Changing Your Mind: Are Science and Religion Compatible?

 
Clay Shirky used to think that science and religion were compatible. That doesn't mean all religious beliefs, of course, because some of them like Young Earth Creationism are not compatible with science. He has changed his mind ... [Religion and Science].

Since we couldn't rely on the literal truth of the Bible, we needed a fallback position to guide our views on religion and science. That position was what I'll call the Doctrine of Joint Belief: "Noted Scientist X has accepted Jesus as Lord and Savior. Therefore, religion and science are compatible." (Substitute deity to taste.) You can still see this argument today, where the beliefs of Francis Collins or Freeman Dyson, both accomplished scientists, are held up as evidence of such compatibility.

Belief in compatibility is different from belief in God. Even after I stopped believing, I thought religious dogma, though incorrect, was not directly incompatible with science (a view sketched out by Stephen Gould as "non-overlapping magisteria".) I've now changed my mind, for the obvious reason: I was wrong. The idea that religious scientists prove that religion and science are compatible is ridiculous, and I'm embarrassed that I ever believed it. Having believed for so long, however, I understand its attraction, and its fatal weaknesses.

Read the rest of the article to find out why the "Doctrine of Joint Belief" is not based on logic.

In the war between "arrogant" atheists and accommodationist atheists (formerly called "appeasers"), Clay Shirky has shifted sides.

Saying that the mental lives of a Francis Collins or a Freeman Dyson prove that religion and science are compatible is like saying that the sex lives of Bill Clinton or Ted Haggard prove that marriage and adultery are compatible. The people we need to watch out for in this part of the debate aren't the fundamentalists, they're the moderates, the ones who think that if religious belief is made metaphorical enough, incompatibility with science can be waved away. It can't be, and we need to say so, especially to the people like me, before I changed my mind.

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Changing Your Mind: Are Scientific Theories Falsifiable?

 
Rebecca Goldstein is a philosopher at Havard University (USA). She used to think that Karl Popper's view of how science is done was correct. Now she's changed her mind ... [Falsifiability]

Said Popper: The criterion of the scientific status of a theory is its falsifiability.

For most scientists, this is all they need to know about the philosophy of science. It was bracing to come upon such a clear and precise criterion for identifying scientific theories. And it was gratifying to see how Popper used it to discredit the claims that psychoanalysis and Marxism are scientific theories. It had long seemed to me that the falsifiability test was basically right and enormously useful.

But then I started to read Popper’s work carefully, to teach him in my philosophy of science classes, and to look to scientific practice to see whether his theory survives the test of falsifiability (at least as a description of how successful science gets done). And I’ve changed my mind.

....

...scientists don’t, and shouldn’t, jettison a theory as soon as a disconfirming datum comes in. As Francis Crick once said, “Any theory that can account for all of the facts is wrong, because some of the facts are always wrong.” Scientists rightly question a datum that appears to falsify an elegant and well-supported theory, and they rightly add assumptions and qualifications and complications to a theory as they learn more about the world. As Imre Lakatos, a less-cited (but more subtle) philosopher of science points out, all scientific theories are unfalsifiable. The ones we take seriously are those that lead to “progressive” research programs, where a small change accommodates a large swath of past and future data. And the ones we abandon are those that lead to “degenerate” ones, where the theory gets patched and re-patched at the same rate as new facts come in.

Many people agree with Rebecca Goldstein but I still hear from lots of Popperians. It's very annoying to see my fellow scientists attack Intelligent Design Creationism on the grounds that it doesn't conform to Popper's idea of science—it's not falsifiable. That's true but irrelevant. Much of the best kinds of science also don't conform to Popper's ideas.

Much of evolutionary theory is not falsifiable in the true Popperian sense.

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Changing Your Mind: Are Humans Evolving?

Steven Pinker, a psychologist at Harvard University (USA) used to think that humans had stopped evolving. Now he's changed his mind ... [Have Humans Stopped Evolving?]

Ten years ago, I wrote:

For ninety-nine percent of human existence, people lived as foragers in small nomadic bands. Our brains are adapted to that long-vanished way of life, not to brand-new agricultural and industrial civilizations. They are not wired to cope with anonymous crowds, schooling, written language, government, police, courts, armies, modern medicine, formal social institutions, high technology, and other newcomers to the human experience.

