Sedimentology on Mars: wet or dry gravity flows?

Once again, the 'water on Mars' subject made it to the headlines: researchers claim that recent gully activity that took place in the last few years (as documented by photographs taken in 1999 and 2005) suggests that watery sediment flows (debris flows) are shaping the planet's surface as we speak.

The problem is, of course, that it is difficult to keep water liquid in an environment where the temperature is usually way below 0 degrees Celsius and the atmospheric water vapor pressure is also very low. And, as far as I am concerned, the morphology of the gullies and of the associated deposits does not rule out deposition from dry granular flows at all. Of course, several papers have been written on the subject; here is, for example, an opinion from Allan Treiman (2003):

The salient features of the Martian gullies [Malin and Edgett, 2000, 2001] are consistent with their origin as dry flows of eolian sediment: gully deposits are fine granular material (erodable by wind); eolian sediment are available where gullies form; the distribution of gullies are consistent with deposition of sediment from wind; and the orientations of gullies are similarly consistent with wind patterns. Further, it is clear that granular materials can flow as if they were Bingham liquids, and granular flows can produce landforms with all of the geomorphic features of Martian gullies. No known data concerning the gullies (chronological, geomorphic, or geologic) falsify this hypothesis, so it is worth further investigation.

I just find it interesting that, by the time the story reaches the media, all the uncertainties disappear, and the story is unequivocal: watery flows must occur on Mars today, period.

Természettudományos oldalak a Transindex-en

Itt (a lap alján). Végre. A sok humán kutatói oldal után itt volt az ideje, hogy azok is teret és reklámot kapjanak, akik 'földhözragadtabb' dolgokkal foglalkoznak. De komolyan foglalkoznak. És más kutatók (azaz az ISI) által is számontartott lapokban közölnek.

John McPhee on geological language

Started reading John McPhee's tetralogue on geology, Annals of the Former World. Here is a memorable sampling of the thick sediments of geological language (p. 33):

As years went by, such verbal deposits would thicken. Someone developed enough effrontery to call a piece of our earth an epieugeosyncline. There were those who said interfluve when they meant between two streams, and a perfectly good word like mesopotamian would do. A cactolith, according to the American Geological Institute's Glossary of Geology and Related Sciences, was a "quasi-horizontal chonolith composed of anastomosing ductoliths, whose distal ends curl like a harpolith, thin like a sphenolith, or bulge discordantly like an akmolith or ethmolith." The same class of people who called one rock serpentine called another jacupirangite. Clinoptilolite, eclogite, migmatite, tincalconite, szaibelyite, pumpellyite. Meyerhofferite. The same class of people who called one rock paracelsian called another despujolsite. Metakirchheimerite, phlogopite, ktzenbuckelite, mboziite, noselite, neighborite, samsonite, pigeonite, muskoxite, pabstite, aenigmatite. Joesmithite.

He could have included turbidite, tsunamite, tempestite, unifite, homogenite, debrite, hyperpycnite, and contourite as well. As if this wasn't enough, there are sedimentary geologists who suggest introducing new 'ites' (PDF link) like gravite and densite.

Bullshite.

Bedforms in Matlab - everything you wanted to know about ripple marks and cross beds

David Rubin's bedform-generating code has been implemented in Matlab (in fact, it has been out there for a while). It is a great learning, teaching, and research tool that can be downloaded as part of an USGS open file report. Strongly recommended to anyone having some interest in sedimentary structures, bedforms, and cool Matlab graphics.

That reminds me of something else: it would be nice to have a Matlab version running on Intel Macs. I hope Mathworks will keep its promises and have something ready by early 2007. Having to reboot the iMac in Windows XP is an acceptable solution, but I could live without it [although even Windows XP looks OK on this kind of hardware :) ].

Let a thousand academic flowers bloom

The ongoing debate about whether there is need for a new university in Cluj that would roughly correspond to the former Bolyai University should consider what we know about higher education systems that work pretty well. Here are, for example, some recommendations from The Economist:

As it happens, we already possess a successful model of how to organise higher education: America's. That country has almost a monopoly on the world's best universities (see table 1), but also provides access to higher education for the bulk of those who deserve it. The success of American higher education is not just a result of money (though that helps); it is the result of organisation. American universities are much less dependent on the state than are their competitors abroad. They derive their income from a wide variety of sources, from fee-paying students to nostalgic alumni, from hard-headed businessmen to generous philanthropists. And they come in a wide variety of shapes and sizes, from Princeton and Yale to Kalamazoo community college.

