attacking Wellington's center. That attack was driven back and the retreat of the elite Imperial Guard triggered a general retreat of all French forces. Wellington signaled a general advance that didn't stop until the allies reached Paris.
Note the Prussians attacking from the East (right) the French corps under Grouchy had not prevented Blücher from carrying out his promise to support Wellington. The French were doomed as long as Wellington held out until the end of the day and that's what happened.
I've been to the battlefield twice. Here's a photo from 2010 when I went with my daughter, son-in-law, and newly born granddaughter. The big hill behind them was made for tourists so they could get an overview of the battlefield from the top. Most people think it ruined the site.
There are monuments to various military leaders all over the battlefield. Most of the thousands of men who died that day have no monuments to mark where they fell. One of Ms. Sandwalk's distant cousins, Isabella Hood, was married to John Whyte of the British Dragoons. He died at Waterloo. His wife moved to Canada.
Watch Jeffrey Tomkins of The Institute for Creation Science teach us about the very latest (not!) research in genomics. I haven't bothered counting the errors and misrepresentations in this video. I'm pretty sure it would take me a lot longer than 17 minutes to show where he is wrong. That's the problem.
Click on the figure below the video to show the human/chimp sequence comparison for chromosome 2 (top) and chromosome 7 (bottom). Note that the red dots fluctuate between 98-99% across the entire lengths except for a few gaps and duplications. Keep your eye on the figure as you listen to Jeffrey Tomkins tell us how the real difference is 66-85%.
Also, note how this level of similarity extends all across chromosome 2 where the comparison is to two separate chimp chromosomes. Examine the figure while Tomkins explains that the chromosome fusion idea is wrong.
After the defeat at Ligny, the Prussians retreated in good order to Wavre and by Saturday, June 17th a large part of the Prussian army had reached that town.
Meanwhile, Wellington had massed his forces on the ridge south of Mont St. Jean and he was fortifying the farm at Hougoumont on his right and the village of Papelotte on his left. In addition, he placed a garrison in La Haye Sainte, a farm right in front of his center on the main road to Brussels. As usual, most of Wellington's troops were posted on the reverse slope of the ridge where they could not be easily seen by the advancing French army and they were partially protected from cannon fire.
The map on the right (above) shows the positions of the armies on each day. As you can see, the Prussians were well-positioned to come to the aid of Wellington by advancing troops from Wavre toward the battlefield at Mont St. Jean (Waterloo). Wellington and Blücher were in touch during this day of preparation and Blücher promised to attack the French right on the following day.
The map on the right (above) shows Grouchy marching off to the East but this is not accurate. Grouchy did keep in touch with the Prussians retreating down the road to Wavre and there was a battle at Wavre the next day. However, Grouchy did not press the Prussians as hard as he should have and he did nothing to prevent them from coming to the aid of Wellington the next day. All historians agree that this failure on the part of Grouchy played a major role in Napoleon's defeat. The second map is a bit better.
Napoleon joined Ney at Quatre-Bras and pursued the Anglo-Dutch army down the road to Brussels. The French were not able to bring up their forces very quickly so they were not in position to attack on the 17th.
By that evening the French had amassed 48,000 infantry, 14,000 cavalry, and 250 guns. Wellington's force consisted of 50,000 infantry, 11,000 cavalry, and 150 guns. The Prussians committed 48,000 men out of a force twice that size.
There was a heavy rain that evening. The men huddled in their tents knew that the decisive battle would be fought the next day and thousands of them would never live to see another night.
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?
Napoleon's Army of the North had crossed the Belgian frontier and was advancing toward Brussels. Napoleon had surprised the allied armies with his rapid advance and now they choose the risky strategy of a forward concentration in the face of an enemy attack. The Prussians had an easier task since they choose to concentrate their army at Ligny covering their supply lines to the East. The forward outposts fall back to Ligny under pressure from the French right under Grouchy. [see Battle of Waterloo]
On Thursday evening Wellington attended a ball given by the Duchess of Richmond in Brussels and it wasn't until the early hours of Friday the 16th that he gave orders to concentrate the Anglo-Dutch army at Quatre-Bras. Prince Orange was ordered to hold Quatre-Bras until the rest of the army arrived.
Wellington's strategy was to stay in contact with the Prussians at Ligny where the combined armies could defeat Napoleon. Napoleon's goal was to prevent the allied armies from supporting each other and crush one of them with overwhelming superiority of numbers. As it turned out, neither strategy succeeded on Friday, June 16th.