And:

Are we still evolving? Biologically, probably not much. Evolution has no momentum, so we will not turn into the creepy bloat-heads of science fiction. The modern human condition is not conducive to real evolution either. We infest the whole habitable and not-so-habitable earth, migrate at will, and zigzag from lifestyle to lifestyle. This makes us a nebulous, moving target for natural selection. If the species is evolving at all, it is happening too slowly and unpredictably for us to know the direction. (How the Mind Works)

...

New results from the labs of Jonathan Pritchard, Robert Moyzis, Pardis Sabeti, and others have suggested that thousands of genes, perhaps as much as ten percent of the human genome, have been under strong recent selection, and the selection may even have accelerated during the past several thousand years. The numbers are comparable to those for maize, which has been artificially selected beyond recognition during the past few millennia.

If these results hold up, and apply to psychologically relevant brain function (as opposed to disease resistance, skin color, and digestion, which we already know have evolved in recent millennia), then the field of evolutionary psychology might have to reconsider the simplifying assumption that biological evolution was pretty much over and done with 10-000 — 50,000 years ago.

I'm glad he's changed his mind but it's for the wrong reasons.

Evolution, human or otherwise, cannot ever be stopped. Pinker, like the true adaptationist he is, cannot conceive of any evolution mechanism other than natural selection. Even if his original writings were correct, all he said is that natural selection may have stopped. Evolution by random genetic drift—the most frequent form of evolution—never stops.

It's interesting to see Pinker make the connection between the presumed stoppage of human evolution after the shift from hunter-gatherer mode, and evolutionary psychology. I never really thought about it before but that connection is a basic assumption in most of the the just-so stories promoted by evolutionary psychologists. If there has been lots of recent selection in human populations then it becomes more difficult to attribute our current "primitive" behavior to old adaptations that took place 100,000 years ago.

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[Photo Credit: CivilBrights]

Changing Your Mind: Alan Alda Converts from Atheism to Agnosticism

 
Alan Alda has changed his mind. He used to be an atheist but now he prefers to call himself an agnostic [ So far, I've changed my mind twice about God].

But, slowly I realized that in the popular mind the word atheist was coming to mean something more: a statement that there couldn't be a God. God was, in this formulation, not possible, and this was something that could be proved. But I had been changed by eleven years of interviewing six or seven hundred scientists around the world on the television program Scientific American Frontiers. And that change was reflected in how I would now identify myself.

The most striking thing about the scientists I met was their complete dedication to evidence. It reminded me of the wonderfully plainspoken words of Richard Feynman who felt it was better not to know than to know something that was wrong. The problem for me was that just as I couldn't find any evidence that there was a god, I couldn't find any that there wasn't a god. I would have to call myself an agnostic. At first, this seemed a little wimpy, but after a while I began to hope it might be an example of Feynman's heroic willingness to accept, even glory in, uncertainty.

I think he's dead wrong about the meaning of the word atheism. I think it means that you have not accepted theism and therefore you are "without a belief in God." I see the word atheism as similar to words like "a-toothfairyism" or "a-SantaClausism." You don't believe in Santa Claus so you are an "a-SantaClausist." It does not mean you are committed to the concept that there could not possibly be a Santa Claus.

It would be silly to label yourself an agnostic with respect to belief in Santa Claus. Nobody, especially Christians, goes around announcing that they are agnostic about the existence of the Greek Gods. You don't believe in them, full stop.

There is a version of agnosticism that's perfectly acceptable. John Wilkins, among others, promotes this definition of agnosticism. True agnostics claim that it is impossible to prove one way or the other whether God exists, just as it's impossible to prove one way or the other whether the tooth fairly exists. All rational people are agnostics in this sense. Some of them are also atheists. Alan Alda appears to be both an atheist and an agnostic, just like Richard Dawkins. Alan Alda is a wimp for letting non-atheists redefine atheism and then abandoning his position because of that incorrect definition.

It's not an either/or situation, in my opinion (Wilkins disagrees). You can, and should, be both an atheist and an agnostic.