This survey will offer two pieces of advice for countries that are trying to create successful higher-education systems, be they newcomers such as India and China or failed old hands such as Germany and Italy. First: diversify your sources of income. The bargain with the state has turned out to be a pact with the devil. Second: let a thousand academic flowers bloom. Universities, including for-profit ones, should have to compete for customers. A sophisticated economy needs a wide variety of universities pursuing a wide variety of missions. These two principles reinforce each other: the more that the state's role contracts, the more educational variety will flourish.

I especially like that "a sophisticated economy needs a wide variety of universities pursuing a wide variety of missions". Contrast that with what is going on in Romania. Cluj, the most important cultural center in Transylvania, is almost entirely dominated by a single but huge academic institution, that is, Babes-Bolyai University. There are about 45,500 students at UBB, and it is essentially the only institution in Transylvania that has some real scientific output (that is, publications in ISI journals). Not a lot of scientific output, taking into account the number of faculty, but certainly light-years ahead of any other place pretending to produce science.

So wouldn't it make sense to diversify a bit the academic picture and re-create an institution that already has some respectable history? The new Bolyai University would not be an institution against the present-day UBB; and it clearly should not be solely focused on local and Hungarian issues. Ideally, it would result in a healthy competition, and it would give a chance to the Hungarian community in Transylvania to have a real center of excellence in research and higher education.

That would be the real multiculturalism. A relatively small but quality-driven institution of higher education is better than a giant degree-machine whose leaders seem to think that just pointing out how many thousands of students study in how many different languages shows how good the institution is. The best universities in the world are famous not for the sheer numbers of their students or faculty, and the number of languages that are used on campus, but for the quality and impact of research and teaching. And by that standard, I am sorry to say, Babes-Bolyai has a long way to go.

Seed Magazine and Science Blogs

Just wanted to take note of two new (that is, new to me) developments on the science-friendly web. Seed Magazine now has a nice website. They also gave home to a number of good science blogs at ScienceBlogs. See also my updated link list in the sidebar. Exciting stuff.

Digital Earth

Last weekend I discovered (1) that Google Earth was even more amazing than I had previously thought [and now they have a Mac version as well!]; and (2) there is a lot more out there in terms of digital geography if you look a bit harder.

Here is for example this USGS site from which you can download (with some patience) not only the usual satellite imagery but digital elevation models (DEMs) as well, for pretty much the whole globe [thanks to my friend Radu Girabcea for pointing me to it]. Once you've got a DEM, you can use 3dem, a nice little piece of freeware to display the elevation models in 2D and 3D and to drape georeferenced images over the topography. DEMs are available (for free -- at least at this point) with a ~10 m resolution for most of the US and a ~30 m resolution for other areas (I was especially excited to savor the detailed topography of the Carpathians -- the more familiar you are with a place, the more illuminating it can be if you examine the morphology).

Another thing worth taking a look at is NASA's version of Google Earth, that is, World Wind. With one click, you can switch from Landsat images to USGS topographic maps [although I often have problems with the server connection]. Can it get a lot better than this?

The culture of science

[this article was published in Ad Astra in 2004]

An interview grabbed my attention in a Romanian newspaper a few months ago. A "researcher" claimed that, in his book entitled "The Final Truth", he presented a theory that "bridges the gaps between the idealistic, materialistic and ezoteric worldviews"; that thoughts cannot arise in the human brain, they must come from somewhere else; that Darwininan evolution is wrong; that there must be another Universe that "consists of electromagnetic waves of higher frequencies"; and that this high-frequency Universe is the source of all human thought, UFOs, religion, astrology and paranormal phenomena.

The fact that somebody, who by all means would satisfy most criteria for the recognition of a crackpot, comes up with a handful of ideas that are either age-old or simply silly and tries to sell them as revolutionary scientific results is not new and would not grab my attention anymore. It was the style of presentation that forced me to think about this article a bit longer: the editor (and interviewer) tried to create an aura of scientific authenticity by saying that people from Chalmers University in Goteborg, Sweden and the Hungarian Academy of Science "expressed interest" in the book; and by mentioning that the author has spent many years doing research on these subjects in Sweden. I could not resist writing a letter to the newspaper and pointing out that the "research" of this gentleman is far from being science and, if presented at all, it should be presented accordingly, either as metaphysics or philosophy (of the sloppiest kind, I must add), or as just another muddled rambling about other-worldly energies and paranormal nonsense. But not as science and a Nobel-prize-worthy intellectual achievement.

