The Nature of Science

Showing posts with label Science. Show all posts

More Expert Opinion on Junk DNA from Scientists

The Nature issue containing the latest ENCODE Consortium papers also has a New & Views article called "Genomics: ENCODE explained" (Ecker et al., 2012). Some of these scientist comment on junk DNA.

For exampleshere's what Joseph Ecker says,

One of the more remarkable findings described in the consortium's 'entrée' paper is that 80% of the genome contains elements linked to biochemical functions, dispatching the widely held view that the human genome is mostly 'junk DNA'. The authors report that the space between genes is filled with enhancers (regulatory DNA elements), promoters (the sites at which DNA's transcription into RNA is initiated) and numerous previously overlooked regions that encode RNA transcripts that are not translated into proteins but might have regulatory roles.

And here's what Inês Barroso, says,

The vast majority of the human genome does not code for proteins and, until now, did not seem to contain defined gene-regulatory elements. Why evolution would maintain large amounts of 'useless' DNA had remained a mystery, and seemed wasteful. It turns out, however, that there are good reasons to keep this DNA. Results from the ENCODE project show that most of these stretches of DNA harbour regions that bind proteins and RNA molecules, bringing these into positions from which they cooperate with each other to regulate the function and level of expression of protein-coding genes. In addition, it seems that widespread transcription from non-coding DNA potentially acts as a reservoir for the creation of new functional molecules, such as regulatory RNAs.

If this were an undergraduate course I would ask for a show of hands in response to the question, "How many of you thought that there did not seem to be "defined gene-regulatory elements" in noncoding DNA?"

I would also ask, "How many of you have no idea how evolution could retain "useless" DNA in our genome?" Undergraduates who don't understand evolution should not graduate in a biological science program. It's too bad we don't have similar restrictions on senor scientists who write News & Views articles for Nature.

Jonathan Pritchard and Yoav Gilad write,

One of the great challenges in evolutionary biology is to understand how differences in DNA sequence between species determine differences in their phenotypes. Evolutionary change may occur both through changes in protein-coding sequences and through sequence changes that alter gene regulation.

There is growing recognition of the importance of this regulatory evolution, on the basis of numerous specific examples as well as on theoretical grounds. It has been argued that potentially adaptive changes to protein-coding sequences may often be prevented by natural selection because, even if they are beneficial in one cell type or tissue, they may be detrimental elsewhere in the organism. By contrast, because gene-regulatory sequences are frequently associated with temporally and spatially specific gene-expression patterns, changes in these regions may modify the function of only certain cell types at specific times, making it more likely that they will confer an evolutionary advantage.

However, until now there has been little information about which genomic regions have regulatory activity. The ENCODE project has provided a first draft of a 'parts list' of these regulatory elements, in a wide range of cell types, and moves us considerably closer to one of the key goals of genomics: understanding the functional roles (if any) of every position in the human genome.

The problem here is the hype. While it's true that the ENCODE project has produced massive amounts of data on transcription binding sites etc., it's a bit of an exaggeration to say that "until now there has been little information about which genomic regions have regulatory activity." Twenty-five years ago, my lab published some pretty precise information about the parts of the genome regulating activity of a mouse hsp70 gene. There have been thousands of other papers on the the subject of gene regulatory sequences since then. I think we actually have a pretty good understanding of gene regulation in eukaryotes. It's a model that seems to work well for most genes.

The real challenge from the ENCODE Consortium is that they question that understanding. They are proposing that huge amounts of the genome are devoted to fine-tuning the expression of most genes in a vast network of binding sites and small RNAs. That's not the picture we have developed over the past four decades. If true, it would not only mean that a lot less DNA is junk but it would also mean that the regulation of gene expression is fundamentally different than it is in E. coli.

[Image Credit: ScienceDaily: In Massive Genome Analysis ENCODE Data Suggests 'Gene' Redefinition.

Ecker, J.R., Bickmore, W.A., Barroso, I., Pritchard, J.K. (2012) Genomics: ENCODE explained. Nature 489:52-55. [doi:10.1038/489052a]
Yoav Gilad
& Eran Segal

Only Young Scientists Overthrow Old Concepts?

Max Planck once said ...

A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.

This does not conform to my experience in the biological sciences.

I think that what usually what happens is that a new way of thinking is promoted by well-established investigators. Gradually other scientists are convinced by the evidence to change their minds and the new scientific truth spreads within the community.

When a substantial number of scientists are converted, they start teaching the new concept in graduate and undergraduate courses. This produces a young generation who never heard of the old "truth."

If I'm correct then a new generation of scientists grows up familiar with the new scientific truth but only because the established scientists converted and started training the next generation properly.

When it comes to challenging old established concepts in a discipline I find that initially the younger scientists are often quite conservative unless they just happen to be working on that problem. This shouldn't be a surprise since our young investigators have their hands full just establishing themselves in their field. They don't have time to think about what's going on in the rest of the discipline. In fact, it might be detrimental to their careers to challenge most established concepts.

As I'm writing this I'm having trouble coming up with examples in biology. Most of the conceptual shifts that come to mind are ongoing controversies where it still isn't clear that the new scientific truth will replace the old one. I'm thinking of evo-devo, challenges to evolutionary theory, junk DNA, chemiosmotic theory, metabolism & thermodynamics, the tree of life, photosynthesis, and even new ways of teaching.

Can anyone think of examples were the shift has been completed so we can test the Max Planck hypothesis?

How about the shift from thinking that genes were proteins to genes are DNA?

A History of Science Blogging

Blogs have been around for more than a decade but it's still not clear what purpose they serve (if any). We still don't know how to distinguish a science blog from other types of blogs—perhaps it's foolish to try.

Bora Zivkovic of A blog Around the Clock has written a short history of science blogging [Science Blogs – definition, and a history]. It's well worth reading since Bora has been active for a long time and he's very well connected to the science blogging community.

Here's how he describes the category that applies to Sandwalk.

The earliest science bloggers were those who started out doing something else online – updating their websites frequently, or participating in Usenet groups – then moving their stuff to blogging software once it became available in the late 1990s and early 2000s.

As much of the early online activity focused on countering anti-science claims, e.g., the groups battling against Creationism on Usenet, it is not surprising that many of the early science bloggers came out of this fora and were hardly distinguishable in form, topics and style from political bloggers. They brought a degree of Usenet style into their blogs as well: combative and critical of various anti-science forces in the society.

In my case the usenet groups were talk.origins and sci.bio.evolution. Both of those groups are hosted on a server in my office; talk.origins is still very active but sci.bio.evolution isn't.

PZ Myers is the most famous talk.origins veteran. He's the one who convinced me to start a blog back in 2006 when I realized that blogs had many advantages over usenet, especially images. I don't know how many other talk.origins veterans have a blog. Can you help me out? Here's a partial list. (Some of these blogs are not science blogs.)

PZ Myers: Pharyngula
John Wilkins: Evolving Thoughts
Jeffrey Shallit: Recursivity
Jim Lippard: The Lippard Blog
various people: Panda's Thumb
John (catshark) Pieret: Thoughts in a Haystack
Troy Britain: Playing Chess with Pigeons

I know there are many more but I just can't remember them right now.