Ney held the Anglo-Dutch troops at bay around Quatre-Bras in a tough battle with heavy losses. He eventually took the crossroads at Quatre-Bras only to be driven back when Wellington arrived with fresh troops. Meanwhile, Napoloeon attacked the Prussians at Ligny with Grouchy's corps and the reserve that had been under his personal command. The Prussians were defeated but not destroyed [Battle of Ligny].
The map (left) shows the positions on Friday evening as the Prussian center collapses. It also shows the wandering of D'Erlon's corps that never got into either battle. It it had attacked the flank of the Prussian army Napoleon might have gained a decisive victory and if it had supported Ney it could have prevented Wellington's army from using the crossroads at Quatre-Bras. [see Waterloo: Myth and Reality]
Now comes one of the decisive moments of the Waterloo campaign. Blücher's Prussians retreated in orderly fashion on Wavre where he could remain in touch with Wellington who was forced to fall back to Wavre after the position at Quatre-Bras became untenable. Grouchy was ordered to pursue Blücher and prevent the Prussians from supporting the Anglo-Dutch army. Grouchy failed to do this because his corps did not move quickly and was confused about the direction of the Prussian retreat. As we shall see, Grouchy's failure is blamed for the defeat at Waterloo two days later.
Meanwhile, Wellington was able to fall back to a defensive position at Waterloo where he waited for the French army.
"Ligny by Ernest Crofts (1875). This representation of the battle shows Napoleon surrounded by his staff surveying the battlefield while columns of infantry advance to the front. The windmill at Brye on a hill, north west from Ligny, was a good vantage point and Blücher made it his headquarters during the battle, hence in this context it is an iconic symbol of Napoleon's victory." [Battle of Ligny]
Summoned to Waterloo: Brussels, dawn of June 16, 1815 by Robert Alexander Hillingford. Officers leaving the Duchess of Richmond's ball.
Quatre Bras (Black Watch at Bay) by William Barnes Wollen
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]
It was 200 years ago today that Napoleon's army crossed the Belgian border at Charleroi and advanced on Quatre-Bras in order to split the Prussian and British armies. By occupying the central position, Napoleon hoped to defeat each army separately and occupy Brussels and the channel ports.
Neither Blücher nor Wellington were expecting such a rapid advance so Napoleon gained the element of surprise in the opening days of the campaign [Battle of Waterloo].
The Prussian outposts were quickly overrun and the army was ordered to assemble at Ligny. Napoleon's right, under Marshal Grouchy, pursued the retreating Prussians while the left, under Marshal Ney, marched on Quatre Bras in order to prevent the British army from uniting with the Prussians.
It's particularly important to note that just presenting correct scientific facts isn't enough to correct myths and misinformation. You need to discuss the misinformation and show why it is wrong. This method is supported by numerous studies.
What it means is that if you want to correct misinformation about evolution, you have to address the false beliefs of your audience. You can't correct the beliefs of evolution deniers without bringing up the various forms of creationism and showing why they are wrong. In other words, teach the controversy.
Some of my American friends tell me that this is legally impossible in American schools. If they are right, then creationism wins. Ironically, by using the courts to keep all mention of creationism out of the public schools, these friends are playing right into the hands of the anti-evolution crowd and making it impossible to debunk their myths and misconceptions.
The meeting is on Sunday evening at 7:00 pm at The Franklin House, 263 Queen St. in Sreetsville. This is a relatively new Café Scientifique so new people are more than welcome. The talk is very informal (no slides or powerpoint) and there will be lots of time for discussion and debate. I'm told that various "refreshments" will be available to help make the evening more enjoyable.
Stephen Jay Gould wrote a book about the role of chance in evolution. He called it "Wonderful Life." On the surface it's a book about the Burgess Shale and the Cambrian explosion but there's a powerful message as well. Gould is interested in why some species survive while others go extinct. Are the survivors better adapted than the losers of is it a matter of luck? We could answer this question if we could carry out an experiment.
I call this experiment "replaying life's tape." You press the rewind button and, making sure you thoroughly erase everything that actually happens, go back to any time and place in the past—say, to the seas of the Burgess Shale. Then let the tape run again and see if the repetition looks at all like the original. If each replay strongly resembles life's actual pathway, then we must conclude that what really happened pretty much had to occur. But suppose that the experimental versions all yield sensible results strikingly different from the actual history of life? What could we then say about the predictability of self-conscious intelligence? or of mammals? or of vertebrates? or of life on land? or simply of multicellular persistence for 600 million years?
Stephen Jay Gould (1989) pp. 48-50
