An intelligent judge against Not-So-Intelligent Design

Judge John E. Jones III finally has a decision in the Pennsylvania creationism trial. How refreshing is to see a judge (and not any judge, but a conservative Republican appointed by George W. Bush) not falling into the trap of ‘equal time’ and ‘balanced judgment’ (see for example this story). He is simply extremely clear that intelligent design is not science, regardless of how hard some people try to masquerade it like that. Of course, I cannot be as eloquent as Carl Zimmer is:

“Journalists would do well to print Judge Jones’s decision out and read it carefully. It’s not up to a journalist to decide which side is right in a genuine scientific controversy. But it’s wrong to let people use an article as a soapbox where they can make grand pronouncements about science, without looking into whether the science actually backs them up. Judge Jones fact-checked intelligent design and found it wanting. He did not shy away from this realization with worries that he was somehow being one-sided. Justice holds a balance in her hand, but balance is not what she seeks. Instead, she weighs the evidence to see which way it tips.”

I am responsible for typing the last two sentences in bold. I just like them a lot.

The fractal nature of Einstein’s and Darwin’s letter writing

Power laws are gathering quite some attention again, thanks to a few new papers (e.g., this one and this one) by Albert-László Barabási and his coworkers, published in Nature. Cosma Shalizi and others disagree: once again, just because some dataset on a log-log plot looks like you could easily fit a straight line to it, it is not safe to conclude that it is a power-law distribution.

One of the papers looks at the letter-writing habits of Darwin and Einstein, and concludes that the response times have a power-law distribution with an exponent of 3/2. The other “reports that the probability distribution of time intervals between consecutive emails sent by a single user and time delays fro eamil replies follow a power law”. Shalizi and Stouffer et al. claim that these are in fact lognormal distributions.

I am wondering if you could ever get a paper published in Nature that looks at some dataset, shows that it has normal or lognormal distribution, draws some overarching and universal conclusions from that, and… and that’s it.

Or, to translate it to the much more mundane language of geologists, that only applies to dirt, not to Einstein’s letters: there is no interesting story in showing that bed thicknesses or sedimentary body sizes have a lognormal distribution, but if it’s a power law, suddenly you can talk about the “scale-independent physics of turbidite deposition” and the importance of non-equilibrium thermodynamics in the geometries of deltas and everything else under the sun.

That’s why power laws are great.

Hurricanes and barrier islands

Here is the reason why one should think twice about buying or building a house on a barrier island that is in hurricane country. This USGS website also shows convincingly that Hurricane Rita should not be misunderestimated 🙂 just because it barely touched the Houston-Galveston area. It did plenty of damage where the right-front qaudrant made landfall – things would have been very different around here if Rita made landfall at Galveston or a bit to the West of Galveston.

And these images of a barrier island that migrates landward as hurricanes go over it make you wonder how much of the geologic record of barrier islands (and beaches in general) actually consist of fairweather deposits. Everything seems to be moving and redepositing during these storms.

Dawkins against Intelligent Design

Richard Dawkins (this time with Jerry Coyne of the University of Chicago) explains it again, in probably the most clear language you can find, why intelligent design should not be taught alongside evolution in science classes:

What is wrong with the apparently sweet reasonableness of “it is only fair to teach both sides”? The answer is simple. This is not a scientific controversy at all. And it is a time-wasting distraction because evolutionary science, perhaps more than any other major science, is bountifully endowed with genuine controversy.

Among the controversies that students of evolution commonly face, these are genuinely challenging and of great educational value: neutralism versus selectionism in molecular evolution; adaptationism; group selection; punctuated equilibrium; cladism; “evo-devo”; the “Cambrian Explosion”; mass extinctions; interspecies competition; sympatric speciation; sexual selection; the evolution of sex itself; evolutionary psychology; Darwinian medicine and so on. The point is that all these controversies, and many more, provide fodder for fascinating and lively argument, not just in essays but for student discussions late at night.

Intelligent design is not an argument of the same character as these controversies. It is not a scientific argument at all, but a religious one. It might be worth discussing in a class on the history of ideas, in a philosophy class on popular logical fallacies, or in a comparative religion class on origin myths from around the world. But it no more belongs in a biology class than alchemy belongs in a chemistry class, phlogiston in a physics class or the stork theory in a sex education class. In those cases, the demand for equal time for “both theories” would be ludicrous. Similarly, in a class on 20th-century European history, who would demand equal time for the theory that the Holocaust never happened?