The other thing that Bora points out is that many science bloggers were connected to each other in different ways. Often we had met in person—this is certainly true of the talk.origins veterans. The early blogs were characterized by in jokes and incestuous cross links.

This has now disappeared as a whole new generation of science bloggers have entered the blogosphere, although there's still a certain amount of personal contact (see Evolution and Poutine and Beaver Tails.) I don't know if this is important or not. Blogger cliques can be a good thing and a bad thing.

The Trouble with Scientism?

Philip Kitcher is a philosopher who specializes in the philsophy of science. He is a professor at Columbia University in New York, USA. He's well known in the atheist, skeptical community and he's an outspoken critic of creationism.

He just published an article in The New Republic entitled: The Trouble with Scientism: Why history and the humanities are also a form of knowledge.

Many of the debates on the issue of "scientism" depend on how you define "science." As you can see from the subtitle of his essay, it's about the two cultures. Kitcher separate the search for knowledge in the humanities from the search for knowledge in the natural sciences. Here's what he says ...

It is so easy to underrate the impact of the humanities and of the arts. Too many people, some of whom should know better, do it all the time. But understanding why the natural sciences are regarded as the gold standard for human knowledge is not hard. When molecular biologists are able to insert fragments of DNA into bacteria and turn the organisms into factories for churning out medically valuable substances, and when fundamental physics can predict the results of experiments with a precision comparable to measuring the distance across North America to within the thickness of a human hair, their achievements compel respect, and even awe. To derive one’s notion of human knowledge from the most striking accomplishments of the natural sciences easily generates a conviction that other forms of inquiry simply do not measure up. Their accomplishments can come to seem inferior, even worthless, at least until the day when these domains are absorbed within the scope of “real science.”

It's clear the he thinks of "science" as something that only natural scientists do. This is a different definition that the one I prefer. I think of "science" as a way of knowing that involves evidence, skepticism, and rationalism. I agree with Rush Holt [Rush Holt on Science and Critical Thinking] that critical thinking is an important part of science as a way of knowing and I agree with him that the scientific approach can be used everywhere—even in philosophy departments.

Kitcher's view is different. That leads him to define scientism as ...

The problem with scientism—which is of course not the same thing as science—is owed to a number of sources, and they deserve critical scrutiny. The enthusiasm for natural scientific imperialism rests on five observations. First, there is the sense that the humanities and social sciences are doomed to deliver a seemingly directionless sequence of theories and explanations, with no promise of additive progress. Second, there is the contrasting record of extraordinary success in some areas of natural science. Third, there is the explicit articulation of technique and method in the natural sciences, which fosters the conviction that natural scientists are able to acquire and combine evidence in particularly rigorous ways. Fourth, there is the perception that humanists and social scientists are only able to reason cogently when they confine themselves to conclusions of limited generality: insofar as they aim at significant—general—conclusions, their methods and their evidence are unrigorous. Finally, there is the commonplace perception that the humanities and social sciences have been dominated, for long periods of their histories, by spectacularly false theories, grand doctrines that enjoy enormous popularity until fashion changes, as their glaring shortcomings are disclosed.

That's a really stupid definition of scientism. I don't know anyone who actually thinks like that. Do you know any "natural science imperialists" who dismiss the humanities and the social sciences?¹

I believe that people in the humanities and social sciences use the same approach as those in the natural sciences. I call that way of knowing "science" but if someone wants to come up with a better name, I'm all ears. As far as I'm concerned, science (as I define it) is the ONLY way of knowing that has actually been successful in discovering true knowledge. I guess that makes me guilty of "scientism."

It's very easy to refute scientism as I define it. All you have to do is show that there's some other way of knowing that produces universal truths or true knowledge. Perhaps philosophers have discovered truths using some other way of knowing?

1. I criticize evolutionary psychology. The reason why I'm so critical is precisely because they don't conform to the scientific way of knowing. They are not doing "good science" by any definition of the word "science."

Rush Holt on Science and Critical Thinking

I don't know Rush Holt from Adam. I'm told that he's a US Congressman from New Jersey but I find that difficult to believe. :-)

Here's an interview he gave with The Humanist: Thinking Like a Scientist.

The Humanist: How do you define critical thinking?

Rush Holt: Let me define instead what I like to call “thinking like a scientist.” It’s asking questions that can be answered based on evidence; it’s expressing questions in a way that allows someone to check your work. If you don’t have both of those elements, it’s too easy to fool yourself or to get lazy in your thinking. I wouldn’t say that critical thinking is hard thinking, because I don’t want to discourage people from doing it, but like anything else, it’s easier if you practice.

Third graders, for example, are often very good at thinking like scientists. Like scientists, they know that if you ask how something works, what something means, or how something happens, you should do it in a way that allows for more than just pure thinking. There should be some evidence, something empirical. You should form your question so that it allows someone else to ask that same question and observe the evidence to see if they get the same answer as you do. And that’s the essential part of critical thinking. If you say, “I’ve been thinking about this deeply and, by golly, now I understand it,” but then you try to explain it to someone else and can’t, then you probably don’t understand it … or it’s not very reliable knowledge.

I keep trying to get science taught in a way that, even if you can’t remember a single Latin term or are a klutz at solving equations, you’ve learned how to frame questions and sift evidence. I talk about verification but another way of putting it is: be ready for the cross-examination. Prepare to explain yourself.

The Humanist: How valuable is critical thinking to everyday life?

Holt: It’s invaluable, whether you’re making a consumer decision like which laundry detergent to buy or whether you’re trying to decide what career you want to pursue. There are ways to ask yourself both what you’re trying to accomplish and how to measure whether you’ve accomplished it. If you’re able to express it that way, then you’re thinking critically.

This is important on every level, not just on a personal level, not just in regards to consumer decisions or life choices. I think it’s quite likely we wouldn’t have invaded Iraq if more people in the CIA or in Congress had been thinking critically and asking, “What’s the evidence? You say Saddam Hussein is doing things that will hurt our national interests. Now tell me exactly: what is he doing? Does he have chemical weapons, nuclear weapons? Where’s the evidence?” Of course, there wasn’t any.

This is important stuff. I think of "science" as a way of knowing but it can also be thought of as a way of thinking. It's intimately associated with critical thinking.

In this sense, "science" is not confined to the so-called "natural sciences" but it can be applied to everything that requires a search for reliable truth. Everybody should be thinking like a scientist and that includes politicians and philosophers. In my experience, there is no other way of knowing that has a proven track record.

[Hat Tip: RichardDawkins.net]

Dysfunctional Science

Carl Zimmer, one of the top science writers in the world, has written an article for the New York Times with the following provocative title: A Sharp Rise in Retractions Prompts Calls for Reform. It's partly about the rise in the rate of retractions¹ in scientific journals. This is a serious problem and it's hard to figure out the underlying cause, in spite of the fact that many of the people who comment think they know the answer.

But there's much more to this story as Carl explains on his blog [Dysfunctional science: My story in tomorrow’s New York Times].

In tomorrow’s New York Times, I’ve got a long story about a growing sense among scientists that science itself is getting dysfunctional. For them, the clearest sign of this dysfunction is the growing rate of retractions of scientific papers, either due to errors or due to misconduct. But retractions represent just the most obvious symptom of deep institutional problems with how science is done these days–how projects get funded, how scientists find jobs, and how they keep labs up and running.

