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.

The Catholic Church: a step in the wrong direction

When defenders of evolution try to be sympathetic towards people of faith, and show that evolution and faith are clearly compatible, they often quote what pope John Paul II stated in 1996: that “evolution is more than a hypothesis”. I did that as well a while ago.

Well, that relatively open-minded approach might change, or has already changed, with the new boss in the Vatican. Christoph Schönborn, archbishop of Vienna, has written an op-ed article for the New York Times, and according to cardinal Schönborn,

Evolution in the sense of common ancestry might be true, but evolution in the neo-Darwinian sense – an unguided, unplanned process of random variation and natural selection – is not. Any system of thought that denies or seeks to explain away the overwhelming evidence for design in biology is ideology, not science.

Pretty disappointing statements from a man of higher learning. And it is ridiculous that a high priest of the Catholic Church is claiming that mainstream biologists (that is, ~99.999 percent of all biologists who matter) are doing ideology, not science. How on earth is he qualified to decide what is science and what is not in biology? Does he have a PhD in biology? No. Did he publish any scientific papers in biology? No. Did he spend most of his life studying, teaching, and spreading religious ideology? Yes. So who is doing science, and who is doing ideology?

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.

UFOs on ABC

A few weeks ago I started watching a 2-hour long special on ABC about UFO-s — but I couldn’t stand watching it for a long time; there was too much of the usual mystical stuff and the skeptical viewpoint was hardly given any consideration. Chris Mooney writes about the program at CSICOP’s home page, and concludes that

“through the use of selective skepticism, journalistic “balance,” and haphazard suspension of disbelief, ABC and Peter Jennings manage to keep the sense of “mystery’ alive. In light of the difficulty of positively proving any existing UFO claim, that’s probably the most they could possibly accomplish.”

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.