Talking about Dawkins: in the September issue of Discover magazine, there is an article about him entitled “Darwin’s Rottweiler – Sir Richard Dawkins: Evolution’s fiercest champion, far too fierce“. The author, Stephen S. Hall, paints an overall positive picture about Dawkins, but, as he makes it clear already in the title, he thinks that Sir Richard is “far too fierce”. This is how the article ends:

This recusal underlines the most obvious contradiction about Richard Dawkins and the cultural war in which he has so much to contribute: You can be the world’s greatest apostle of scientific rationalism, but if you come across as a rottweiler, Darwin’s or anybody else’s, when you enter that marketplace, it’s very hard to make the sale.

Well, first of all, in most of his writings and talks, Dawkins does not come across to me as a rottweiler. Read the quotation above: is there any barking and biting in it? I don’t think so. It just states facts and draws conclusions that make sense to any reasonable person. 99% percent of his books consist of crystal-clear explanations of how evolution or science in general work. The remaining 1% is similarly well-written and convincing – it just happens that a lot of people are offended because it makes them uncomfortable. Should he never talk about religion just because some people get offended? There are incredibly few people who have the intellect and courage to talk about these issues honestly; even if you disagree sometimes with him, why should one of the most eloquent guys shut up?

At times when American science education is endangered by a few politically powerful, but scientifically challenged people, we would need to clone professor Dawkins, not to tame him. When it comes to speaking the truth in clear and honest terms, I wish we had more rottweilers of the calibre of Dawkins and fewer lapdogs that never bark and never bite.

When a ‘balanced view’ is wrong, wrong, wrong

Time magazine has a cover story about the “Evolution wars”, that is, the controversy surrounding the teaching of intelligent design alongside evolution in schools. Again, thanks to the lame and stupid idea of ‘we are not taking sides’ that dominates present-day American journalism, anti-evolutionists are given about the same space and consideration as virtually all the biologists and scientists combined, Michael Behe’s and a baptist theologian’s opinion having apparently the same weight as that of Steven Pinker or Francis Collins. I am sure Behe and co. are celebrating: this is what they wanted, to have a credibility in the eyes of the media that equals that of some of the best scientists around.

Anyway, I just want to take note here of Pinker’s short but, as usual, crystal-clear answer to the question “Can you believe in God and evolution?”:

The theory of natural selection explains life as we find it, with all its quirks and tragedies. We can prove mathematically that it is capable of producing adaptive life forms and track it in computer simulations, lab experiments and real ecosystems. It doesn’t pretend to solve one mystery (the origin of complex life) by slipping in another (the origin of a complex designer).

Many people who accept evolution still feel that a belief in God is necessary to give life meaning and to justify morality. But that is exactly backward. In practice, religion has given us stonings, inquisitions and 9/11. Morality comes from a commitment to treat others as we wish to be treated, which follows from the realization that none of us is the sole occupant of the universe. Like physical evolution, it does not require a white-coated technician in the sky.

Darwin on geology and epistemology

Here is a geology quote that Michael Shermer seems to like a lot (for example, in this book). It is from a guy called Darwin:

About thirty years ago there was much talk that geologists ought only to observe and not theorize; and I well remember someone saying that at this rate a man might as well go into a gravel-pit and count the pebbles and describe the colours. How odd it is that anyone should not see that all observation must be for or against some view if it is to be of any service!

On cumulative probability curves

Let’s go back to some good old science subjects and take some notes about sediments, something I am supposed to be an expert in.

One of my favorite pastimes lately is collecting examples from the geological literature in which the statistical analysis went incredibly wrong. Take for example the papers dealing with grain-size distributions that advertise cumulative probability plots as the best technique to identify subpopulations in a mixed distribution. Here is what G.S. Visher says in his 1969 paper on “Grain size distributions and depositional processes” (Journal of Sedimentary Petrology, v. 39, p. 1074-1106):

“The most important aspect in analysis of textural patterns is the recognition of straight line curve segments. In figure 3 four such segments occur on the log-probability curve, each defined by at least four control points. The interpretation of this distribution is that it represents four separate log-normal populations. Each population is truncated and joined with the next population to form a single distribution. This means that grain size distributions do not follow a single log-normal law, but are composed of several log-normal populations each with a different mean and a standard deviation. These separate populations are readily identifiable on the log-probability plot, but they are difficult to precisely define on the other two curves.” (p. 1079)

I am wondering if this tendency to see straight line segments in cumulative probability plots and to give them some special significance is a syndrome restricted only to geologists – whose abilities for pattern recognition are excellent in general – or one could find such examples from other fields as well. The fact that a certain distribution looks like a straight line on a cumulative plot does not mean that mixtures of the same type of distribution will plot as straight line segments. The excellent sedimentologist Robert Folk has pointed this out in a 1977 discussion of a paper coauthored by Visher (in which they try to prove that the Navajo Sandstone is not an eolian deposit – yeah, right):

“A general defect of the Visher method is exemplified by Kane Creek #2, which is shown as consisting of four straight line segments, implying that it is a mixture of four populations. It can be proved by anyone using probability paper and ordinary arithmetic that such kinky curves can be made by a simple mixing of two (not four) populations that are widely separated; the ‘flat’ portions represent the gaps in the distribution. Furthermore, mixing of populations on probability paper results in smoothly curving inflexions, not angularly joined straight-line segments.”