As usual, Carl's got it right. There's something wrong with science, or perhaps I should say there's something wrong with the biological sciences since Sean Carroll doesn't see the same problem in physics [Is Physics Among the Dysfunctional Sciences?].

1. The rate is about 0.04%. Compare this to the rate of fraudulent creationist publications, which is close to 100%.

Is Science Restricted to Methodologial Naturalism?

Maarten Boudry, Stefaan Blancke, and Johan Braeckman have an article coming out in Science & Education on "Grist to the Mill of Anti-evolutionism: The Failed Strategy of Ruling the Supernatural out of Science by Philosophical Fiat."

It relates to the idea that science is limited by its insistence on adhering to methodological naturalism. According to this view, science cannot investigate the supernatural. The view is popular among some who oppose creationism since it means that creationism can't be scientific, by fiat. It's also important for accommodationists because it allows science and religion to co-exist in separate magisteria.

I oppose such a definition of science but, up until a few years ago, I was always told that my opinion is irrelevant since all philosophers, and many scientists, agree that science is limited by methodological naturalism. That's why I was so delighted to meet the philosophers from Gent. Finally there was another point of view opposed to the methodological naturalism limitation. Now those who promote this limitation on science have to honestly admit that it's just their opinion and not a universally accepted definition of science.¹

Good News from Gent
Methodological Naturalism
Methodological Naturalism - How Not to Attack Intelligent Design Creationism
Here Be Dragons
An Interview with Maarten Boudry

Here's the abstract of the Science & Education paper.

According to a widespread philosophical opinion, science is strictly limited to investigating natural causes and putting forth natural explanations. Lacking the tools to evaluate supernatural claims, science must remain studiously neutral on questions of metaphysics. This (self-imposed) stricture, which goes under the name of ‘methodological naturalism’, allows science to be divorced from metaphysical naturalism or atheism, which many people tend to associate with it. However, ruling the supernatural out of science by fiat is not only philosophically untenable, it actually provides grist to the mill of anti-evolutionism. The philosophical flaws in this conception of methodological naturalism have been gratefully exploited by advocates of intelligent design creationism to bolster their false accusations of naturalistic bias and dogmatism on the part of modern science. We argue that it promotes a misleading view of the scientific endeavor and is at odds with the foremost arguments for evolution by natural selection. Reconciling science and religion on the basis of such methodological strictures is therefore misguided.

And here's a brief summary of their position ...

A widespread philosophical opinion conceives of methodological naturalism as an intrinsic and self-imposed limitation of science, as part and parcel of the scientific enterprise by definition. According to this view (Intrinsic Methodological Naturalism or IMN) – which is the official position of both the National Center for Science Education and the National Academy of Sciences and has been adopted in the ruling of Judge John E. Jones III in the Kitzmiller vs. Dover case – science is simply not equipped to deal with the supernatural and hence has no authority on the issue.3

In our view, however, methodological naturalism is a provisory and empirically anchored commitment to naturalistic causes and explanations, which is in principle revocable in light of extraordinary evidence (Provisory or Pragmatic Methodological Naturalism – PMN). Methodological naturalism thus conceived derives its rationale from the impressive dividends of naturalistic explanations and the consistent failure of supernatural explanations throughout the history of science.4

The distinction between Intrinsic Methodological naturalism (IMN) and Pragmatic Methodological Naturalism (PMN) is important. PMN is a conclusion based on centuries of scientific evidence strongly suggesting that natural explanations are sufficient to explain all phenomena. Those investigations include looking onto possible supernatural explanations.

Scientists have actually investigated possible miracles and found no evidence for them. Scientist have actually investigated the supernatural explanation for a world-wide deluge and refuted it. And if someone says that God made bacterial flagella, real scientists will try and find out whether that's true instead of just throwing up their hands and claiming that such an explanation is outside of science.

The implications of PMN are profound. It means that science and religion really are in conflict.

1. Of course the accommodationists will admit no such thing as I'm sure you are about to see in the comments. Such an admission would require them to say that they mislead Judge Jones in the Dover trial.

Happy Birthday Charles Darwin

[Reposted from 2008.]

Charles Robert Darwin was born on this day in 1809. Darwin was the greatest scientist who ever lived.

In honor of his birthday, and given that this is a year of politics in America, I thought it would be fun to post something about Darwin's interactions with politicians. The historical account is from Janet Browne's excellent biography (Brown 2002).

William Gladstone (photo below) was an orthodox Christian. He was not a fan of evolution. In March 1877 Gladstone was leader of the Liberal party and a former Prime Minister of the most powerful country in the world. He was spending the weekend with John Lunnock—a well-known liberal—and a few other friends, including Thomas Huxley.

They decided to walk over to Darwin's House in Downe. This was 18 years after the publication of Origins and Darwin was a famous guy. The guests were cordially received by Darwin and his wife Emma. Darwin and Emma were life-long liberals and they were honored by Gladstone's visit. A few days later, Darwin wrote a note to his friend saying,

Our quiet, however, was broken a couple of days ago by Gladstone calling here.—I never saw him before & was much pleased with him: I expected a stern, overwhelming sort of man, but found him as soft & smooth as butter, & very pleasant. He asked me whether I thought that the United States would hereafter play a much greater part in the history of the world than Europe. I said that I thought it would, but why he asked me, I cannot conceive & I said that he ought to be able to form a far better opinion,—but what that was he did not at all let out.

A few years later Gladstone sent Darwin one of his essays on Homer. Darwin gratefully acknowledged the gesture.

In 1881, when Gladstone was Prime Minister again, Darwin and some of his friends petitioned Gladstone to award a pension to Alfred Russel Wallace, who was in dire financial straits at the time. Gladstone granted the request. Two months later Gladstone offered Darwin a position as trustee of the British Museum but Darwin declined. (Remember, Gladstone did not agree with Darwin about evolution, or religion.)

When Darwin died, Gladstone was instrumental in arranging for him to be buried in Westminster Abbey. The funeral was held on April 26, 1882. William Gladstone was too busy to attend. He went to a dinner at Windsor.

Brown, J. (2002) Charles Darwin: The Power of Place (Vol. II). Alfred A. Knopf, New York (USA)

Was Newton the Greatest Scientist Who Ever Lived?

Most of us know that Charles Darwin was the greatest scientist who ever lived but one still finds the occasional misguided physicist/mathematician who thinks that the honor should go to an eighteenth century Englishman named Isaac Newton (1642-1727) [Top Five Dead Scientists] [Westminster Abbey: Darwin vs Newton] [Books by Charles Darwin] [Why I'm Not a Darwinist].

Now we have more direct evidence.¹ The Israel National Library has just put a pile of Newton's writings on line [Israel National Library uploads trove of Newton's theological tracts ]. We get to see direct example of how Newton thinks like a scientist.

My favorite is Newton's predictions about when the apocalypse will take place. He starts his calculation with the crowing of Charlemagne as Holy Roman Emperor in 800 AD and goes downhill from there [Newton on the date 2060 (early 18th century)].