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[Photo Credit: M*A*S*H]

Changing Your Mind: The Limits Of Darwinian Reasoning

 
Marc D. Hauser is a biologist and psychologist at Harvard University (USA). He is beginning to see the error of his adaptationist ways [The Limits Of Darwinian Reasoning].

Let me be clear about the claim here. I am not rejecting Darwin’s emphasis on comparative approaches, that is, the use of phylogenetic or historical data. I still practice this approach, contrasting the abilities of humans and animals in the service of understanding what is uniquely human and what is shared. And I still think our cognitive prowess evolved, and that the human brain and mind can be studied in some of the same ways that we study other bits of anatomy and behavior. But where I have lost the faith, so to speak, is in the power of the adaptive program to explain or predict particular design features of human thought.

Although it is certainly reasonable to say that language, morality and music have design features that are adaptive, that would enhance reproduction and survival, evidence for such claims is sorely missing. Further, for those who wish to argue that the evidence comes from the complexity of the behavior itself, and the absurdly low odds of constructing such complexity by chance, these arguments just don’t cut it with respect to explaining or predicting the intricacies of language, morality, music or many other domains of knowledge.

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Changing Your Mind: The Obligations and Responsibilities of The Scientist

 
Leon Lederman is a physicist and a Nobel Laureate. He has changed his mind about the The Obligations and Responsibilities of The Scientist.

The role of the Professor, reflecting the mission of the University, is research and dissemination of the knowledge gained. However, the Professor has many citizenship obligations: to his community, State and Nation, to his University, to his field of research, e.g. physics, to his students. In the latter case, one must add to the content knowledge transferred, the moral and ethical concerns that science brings to society. So scientists have an obligation to communicate their knowledge, popularize, and whenever relevant, bring his knowledge to bear on the issues of the time. However, additionally, scientists play a large role in advisory boards and systems from the President's Advisory system all the way to local school boards and PTAs. I have always believed that the above menu more or less covered all the obligations and responsibilities of the scientist. His most sacred obligation is to continue to do science. Now I know that I was dead wrong.

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Changing Your Mind: Maybe Human Races Do Exist After All

 
Mark Pagel is an evolutionary biologist who used to buy into the idea that human races did not exist [We Differ More Than We Thought].

The last thirty to forty years of social science has brought an overbearing censorship to the way we are allowed to think and talk about the diversity of people on Earth. People of Siberian descent, New Guinean Highlanders, those from the Indian sub-continent, Caucasians, Australian aborigines, Polynesians, Africans — we are, officially, all the same: there are no races.

Now, in 2007, he changed his mind ...

What this all means is that, like it or not, there may be many genetic differences among human populations — including differences that may even correspond to old categories of 'race' — that are real differences in the sense of making one group better than another at responding to some particular environmental problem. This in no way says one group is in general 'superior' to another, or that one group should be preferred over another. But it warns us that we must be prepared to discuss genetic differences among human populations.

Good for him. Better late than never, I say.

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Changing Your Mind: The Fallacy of Hypothesis Testing

 
The Edge has asked people to describe whether they have changed their mind about anything and if so, why? It's the Annual Question for 2008.

Some of the replies are worth discussing. For example, Irene Pepperbreg has changed her mind about the meaning of the scientific method [The Fallacy of Hypothesis Testing]. I think she makes some good points, notably ....

Third, I've learned that the scientific community's emphasis on hypothesis-based research leads too many scientists to devise experiments to prove, rather than test, their hypotheses. Many journal submissions lack any discussion of alternative competing hypotheses: Researchers don't seem to realize that collecting data that are consistent with their original hypothesis doesn't mean that it is unconditionally true. Alternatively, they buy into the fallacy that absence of evidence for something is always evidence of its absence.

I'm all for rigor in scientific research — but let's emphasize the gathering of knowledge rather than the proving of a point.

I think this is a serious problem in science today. There are too many papers being published without any serious discussion of competing explanations. There are too many papers that fail to critically examine their own basic assumptions or the possible flaws in their experiments.

There may be a reason for this behavior—scientists don't want to draw attention to possible flaws in their work for fear that the granting agency will find out—but that doesn't excuse it. Scientific rigor demands that you present both sides of a scientific debate in a fair and unbiased manner. The failure to address the arguments of your opponents is nothing less than failing to be a good scientist.

