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.