In the instance displayed on this manuscript folio, Newton calculates a tentative date using the 1260 days (taken to be years) from Daniel in part to counter the claims of some of his contemporaries, who claimed that the end would come in the seventeenth or eighteenth century. Newton stood apart from contemporary interpreters who were predicting the imminent restoration of the Jews, the fall of the Catholic Church and the Second Coming of Christ. Nevertheless, Newton’s own fervent belief in these prophetic events is not in doubt. The abbreviation “A.C.” stands for Anno Christi (“the year of Christ”).
So then the time times and half a time are 42 months or 1260 days or three years and an half, reckoning twelve months to a year and 30 days to a month as was done in the Calendar of the primitive year. And the days of short lived Beasts being put for the years of lived [sic] kingdoms, the period of 1260 days, if dated from the complete conquest of the three kings A.C. 800, will end A.C. 2060. It may end later, but I see no reason for its ending sooner. This I mention not to assert when the time of the end shall be, but to put a stop to the rash conjectures of fanciful men who are frequently predicting the time of the end, and by doing so bring the sacred prophesies into discredit as often as their predictions fail. Christ comes as a thief in the night, and it is not for us to know the times and seasons which God hath put into his own breast.

There's lots more where this came from but I don't want to embarrass the Newton supporters any further.

By way of contrast, the real greatest scientist who ever lived was a non-believer who never would have treated the Bible as a scientific authority.

1. The information isn't new. It's just that we can now see for ourselves that Isaac Newton was remarkably unscientific in most of his writings.

P.S. Some losers are going to argue that Newton was still the greatest scientist and we should ignore the fact that his religious beliefs made him write many stupid anti-science treatises. That's like saying that Young Earth Creationists (like Newton) can be good scientists even though they believe the Earth is only 6000 years old.

Haught vs Coyne: The Letter

As most of you know, John Haught originally tried to prevent the release of the video of their debate. You can read the history on Jerry Coyne's blog: Theologian John Haught refuses to release video of our debate.¹

You might have missed John Haught's open letter buried in the comments (#122), so here it is. You can also read Jerry's reply. Read Coyne vs. Haught - advantage, Coyne for a third party perspective on whether Coyne's behavior was appropriate.

The facts are clear, as far as I'm concerned. The sophisticated Roman Catholic theologian chose to step into the fire pit of real debate and got badly burned. Now he's whining because the fire didn't play by his rules. Maybe he thought he would be protected just like Shadrach, Meshach, and Abednego?

Seriously, we all know what this is about. It's not about whether science and religion are compatible—they aren't. It's about giving religious views special privileges that we don't give to any other viewpoints. It's about the unwritten rule that we aren't supposed to criticize someone's personal faith.

For decades that unwritten rule has given carte blanche to religious leaders who can say whatever they want about scientists and atheists knowing that they won't be challenged to defend those views. That's changing in the 21st century. John Haught seems to have just discovered that his special privileges have been revoked.

He doesn't get out very much.

An open Letter to Jerry Coyne:

Dear Jerry,

Your distorted reading of my motivation for not releasing the video of our conversation in Kentucky has given birth to an inordinate number of hostile letters to me. Because of misleading statements on your website (11/1/2011), I have received a considerable amount of hate mail, often laced with obscenities, though often also tempered with inquisitive politeness. The mail mostly complains about my “cowardly” reneging on an alleged agreement that you falsely assume I made to post online the video of our panel at the University of Kentucky. When I was in Kentucky I was never asked to do so. Later, after reflecting on what to me was a most unfortunate event, I wrote to Prof Rabel requesting that any video not be released.

Anyway, Jerry, your own words impute cowardice to me for this refusal, but how do you know that’s the reason for my reluctance? Here is a typical reaction stirred up by your remarks: “What a pathetic, sociopathic dweeb you are. Hiding behind your sick belief system you call a religion. You are an insult to academia, and a dim bulb for the uninformed masses. You deserve the insults you are getting and should be fired. Coward, liar and fool you are, loser. And no doubt a Republican too!” (I’m tempted to say that I can live with every accusation except the last.)

I want to make it clear that Rob Rabel at the University of Kentucky has confirmed that I never gave permission before or after the panel to post the video. You need to make this clear to your audience. I never broke the agreement that you have unkindly caused your readers to assume I made.

However, the more interesting issue has to do with my reasons for refusing permission to post the video, and whether it was wrong for me to do so. I have no regrets about anything I had to say during the panel, and if you agree to post this letter on your site I will be happy to have the video released unedited, for public scrutiny. Those who are reading this blog are free to look at other videos of my comments on science and religion available online. They will see that I have no need to hide my views from the public, and in fact I am quite eager to have my thoughts made available provided they are presented accurately and fairly.

Why then do I hesitate in this case? It has to do with you alone, Jerry, not anyone else, including myself. I have had wonderful conversations with many scientific skeptics over the years, but my meeting with you was exceptionally dismaying and unproductive. I mentioned to you personally already that in my view, the discussion in Kentucky seldom rose to the level of a truly academic encounter. I agree that it was probably entertaining to the audience who gave us a standing ovation at the end. Nevertheless, instead of being flattered by this I went away terribly discouraged at what had just taken place. I wish to emphasize that I do not exempt myself from criticism.

The event at the University of Kentucky did not take place in the way I had expected. My understanding was that each speaker was to provide a curt 25-minute presentation of how he understood the relationship between science and theology. I did just this, and I have no objection to having that presentation made public. People who attended the event, moreover, can testify that in my presentation I avoided talking about or criticizing you personally. Instead I was content to make some very general remarks about why I consider science completely compatible with theology as I understand it.

When Robert Rabel of the Gaines Center at the University of Kentucky, a true gentleman who remains far above reproach in all of this, contacted me last summer and invited me to participate in the event, he asked me for names of people who would differ from my own position. I recommended you as someone who would definitely have a different perspective, to say the least. Prof. Rabel informed me that you agreed to participate with the qualification that you did not want to debate me, but simply to lay out your own way of looking at science and religion. I took this to mean that you would do something parallel to what I did in my presentation.

Instead, you used the event primarily to launch a sneering and condescending ad hominem. Rather than using your 25 minutes as an opportunity to develop constructively your own belief that science and religion are always and inevitably in conflict, you were content simply to ridicule rather than refute several of my own ideas, as you interpreted them. On the other hand, my own presentation, as those who watch the video will see, was a dispassionate attempt to have the audience understand some of the reasons why the new scientific picture of the universe is so troubling to many traditionally religious people. I don’t believe that at any point in that presentation I resorted to ridicule, or that I focused on, much less misrepresented, anything you have written. Instead, I argued in a purely academic way that scientism is simply unreasonable. This was clearly my main point, and I was expecting you to respond to it in an academic manner as well.

Rather than answering my point that scientism is logically incoherent–which is really the main issue–and instead of addressing my argument that the encounter with religious truth requires personal transformation, or for that matter instead of responding to any of the other points I made, you were content to use most of your time to ridicule several isolated quotes from my books. I was absolutely astounded by your woeful lack of insight into, or willingness to grapple with, the real meaning of these passages. Sophisticated argument requires as an essential condition that you have the good manners to understand before you criticize. Your approach, on the other hand was simply one of “caricature and then crush.” Citation of a few isolated sentences or paragraphs, the meaning of which requires reading and understanding many chapters, is hardly useful criticism. You grossly distorted every quotation you used, and then you coated over your [mis]understanding of these statements with your own uncritical creationist and literalist set of assumptions about the Bible and theology. There was no room for real conversation, as impartial viewers will notice.