Similarly, the failure to recognize the possible flaws in one's own explanation is the mark of a bad scientist.

While Irene Pepperbreg may be right about the flaws in today's method of doing science, I'm not prepared to throw out the baby with the bathwater. Hypothesis-based science is still important. You just have to form the right hypotheses and put your work in context. The problem, in my opinion, isn't that hypothesis testing is a fallacy: the problem is that it's not being done properly.

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Open Lab 2007

 
Open Lab 2007 is about to be published. The book contains the best articles from science blogs in 2007.

There were 486 articles nominated and the judges selected 53 for publication [Open Lab 2007 - the winning entries for you to see!]. The winners come from a wide selection of science blogs; 20 of them are part of the SEED group (ScienceBlogs^TM) and 33 are from other science blogs.

For the second year in a row there won't be any of my Sandwalk postings in the Open Lab anthology.

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Oops! The Rapture Didn't Happen

 
There was supposed to be a rapture last month but the prediction didn't come true. Either that or it did come true and only a small number of people were raptured, not including the prophet.

In case anyone is interested, here's how our prophet explains his little mistake [Are You Rapture Ready]. I assume he's apologizing to all those people who gave away everything in the expectation that they would soon be in heaven.

I offered to take some of those worldly goods off their hands but I couldn't find anyone who was expecting to be raptured. I guess I don't hang out with the right kinds of people.

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Iowa Caucuses

 
In a few days about 100,000 people will get together in Iowa to elect the next President of the United States. At least I think that's what the caucuses are all about. It's all very confusing. Apparently there are some other states like New Hampshire and South Carolina that have to confirm the Iowa result before it becomes official.

American politics is so confusing. None of this stuff is in the Constitution so I can't check the rules.

Anyway, since those few Iowa citizens are going to have such an important role in choosing the new leader of the free world (sic) I thought you might be interested in seeing how one of them is struggling to make up his mind. John Logsdon of Sex, genes & evolution has written about his quandary [Caucus Conundrum: Considering Compelling Candidates]. Why not pay him a visit and help him decide?

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You Think *You* Have a Tough Job? ....

 

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[Hat Tip: Canadian Cynic]

Airport Security and Liquid Contraband

 
The other day I saw a photograph of an airport security guard standing in front of dozens of large plastic bags full of confiscated liquids. The bags were stacked in a corridor and passengers were streaming by.

"Isn't this strange," I thought. Those bags are full of potentially dangerous chemicals that could destroy an aircraft yet the security guard seems unconcerned about the potential threat. As it turns out, there are lots of people who think that airport security is a farce. Patrick Smith has written about it in today's New York Times [The Airport Security Follies].

“I would not hesitate to allow that liquid explosives can pose a danger,” Greene added, recalling Ramzi Yousef’s 1994 detonation of a small nitroglycerine bomb aboard Philippine Airlines Flight 434. The explosion was a test run for the so-called “Project Bojinka,” an Al Qaeda scheme to simultaneously destroy a dozen widebody airliners over the Pacific Ocean. “But the idea that confiscating someone’s toothpaste is going to keep us safe is too ridiculous to entertain.”

Yet that’s exactly what we’ve been doing. The three-ounce container rule is silly enough — after all, what’s to stop somebody from carrying several small bottles each full of the same substance — but consider for a moment the hypocrisy of T.S.A.’s confiscation policy. At every concourse checkpoint you’ll see a bin or barrel brimming with contraband containers taken from passengers for having exceeded the volume limit. Now, the assumption has to be that the materials in those containers are potentially hazardous. If not, why were they seized in the first place? But if so, why are they dumped unceremoniously into the trash? They are not quarantined or handed over to the bomb squad; they are simply thrown away. The agency seems to be saying that it knows these things are harmless. But it’s going to steal them anyway, and either you accept it or you don’t fly.

It's about time that we started to protest against the waste of time and effort at airport security lines. This is a huge over-reaction to 9/11 and the fear of terrorism.

Read what John Wilkins has to say on Evolving Thoughts [Follies d'Air]. He puts things into historical perspective and points out that we are not only being inconvenienced by such folly but also surrendering considerable rights and freedoms in the name of "security." You'll appreciate John's ability to link airport security measures with Julius Caesar and the Prussians.