Despite this, multiple straight-line-fitting to cumulative probability plots is fashionable again, although this time it is done on log-log plots of exceedence probability of either bed thickness or fault size data. But this is going to be part of a paper that I am working on right now (in the evenings and weekends…) — so more about this later.

Stem cells & cloning

The first signs that the US is lagging behind in stem cell research started to show: for the first time, “scientists have created nearly a dozen new lines of human embryonic stem (ES) cells that […] carry the genetic signature of diseased or injured patients”, and this did not happen in America, but at Seoul National University in South Korea. Here is an explanation from The New York Times why it is important to get stem cells from cloned embrios rather than from surplus embrios from fertility clinics:

“Stem cells derived from cloned human embryos that are genetically matched to sick patients are potentially much more useful than stem cells derived from surplus embryos at fertility clinics, both for research and for potential treatments. Since cloned embryos carry the genetic makeup of patients with known diseases, scientists can study how those diseases develop from the earliest stages and can perhaps find drug treatments to interrupt the process. And if scientists ultimately succeed in converting the stem cells themselves into replacement tissues to repair damaged organs, those tissues would have the best chance of avoiding rejection by a patient’s immune system if they were genetically matched to the patient through therapeutic cloning.”

Scientists are excited — but, of course, some people immediately expressed their concerns. The president said today that “the use of federal money, taxpayers’ money, to promote science which destroys life in order to save life is – I’m against that.” Destroys life? What life? Using a few cells that happen to come from a fertilized egg in order to save real, living and breathing humans, whose quality of life could be tremendously improved with the potential new techniques — why is that unethical?

It is a lot more unethical to ban this kind of research just because one’s religion declares that life begins at conception. It makes sense to ban reproductive cloning because it is still unsafe. But to ban therapeutic cloning is utter nonsense, and it is really time to shut up for those who have only learned about genetics at Sunday school.

Homeopathy advertised in The New Scientist

The New Scientist talks about “The 13 things that don’t make sense“. Some of the 13 items are at least questionable. For example, it seems to me pretty one-sided to claim that the experimental case for cold fusion is ‘bulletproof’. Bob Park has a much less positive view of the issue, for example here. Also, after reading Brian Greene’s The Fabric of the Cosmos, I thought that inflationary cosmology gave a good explanation for the ‘horizon problem’. According to the New Scientist, “In scientific terms, the uniform temperature of the background radiation remains an anomaly.” The third item that I am quite skeptical about is number 4 – the Belfast homeopathy results:

“MADELEINE Ennis, a pharmacologist at Queen’s University, Belfast, was the scourge of homeopathy. She railed against its claims that a chemical remedy could be diluted to the point where a sample was unlikely to contain a single molecule of anything but water, and yet still have a healing effect. Until, that is, she set out to prove once and for all that homeopathy was bunkum.

In her most recent paper, Ennis describes how her team looked at the effects of ultra-dilute solutions of histamine on human white blood cells involved in inflammation. These “basophils” release histamine when the cells are under attack. Once released, the histamine stops them releasing any more. The study, replicated in four different labs, found that homeopathic solutions – so dilute that they probably didn’t contain a single histamine molecule – worked just like histamine. Ennis might not be happy with the homeopaths’ claims, but she admits that an effect cannot be ruled out.”

I am looking forward to more results that show that homeopathy works. However, scientists and editors and journalists alike should keep in mind that extraordinary claims require extraordinary evidence. I have a feeling that New Scientist’s free advertisment for homeopaths was a bit too early and unnecessary.

The Fabric of the Cosmos

During my recent trip to Boston / MIT, I picked up a copy of “The Fabric of the Cosmos” by Brian Greene, and I read about half of it by now. It is a great reading; I think I am starting to get a vague idea about both how relativity and quantum physics work, subjects that I was utterly ignorant of not long ago. Sometimes the references to the Simpsons and Springfield and agent Mulder and Scully and baseball can be annoying, but overall I am really enjoying this book.

And I am realizing how ‘narrow-minded’ we humans are. Evolution shaped our minds so that we easily understand what is important for our survival, but there was no selective pressure to evolve an understanding of how things work on much larger or much smaller spatial and temporal scales: having some intuitive ideas about what trajectory a thrown piece of rock describes probably had some survival value, but our ancestors did not need to know about the probabilistic nature of the subatomic world in order to get through the hard times.