Instead of trying to convince the audience of the logical coherence and philosophical finality of your belief that science is the only reliable guide to truth, you began by arbitrarily announcing to the audience that John Haught is the chief representative of theology in the conversation of science with religion. You gave no evidence for that, and in fact it is by no means evidently true. I am but one of a great number of theologians involved in the discussion, and many others do not share my views. But your strategy was to show that if the principal figure is stupid, then you need not take his subordinates seriously either. This is a convenient method for shrinking the territory that needs to be covered, but it is hardly a fair way of dealing with all the other theological alternatives to your own belief system.

But let me come to the main reason why I have been reluctant to give permission to release the video. It is not for anything that I said during our encounter, but for a reason that I have never witnessed in public academic discussion before.

I’m still in shock at how your presentation ended up. I was so offended both personally and as an academic by the vulgarity of it all that I did not want other people to have to share what I witnessed that night in October. I still don’t.

I’m referring to the fact that your whole presentation ended up with a monstrous, not to mention tasteless, non sequitur, to give it the kindest possible characterization. You put on the screen a list of all the “evils” you associate with Catholicism: its stance regarding divorce, contraception, priest pedophilia, homosexuality–and I can’t remember what all–as though these have anything at all to do with the topic of the panel or with my own personal views on the relationship of science to theology. The whole focus of your presentation was on me, but when you came to your conclusion you never bothered to find out what my own position regarding your list of Catholic evils might be. I have never witnessed such a blatant smear or malicious attempt to impute guilt by association in all my years in university life.

Your list of Catholic evils, contrary to what you were suggesting, has absolutely nothing logically to contribute to your argument that science is opposed to religion. But even if it did, you never asked me whether I dissent from some or all the items on your list of “evils,” as many Catholics do, and whether such dissent might, in your twisted way of arguing, perhaps make my own position more credible. Your insinuation could only have been that somehow the priest sexual abuse crisis, for example, discredits my views on science and theology. You should be grateful that I have tried to protect the public from such a preposterous and logic-offending way of bringing your presentation to a close.

There is much more to be said, but this is all I will have to say to you or others on this matter. If you are willing to post this letter on your blog, go ahead and ask the Gaines Center to release the video as well. I have no objections now that I have had the opportunity to present my reservations to possible viewers.

Sincerely,

John Haught

1. I'm looking for articles from anyone who thinks that Haught did a good job of making the case for compatibility. Post a link in the comments.

Haught vs Coyne: "Science and Religion: Are They Compatible?"

John Haught and Jerry Coyne "debated" the topic of compatibility at the University of Kentucky on October 12, 2011. If you are interested in this topic you MUST watch the entire video AND the question and answer session.¹

This is a classic confrontation between a "sophisticated" theologian and a scientist who knows what religion really is (in South Chicago).

The sophisticated theologian is John Haught, a Roman Catholic (with all that implies). His talk consisted largely of the claim that there are many different layers of explanation. According to Haught, science, by definition, can only address one layer—the naturalistic layer. He claims that he and his fellow theologians are "explanatory pluralists" whereas atheist scientists are "explanatory monists."

By implication, it's better to be an explanatory pluralist IF THE MULTIPLE LAYERS OF EXPLANATION ACTUALLY EXIST. Haught offers not one iota of evidence for the existence of those multiple layers beyond a childish story about boiling water to make tea. (It's the same story he used in the Kizmiller v. Dover trail.)

Haught does not address alternative definitions of science even though a bit of homework would have shown him that Jerry Coyne doesn't accept his definition of science. Apparently, Haught didn't do his homework. This is surprising since Haught's entire case depends on accepting the idea that science and religion are compatible because science can't address the suprenatural. In other words, compatibility by fiat.

You'd think that a "sophisticated" theologian would be prepared for someone who challenges that definition. Haught wasn't prepared. In fact, even during the Q&A he doesn't seem to have grasped the problem.

Haught conveniently "forgets" to mention anything about his religious beliefs other than that they involve personal revelation (faith). He doesn't tell us what he believes about transubstantiation, miracles, the virgin birth, the efficacy of prayer, the resurrection, the existence of a soul, heaven, hell, angels etc. That's a shame because Jerry Coyne addresses most of those beliefs and argues that they are incompatible with science. Haught will only reveal (in the Q&A) that he doesn't believe in any of the things Coyne addressed in his presentation. One wonders if Haught is really a Roman Catholic.

I'm getting pretty disgusted with those "sophisticated" theologians who hide behind fuzzy notions of religion when you know damn well they believe in a personal god who intervenes in the world. Haught has been playing this game for decades. Either he's a deist—in which case he should come right out and admit it—or he believes in a personal god who does things that possibly conflict with science—in which case he should have the courage to defend his beliefs.

2011 Bale Boone Symposium - Science & Religion: Are They Compatible? from UK Gaines Center on Vimeo.

Science and Religion: Are They Compatible? October 12, 2011 Q+A with Jerry Coyne and John Haught from UK College of Arts & Sciences on Vimeo.

1. There's a special treat in store for those who watch the Q&A. You will get to see an incredibly stupid first question from the moderator. I don't think I could have restrained myself the way Jerry Coyne did.

Alternative Splicing and Why IDiots Don't Understand How Science Works

One of the characteristics of creationists is their inability to understand how science works. For example, in biology, our knowledge of how living things work advances in fits and starts with many hypotheses being tested and rejected before we arrive at a consensus.

At any given point in time there are a number of "works in progress" where scientists have not settled on a definitive model. Many papers will be published and a good number of them will turn out to be wrong. Creationists exploit genuine scientific controversies in two ways: (1) they use them to discredit science, and (2) they selectively quote from those on one side of an issue without mentioning that many other scientists disagree. (Most creationists use both tactics, sometimes in the same paragraph.)

We saw how Jonathan Wells did this in The Myth of Junk DNA. He picked papers that question junk DNA and used them to try and show that the issue has not been settled in spite of what some leading scientists say. This is a valid point, but he goes on to conclude that junk DNA is a myth when the proper conclusion is that scientists haven't reached a consensus but the majority favor junk DNA.

He also selected specific papers that showed evidence of function for some part of the genome without mentioning that this evidence is often disputed. In many cases it isn't clear whether this "evidence" is correct. He ignores controversy when it suits him and exploits it when it's to his benefit.

Some papers have claimed that most of the human genome is transcribed. Wells takes this as evidence that the transcribed DNA is not junk. In this particular case, the objections to this interpretation couldn't be ignored so he spends a page or so dismissing the idea that the data might be wrong and that the conclusion might be wrong. He forgets to mention that the consensus among molecular biologists is that most of the transcript are junk RNA due to accidental transcription. The DNA being transcribed is still junk.

Jonathan M makes a similar mistake in his latest posting [Why the "Onion Test" Fails as an Argument for "Junk DNA"]. The issue is alternative splicing. There are many scientists who think that alternative splicing is widespread in the human genome. Some claim that the vast majority of human genes (>90%) make two or more biologically functional alternative transcripts. This is usually offered as one "explanation" for why humans don't have as many genes as our egos demand [The Deflated Ego Problem]. Fact is, most of us never thought this was a problem in the first place so no "solution" is required.