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[Photo Credit: Tim Boyle/Getty Images from the MSNBC website (Where will all that liquid contraband go?)]

Atheists Are Intolerant and Militant

 
Here's a video from "TheismBeatsAtheism." It's quite well done but still reflects the hollowness of the typical theist. Note that there's a lot of complaining about the "intolerance" and "militancy" of the atheists but very little defense of theism. The best proof they can offer for God's existence is the fact that 80-90% of American believe in him.

The theists are going to have to do better than this. If there is evidence of a supernatural being then let's hear it. I'm sick of those theists who claim that we have to read some "sophisticated" Christian apologetics in order to understand the arguments for God's existence. Those arguments have been around for 2000 years or more and none of them stand up to rational examination. (Note that they never recommend any Hindu books. Why is that? Every religion has their share of "sophisticated" books proving that their particular religion is correct. What does that tell you?)

I like the part where they complain about the universities. Apparently, getting a college education and learning how to think is detrimental to one's belief in a supernatural being. Do they have solutions to this problem, other than promoting ignorance? Yes, they do—more effort on brainwashing young children ought to work. What's interesting is that these theist dudes would complain about brainwashing by other religions¹ but see nothing wrong with Christians doing it.

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1. Especially the Muslim bogeyman. You might be surprised to learn than all Muslims are intolerant and would kill any atheist who lectured to them. I guess it's okay for Christians to be militant and intolerant toward other religions but not okay for atheists. I loathe hypocrisy.

[Hat Tip: Hemant Mehta at Friendly Atheist (These Atheists… They’re Everywhere!)]

DNA Denaturation and Renaturation and the Role of Hydrogen Bonds and Stacking Interactions

 
Several students have written to me with questions about the structure of DNA. The most troubling questions are from students who have read the article I wrote about a paper that measures the stacking interactions in polynucleotides [Measuring Stacking Interactions]. In that posting I wrote ...

The two strands of double- stranded DNA are held together by a number of weak interactions such as hydrogen bonds, stacking interactions, and hydrophobic effects [The Three-Dimensional Structure of DNA].

Of these, the stacking interactions between base pairs are the most significant. The strength of base stacking interactions depends on the bases. It is strongest for stacks of G/C base pairs and weakest for stacks of A/T base pairs and that's why it's easier to melt A/T rich DNA at high temperature. (It is often incorrectly assumed that this is due to having only two hydrogen bonds between A/T base pairs and three between G/C base pairs.)

THEME

Deoxyribonucleic Acid (DNA)Many students have written to say that my statements contradict their Professors and their textbooks. I'm not surprised. The old-fashioned view of DNA denaturation (pre-1990) supposed that the differences between A/T rich DNA and G/C rich DNA were due to the extra hydrogen bond in G/C base pairs. Many of the Professors who teach introductory biochemistry aren't aware of the fact that this view is incorrect. Even more surprising, some of the current textbooks have not bothered to update their material on the structure of DNA.

Here's the story as we know it today. For those students who have written to me, I repeat the caution I mentioned in my reply to you—be sure to check with your Professor before you write any tests. Make sure he/she understands why you are contradicting what was said in class so you don't get marks taken off. It's always better to do this in advance instead of arguing your case after you have lost marks on the test.

Let's look first at what happens when DNA is denatured by raising the temperature.

As the temperature increases, you start to get local unwinding of the double-stranded DNA. This unwinding occurs preferentially in regions where the two strand are held together less strongly. In these regions the strands separate to form bubbles of single-stranded regions. The DNA sequence in these regions is enriched in A/T base pairs because the interactions between the two strands are weaker in A/T rich regions. In G/C rich regions strands are held together more strongly so they don't unwind until higher temperatures.

Incidentally, even at normal cell temperatures the DNA "breathes" and local regions become temporarily unwound. As you might expect, A/T rich regions are more likely to open up than G/C rich regions. This is one of the reasons why transcription initiation bubbles and DNA replication origins are often A/T rich. It's easier for the proteins (RNA polymerase, and origin binding proteins) to create the locally unwound regions.