Here's how Jonathan M describes alternative splicing ....

Alternative Splicing and Genome Size

A second point I made was that the phenomena of alternative splicing and alternative polyadenylation may have some explanatory power when it comes to accounting for the C-value enigma. Alternative splicing allows a single form of a pre-mRNA transcript to be spliced into a number of different forms by skipping exons or by recognizing alternative splice sites. I stated that the level of alternative splicing exhibited in humans (more than 90%, with an average of 2 or 3 transcripts per gene) is much higher than that for C. elegans (about 22%, with less than 2 transcripts per gene), and argued that this may, in part, explain why humans have only marginally more genes than C. elegans, which is otherwise seemingly paradoxical given the complexity of humans as compared to the roundworm.

I don't really understand the connection between alternative splicing and the C-value paradox. How does it explain why closely related species of onion have very different genome sizes?

But that's not the point I want to make. When Jonathan M raised this issue before, I replied, "I don't agree with the facts. I don't think it's true that most human genes produce multiple functional copies of mRNA by alternative splicing."

That prompted the following response ...

On this point, Moran is not just in disagreement with me, he is also out-of-date with the literature by about ten years! As this 2008 article from Science Daily reports,
Nearly all human genes, about 94 percent, generate more than one form of their protein products, the team reports in the Nov. 2 online edition of Nature. Scientists' previous estimates ranged from a few percent 10 years ago to 50-plus percent more recently.

"A decade ago, alternative splicing of a gene was considered unusual, exotic ... but it turns out that's not true at all -- it's a nearly universal feature of human genes," said Christopher Burge, senior author of the paper and the Whitehead Career Development Associate Professor of Biology and Biological Engineering at MIT.
Wang et al. (2008), moreover, report in Nature,
Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon-exon junctions indicated that 92-94% of human genes undergo alternative splicing, ~86% with a minor isoform frequency of 15% or more.

I've written about IDiots and alternative splicing before, especially their inability to understand what they're talking about [Jonathan Wells Weighs in on Alternative Splicing]. But the issue here is somewhat different. It's whether the idea that most human genes are alternatively spliced is a scientific fact or whether it's controversial. Like most IDiots, Jonathan M doesn't understand the subject well enough to know the difference.

Just because there are some papers making truly outlandish claims about alternative splicing doesn't mean they are correct—no matter where those papers are published. In order to understand science you have to dig deeper than that and decide whether the claims have been accepted.

The claim of abundant alternative splicing (i.e. the vast majority of human genes have two or more functional transcripts) has not been accepted. It's a scientific controversy. Hardly any molecular biologist believes that >90% of our genes produce functional alternative transcripts in spite what Jonathan M might believe.

In some cases it's a matter of definition. My colleague, Ben Blencowe, for example, has played a prominent role in promoting the idea that >90% of human genes are alternatively spliced (Pan et al, 2008) but he tells me that this does not mean that all alternative transcripts are functional. He concedes that many of the these transcripts could be due to splicing errors but they still qualify as alternative splicing events.

I don't agree with that definition. Many of us began teaching alternative splicing back in 1980 and putting in textbooks a few years later. "Alternative splicing" always meant "functional" alternatives. It means that the gene produced more that one biologically functional product. The definition changed in the past decade or so, but most people still interpret abundant alternative splicing to mean abundant functional products.

No reasonable molecular biologist could look at the database of spliced transcripts and conclude that most of them have a biological function. (See Two Examples of "Alternative Splicing" to see if you agree.) Most of those transcripts are clearly due to splicing errors just as most of the minor genome transcripts are due to transcription errors. There's just as much junk splicing as there is junk RNA.

Anyone familiar with the subject of alternative transcription knows that the conclusions are controversial. They know that many scientists are skeptical of the claims for massive amounts of functional alternative splicing. They know that those extraordinary claims don't make sense in the light of evolution and are probably wrong. (See A Challenge to Fans of Alternative Splicing.)

Here are some papers from well-known labs attempting to deal with the controversy.

Zhang et al. (2009)

Nonsense-mediated decay is a mechanism that degrades mRNAs with a premature termination codon. That some exons have premature termination codons at fixation is paradoxical: why make a transcript if it is only to be destroyed? One model supposes that splicing is inherently noisy and spurious transcripts are common. The evolution of a premature termination codon in a regularly made unwanted transcript can be a means to prevent costly translation. Alternatively, nonsense-mediated decay can be regulated under certain conditions so the presence of a premature termination codon can be a means to up-regulate transcripts needed when nonsense-mediated decay is suppressed....

We conclude that for recently evolved exons the noisy splicing model is the better explanation of their properties, while for ancient exons the nonsense-mediated decay regulated gene expression is a viable explanation.

Tress et al. (2007)

Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological function of the expressed protein and even to create new protein functions. Alternative splicing has been suggested as one explanation for the discrepancy between the number of human genes and functional complexity. Here, we carry out a detailed study of the alternatively spliced gene products annotated in the ENCODE pilot project. We find that alternative splicing in human genes is more frequent than has commonly been suggested, and we demonstrate that many of the potential alternative gene products will have markedly different structure and function from their constitutively spliced counterparts. For the vast majority of these alternative isoforms, little evidence exists to suggest they have a role as functional proteins, and it seems unlikely that the spectrum of conventional enzymatic or structural functions can be substantially extended through alternative splicing.

Melamud and Moult (2009)

The number of known alternative human isoforms has been increasing steadily with the amount of available transcription data. To date, over 100 000 isoforms have been detected in EST libraries, and at least 75% of human genes have at least one alternative isoform. In this paper, we propose that most alternative splicing events are the result of noise in the splicing process. We show that the number of isoforms and their abundance can be predicted by a simple stochastic noise model that takes into account two factors: the number of introns in a gene and the expression level of a gene. The results strongly support the hypothesis that most alternative splicing is a consequence of stochastic noise in the splicing machinery, and has no functional significance. The results are also consistent with error rates tuned to ensure that an adequate level of functional product is produced and to reduce the toxic effect of accumulation of misfolding proteins. Based on simulation of sampling of virtual cDNA libraries, we estimate that error rates range from 1 to 10% depending on the number of introns and the expression level of a gene.

This is a controversial topic. Some of us believe that alternative splicing in human genes is not particularly widespread and most of the data can be explained as errors in splicing. Others believe that the data is real and most human genes produce multiple transcripts with different biological functions.

It doesn't matter so much which side you pick. What matters is that you understand science well enough to know that the data and the conclusions are disputed. What this means is that you cannot just assume that >90% of human genes are alternatively spliced and use this "fact" to bolster your case for Intelligent Design Creationism.

I'm tempted to say that Jonathan M is "... out-of-date with the literature by about ten years!" but that would be unkind.

Melamud, E. and Moult, J. (2009) Stochastic noise in splicing machinery. Nucleic Acids Res. 37:4873-4886. [doi: 10.1093/nar/gkp471]

Pan, Q., Shai, O., Lee, L.J., Frey, B.J., and Blencowe, B.J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008 Dec;40(12):1413-5. Epub 2008 Nov 2. [doi:10.1038/ng.259]

Tress, M.L., Martelli, P.L., Frankish, A., Reeves, G.A., Wesselink, J.J,, Yeats, C., Olason, P.I., Albrecht, M., Hegyi, H., Giorgetti, A., Raimondo, D., Lagarde, J., Laskowski, R.A., López, G., Sadowski, M.I., Watsonk J.D., Fariselli, P., Rossi, I., Nagy, A., Kai, W., Størling, Z., Orsini, M., Assenov, Y., Blankenburg, H., Huthmacher, C., Ramírez, F., Schlicker, A., Denoeud, F., Jones, P., Kerrien, S., Orchard, S., Antonarakis, S.E., Reymond, A., Birney, E., Brunak, S., Casadio, R., Guigo, R., Harrow, J., Hermjakob, H., Jones, D.T., Lengauer, T., Orengo, C.A., Patthy, L., Thornton, J.M., Tramontano, A., and Valencia, A. (2007) The implications of alternative splicing in the ENCODE protein complement. Proc. Natl. Acad. Sci. USA 104:5495-5500. [doi: 10.1073/pnas.0700800104]

Zhang, Z., Xin, D., Wang, P., Zhou, L., Hu, L., Kong, X., and Hurst, L.D. (2009) Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay. BMC Biol. 7:23-36. [doi:10.1186/1741-7007-7-23]

Is Intelligent Design Creationism a Scientific Theory?

You should recall that Casey Luskin is one of those "serious science bloggers" who strikes fear into the hearts of evolutionary biologists. In fact, we are so afraid of people like Casey Luskin and Jonathan M that we go out of our way to avoid responding to their posts [see: A Reason to Doubt the IDiots].

Luskin's latest posting on Evolution News & Views (sic) is: How Do We Know Intelligent Design Is a Scientific "Theory"?. Here's the main argument ...

ID is a theory of design detection, and it proposes intelligent agency as a mechanism causing biological change. ID allows us to explain how aspects of observed biological complexity, and other natural complexity, arose. And it uses the scientific method to make its claims.

The scientific method is commonly described as a four-step process involving observations, hypothesis, experiments, and conclusion. ID begins with the observation that intelligent agents produce complex and specified information (CSI). Design theorists hypothesize that if a natural object was designed, it will contain high levels of CSI. Scientists then perform experimental tests upon natural objects to determine if they contain complex and specified information. One easily testable form of CSI is irreducible complexity, which can be tested for by reverse-engineering biological structures through genetic knockout experiments to determine if they require all of their parts to function. When scientists experimentally uncover irreducible complexity in a biological structure, they conclude that it was designed.

Praise for Canadian Blood Services

Last week I criticized the Canadian Blood Services for a stupid website called "What's Your Type?" The website associated certain personality traits and diet preferences with your blood type and also gave out false information about the origin of the various blood types [Shame on Canadian Blood Services].

Many people wrote letters to the Canadian Blood Services complaining about the obvious woo. They usually received a form letter saying that the site was not meant to be serious. It was for amusement only and whenever donors showed up for typing they would be told the real science behind blood types. In response to those form letters I wrote to explain that the actual science on the website was wrong—how were they going to explain that as a form of entertainment?

I'm pleased to report that the website is gone [What's Your Type?]. Now you just get a message explaining why you should know your blood type.

I never received a replay from Canadian Blood Services but PZ Myers posts a copy of a letter that some have received.

Dr. Sher has asked me to respond to your recent e-mail regarding our What's Your Type? new donor recruitment program. I understand that you have also sent an e-mail communicating your concerns to www.whatsyourtype@blood.ca and that others from our organization have provided you with specific details in response. I can confirm that the content you object to has been removed from our web site. The marketing materials for this program are being revised.

Thanks again for sharing your views with us.

Ian Mumford
Chief Operating Officer
Canadian Blood Services

Congratulations, Canadian Blood Services. You did the right thing.

Reading Books

Now that I've finished writing my book, I'm back into reading. I have a pile of books that I have to get through before classes start. It's going to be difficult 'cause I'm off to Brussels next week to visit my granddaughter Zoë.

I mostly read non-fiction with an emphasis on science, philosophy, history, theology, and creationism. When I'm finished with a book it's usually full of highlighted text and margin notes and many of the pages have sticky tags for quick reference. Every single one of my books becomes part of my reference library and I almost always consult them again after reading.

I can't imagine how anyone like me could ever make use of an electronic reader. I've got exactly three books on my iPad (Pride and Prejudice, Treasure Island, and Aesop's Fables) and that's only because they came with the kindle app. I will never read them.

A couple of days ago I discovered another thing you can do with a real book (paperback) that you can't do with a kindle or other reader—especially an expensive iPad. It was a horrible book that I had just finished and it felt really, really, good to throw it across the room into the waste basket. I retrieved it later on for future reference but the gesture was immensely satisfying.

[Photo credit: My daughter flew in from Brussels a few days ago on her way to Newark. She had to take care of some business in Toronto so she stayed the night in her old room. I discovered this little scene on her bed after she had left.]

Physicists and Biologists

I've just finished reading evolution: a view from the 21st century by James A. Shapiro. I'll write up a full review later on but right now I just want to quote a passage from near the end of the book. He begins the paragraph with a description of those physicists who entered biology in the 1940s and 50s (e.g. Max Delbrück).

Currently another wave of physical scientists is entering the life sciences. They bring with them a much-needed and fruitful sophistication in observation at the micro level, in mathematical formulation of results, and in computational methods of data analysis. Physicists-turned-biologists have an additional advantage of lacking a formal education in the life sciences; consequently, they have not been taught to exclude from their thinking notions previously concluded to be "impossible." We can only hope that their less prejudiced backgrounds will make it easier for them to develop novel conceptual frameworks to complement the analytical and experimental techniques they are introducing.

This insightful observation has great potential beyond solving the major problems in the biological sciences and I wonder if Shapiro fully appreciates the implications.

I have no formal training in physics. I haven't the foggiest idea what quantum chromodynamics (QCD) is all about, beyond what I can read on Wikipedia. I don't have a firm grasp of general relativity and my math skills are very weak.

However, I understand that physics is grappling with unified field theory and that string theory is going nowhere. I've heard rumors that physicists can't find the Higgs boson, although I can't imagine where they might have put it. I have plenty of experience helping Ms. Sandwalk find her car keys and credit card so I've come up with a brilliant idea.

Why don't I move to physics and solve their problems? I've got all the proper qualifications, "lacking a formal education," "less prejudicial background," and I haven't been taught to exclude impossible things. I bet I could convince half a dozen of my biologist colleagues to abandon the difficult problems of biology in order to help the physicists. It shouldn't take more than a few years.

We need a name for this discovery, let's call it The Shapiro Conjecture.¹

Meanwhile, I welcome all those physicists who know nothing about evolution, protein structure, genetics, physiology, metabolism, and ecology. That's just what we need in the biological sciences to go along with all the contributions made by equally ignorant creationists.

AFTERTHOUGHT: Biologists have been using computers to analyze complex data sets for over fifty years and we're pretty sophisticated at making observations at the micro level. Why do we need physicists to show us these techniques?

1. See The Salem Conjecture.

USA Honors Two Biochemists and an Evolutionary Biologist

The United States has just honored two biochemists, an evolutionary biologist, and some other scientist by issuing stamps to commemorate their achievements [American Scientists (Forever)].