When all of the base interactions are broken, the two strands separate. This is called denaturation. (Local unwinding is not denaturation.)

The base are now exposed to the aqueous environment. Single-stranded DNA is more stable than double-stranded DNA at higher temperature. Note that the edges of the bases will still form hydrogen bonds in this situation. They form hydrogen bonds with water molecules. In fact, they will form many more hydrogen bonds with water than they would form with complementary bases in double-stranded DNA.

As the temperature is lowered, the double-stranded form becomes more stable than the single strand in solution, and the DNA renatures. The first step is a nucleation event where two complementary regions come into contact. Nucleation is the rate-limiting step in renaturation. Once nucleation occurs, the rest of the molecule zips up pretty quickly.

It's easy to follow the denaturation of DNA because there's a difference in the absorbance of ultraviolet light between single- and double-stranded DNA. Single-stranded DNA absorbs more strongly.

In a typical melting curve, you measure the increase in UV absorbance as the temperature increases. This tracks the unwinding and denaturation of DNA. The melting point (T_m) is the temperature at which half the DNA is unwound.

DNA that consists entirely of AT base pairs melts at about 70° and DNA that has only G/C base pairs melts at over 100°. You can calculate the T_m of any DNA molecule if you know the base composition. The simplest formulas just take the overall composition into account and they are not very accurate. More accurate formula will use the stacking interactions of each base pair to predict the melting temperature [Wikipedia: DNA melting].

The question is why is there a relationship between the base composition of DNA and the stability of the double-stranded regions?

The first people to think about this question didn't really understand the role of stacking interactions between base pairs in the middle of double-stranded DNA. They also didn't really appreciate hydrogen bonds. They naively assumed that the differences between G/C rich DNA and A/T rich DNA was due to the fact that G/C base pairs have three hydrogen bonds and A/T base pairs have only two [The Chemical Structure of Double-stranded DNA].

We now know that this explanation doesn't make sense. There is no net loss of hydrogen bonds when DNA is denatured, quite the reverse in fact. There are more hydrogen bonds formed between the bases in single-stranded DNA and water molecules than between base pairs in DNA. There's no reason why single-stranded DNA would renature if formation of double-stranded DNA was driven by the creation of hydrogen bonds between base pairs. For every hydrogen bond between bases you would have to break almost two hydrogen bonds to water molecules.

The most important interactions in double-stranded DNA are the stacking interactions between adjacent base pairs. You can think of this as the interactions of electrons on the upper and lower surfaces of the rings that form the bases.

There are ten possible interactions between adjacent base pairs. The energies of these interactions are shown in the table on the left. The arrows indicate the direction of the DNA stand from 3′→5′ [The Chemical Structure of Double-Stranded DNA].

Note first of all that the strength of these stacking interactions (about 30 kJ mol^-1 on average) are greater than the strength of stability conferred by hydrogen bonds (about 3 4 kJ mol^-1)¹. Assuming there are on average six three hydrogen bonds per in two stacked G/C base pair, the total strength of the hydrogen bonds (18 12 kJ mol^-1) is still much less than the stacking interactions.

Secondly, note that stacking interactions involving G/C base pairs are stronger (more negative) than those involving A/T base pairs. This is why the melting temperature of DNA depends on the base composition. It's not because G/C base pairs have one more hydrogen bond than A/T base pairs, it's because G/C base pairs form stronger stacking interactions.

This is why you can calculate a more accurate melting temperature for oligonucleotides if you use the stacking interactions. It's stacking interactions that determine the stability of double-stranded DNA and it's stacking interactions that are disrupted as the temperature increases and more thermal energy is added to the molecule.

Finally, the paper that I discussed in July [Measuring Stacking Interactions] measured the stacking interactions in single-stranded DNA (poly A). As it turns out, the stacking interactions between single bases are, in some cases, strong enough to force single-stranded DNA into a helical structure. This is further evidence of the importance of stacking interactions in conferring stability to the double helix.

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1. The stability conferred by each hydrogen bond is the difference between the strength of the bond in double-stranded DNA and its strength in when bonded to water. Hydrogen bonds between bases and water molecules typically have strengths of about 25 kJ mol^-1 and hydrogen bonds between base pairs are a bit higher.