Melvin Calvin (1911-1997) is famous for working out an important pathway of carbon fixation known today as the Calvin cycle. This pathway is prominent in photosynthetic bacteria and in chloroplasts. It is often considered to be a fundamental part of photosynthesis, although some workers prefer to maintain the distinction. Calvin won the Nobel Prize in Chemistry in 1961.

Severo Ochoa (1905-1993) received the Nobel Prize in Physiology or Medicine in 1959 along with Arthur Kornberg. Ochoa demonstrated that RNA could be synthesized in vitro using purified RNA polymerase. Later on he helped create synthetic polynucleotides that helped crack the genetic code.

Asa Gray (1810-1888) is best known today as a friend of Charles Darwin and one of the early supporters of evolution in America. He was a botanist at Harvard for most of his career. The website says he "... became the principal American advocate of evolutionary theory in the mid-nineteenth century." I think it would be much more fair to say that Asa Gray was a strong supporter of evolution. He and Darwin had many discussions (by letter) on the mechanisms of evolution.

Can Somebody Please Translate This?

Denise O'Leary has discovered a paper that was written up in Science ~~News~~ Daily: Chromosomes' Big Picture: Similarities Found in Genomes Across Multiple Species; Platypus Still out of Place. She seems to think this causes a problem for evolution.

I couldn't make head nor tail of the posting on Uncommon Descent [Most life forms show S pattern in chromosome lengths, guess which one doesn’t?] but that didn't surprise me because, after all, it was written by an IDiot. However, I was a bit surprised by the Science News report because I couldn't understand it either.

So I looked at the original paper. Here's the reference and abstract.

Li, X., Zhu, C., Lin, Z., Wu, Y., Zhang, D., Bai, G., Song, W., Ma, J., Muehlbauer, G.J., Scanlon, M.J., Zhang, M., and Yu, J. (2011) Chromosome Size in Diploid Eukaryotic Species Centers on the Average Length with a Conserved Boundary. Mol. Biol. Evol. 28: 1901-1911. [doi: 10.1093/molbev/msr011]

Abstract

Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation of living organisms. Although the genome of a species as a whole is important, chromosomes are the basic units subjected to genetic events that coin evolution to a large extent. Now many complete genome sequences are available, we can address evolution and variation of individual chromosomes across species. For example, “How are the repeat and nonrepeat proportions of genetic codes distributed among different chromosomes in a multichromosome species?” “Is there a general rule behind the intuitive observation that chromosome lengths tend to be similar in a species, and if so, can we generalize any findings in chromosome content and size across different taxonomic groups?” Here, we show that chromosomes within a species do not show dramatic fluctuation in their content of mobile genetic elements as the proliferation of these elements increases from unicellular eukaryotes to vertebrates. Furthermore, we demonstrate that, notwithstanding the remarkable plasticity, there is an upper limit to chromosome-size variation in diploid eukaryotes with linear chromosomes. Strikingly, variation in chromosome size for 886 chromosomes in 68 eukaryotic genomes (including 22 human autosomes) can be viably captured by a single model, which predicts that the vast majority of the chromosomes in a species are expected to have a base pair length between 0.4035 and 1.8626 times the average chromosome length. This conserved boundary of chromosome-size variation, which prevails across a wide taxonomic range with few exceptions, indicates that cellular, molecular, and evolutionary mechanisms, possibly together, confine the chromosome lengths around a species-specific average chromosome length.

Here's the challenge. Read the abstract and try and guess what important scientific point the authors are making that deserves publication in a molecular evolution journal. For extra points, read the entire article and see if you can improve your guess. You'll be impressed when you read the discussion and it all becomes clear (not!)

Polaris 25 - The Skeptical Track

Polaris 25 will take place this coming Friday, Saturday, and Sunday (July 15-17) at the Sheraton Parkway Toronto North in Richmond Hill, just north of Toronto. It will celebrate the 45th anniversary of Star Trek. Three of the actors from Stargate SG-1/Stargate Atlantis will be there—that's my favorite TV series (now in re-runs).

The Centre For Inquiry and its Committee for the Advancement of Scientific Skepticism (CASS) has been invited to present a Skeptical Track at the convention. The four speakers are ....

Me (Larry Moran): "What’s the Difference Between Science and Science Fiction?"

Jeffrey Shallit: "Misinformation Theory: How Creationists Abuse Mathematics."

Chris Hassall: "The Evolution of Superstition: People, PCs and Pigeons."

Alex Manafu: "Could Science Prove the Existence of God? (Or, Must Science Be Naturalistic?)"

For more information see Jeffrey Shallit's blog Recursivity: See me at Polaris 2011 in Toronto - July 16 and Michael Kruse's blog at Skeptic North: Skeptical Track at Polaris 25.

The Accommodationist Wars: Winston vs Harris

Robert Winston is a stem cell researcher with a strong interest in science education. Sam Harris is a neuroscientist who writes about the conflict between science and religion.

They recently debated whether science and religion are compatible [Is there any place for religious faith in science?].

This is part of the accommodationist wars. Winston argues that there is no conflict between one's personal religious belief and science.

accommodationist

one who adapts to or compromises with an opposing view

Mirriam-Webster Dictionary
This "war" is supposed to be about whether science and religion are in conflict or whether they are compatible. If they are compatible then it's perfectly reasonable for someone to support scientific reasoning as an important and valid way of knowing while, at the same time, believing the major tenets of some religion. However, as you can see in this debate, the accommodationist position is often confused. It's easy for them to forget the question and stray into other issues that upset them.

One of the things that upset accommodationists isn't the real question but whether it is polite or civil to "attack" the beliefs of legitimate scientists.

As Robert Winston puts it ...

You quote Collins in your book: "as I rounded a corner and saw a beautiful waterfall hundreds of feet high, I knew the search [for God] was over." You write, in commentary, "it is astounding that this passage was written with the intent of demonstrating the compatibility of faith and reason". But he is making his own personal judgement about his circumstances, not preaching to the world. Your writing is lovely, funny, but I don't think the denigration of a serious scientist like Collins does a lot of good. We should be very careful about criticising other scientists, except when their science is clearly at fault.

The problem for Winston is not really whether the scientific approach is consistent with evangelical Christianity but whether it is appropriate to even raise the issue because it "denigrates" compatibilists. As expected, Winston takes a few swaps at the attitude of the New Atheists.

The quotation from Winston also highlights another aspect of the accommodationist wars. Winston focuses on the ability of Francis Collins to "do science" as though that's what it's all about. ("But do his views detract from the outstanding work [Collins] has done?") This is not what the debate is about. As Sam Harris points out, there are Young Earth Creationists who do science but nobody would argue that Young Earth Creationism and science are compatible. Similarly, I have argued that there are scientists who believe in homeopathy and astrology but that does not make those subjects compatible with science.

The debate is about whether the principles of scientific reasoning are in conflict with the beliefs held by people of faith or whether the scientific way of knowing is compatible with another way of knowing that lies outside of science.

Whether one side or the other is being rude doesn't address the question. Whether a scientist can still pipette accurately while believing in silly things isn't relevant.

We need to keep the accommodationists focused on the main point and not on strawmen that have no bearing on the question. It's hard for us to do that but we need to keep trying.

[Photo Credit: David Levene: guardian.co.uk]

[Hat Tip: RichardDawkins.net]