The letter was published, and it generated a series of pro-and-con articles in the Transylvanian newspaper. With the exception of a mathematician, who was slightly critical of "The Final Truth" and its author, everybody, including the editor, were enthusiastic about them. They either said that this was science, my opinion nonwithstanding, or that this was more than science, because it integrates the ‘spiritual dimension’ with what we know from science. Those who argued against my criticisms included a ‘chief psychiatrist’ and a ‘university professor’. After a few months of replies-to-the-replies, the editor finally closed the argument by writing that he was proud of starting these series of articles about "The Final Truth", and the importance of the book was also suggested by the fact that it drew the attention of "American researchers" as well. He just forgot to mention what the "American researchers" had to say about it.

It is true that the newspaper I am talking about is not a major paper in Romania; that it is published in Hungarian, therefore it has a relatively small readership in Transylvania, more precisely in the city of Cluj. I think however that it is diagnostic of the attitudes towards science in this part of Europe. After all, Cluj has one of the largest universities in Europe (more than 40,000 students and 1500 faculty), and I find it worrysome that nobody of the several thousand Hungarian-speaking faculty members and students takes the time to fight such science-bashing or science-degrading nonsense that surfaces from time to time in the media. They either don't know how to tell good science from bad science or pseudoscience, or they do know but they couldn't care less.

It seems to me that back home, science, if the word is understood correctly - as we saw, sometimes it isn't -, is not considered an essential part of being well-read, well-informed, and well-educated. A lot of 'intellectuals' are enthusiastic about science - as long as astrology or chinese medicine are included, as long as great scientists can be used as boosters of national pride, or as long as you do not exclude postmodern literary criticism (the term "literature science"is often used in Hungarian and it gives a hint of how broad the meaning of the word 'science' is in some circles). When I was in high school in a small Transylvanian town near Brasov, math and physics were thought to be important only because at that time (in the eighties) these subjects meant the safest route towards college education. Almost everybody seemed to know that real knowledge and real culture can only come from the study of literature, art and history. And I think this attitude did not change since then, or it even got worse: it is still OK if you don't know what a fractal is or how the genetic machinery inside us works, but you cannot be a real intellectual if you cannot talk about Shakespeare, Ionesco, Derrida or Tarkovsky for at least as long as two beers last at the pub. In their excellent paper on the status of science in post-communist Romania, Liviu Giosan and Tudor Oprea suggest that "culture wars" between the "two cultures" would be "suicidal at best". However, I am afraid that there is no danger of "culture wars" or "science wars" in Romania, simply because the intellectual elite is dominated by people with little or no scientific background and a 'culture of science' does not exist. One obvious piece of evidence is that none of the major Romanian daily newspapers has a science and/or technology section. While 'science writing' has become an exciting profession in the West, it is essentially non-existent in Romania. Yes, Discovery Channel is available in many cities [let's put aside now the fact that not all of its programs are scientific] and I hear there is even a Romanian edition of Scientific American, but, to put it mildly, there is a lot of room for improvement in making science more socially accepted, better understood, and part of mainstream culture.

More reliable than my little pieces of anecdotic evidence are the results of a recent study prepared for the European Commision: an Eurobarometer report on "public opinion in the countries applying for European Union membership". There are several statistics that suggest a positive attitude towards science in the candidate countries in general, including Romania. For instance, 78 % of Romanians (81 % on average in the thirteen countries) agree with the statement that "science and technology are making our lives healthier, easier and more comfortable". Also, 74 % think that "even if it brings no immediate benefits, scientific research which adds to knowledge, is necessary and should be supported by government", and scientists are regarded by 51 % of the respondents as having a highly prestigious profession. Other numbers however are less encouraging. In the category of "knowledge of fundamental scientific facts", the average number of correct answers given by participants in Romania is significantly below the average in the EU or in many other Eastern European countries. Compared to the rest, Romanians did poorly in in recognizing the scientifically correct method for drug testing (15 % correct answers compared to more than 30% in most other countries).

I am not convinced that these differences are extremely important or disconcerting. The gaps between statistics on science in Romania and in other candidate countries or the EU increase from barely significant to orders of magnitude as one goes from the attitudes and knowledge among the population to governmental investments in R&D and to the number of scientific publications. To add only one number to the detailed analysis by Giosan and Oprea (2003): the gross domestic expenditure on R&D in the field of natural sciences in 2000 was 12.1 million euros in Romania, compared to 59.1 million in Hungary, 185.9 million in the Czech Republic, and 261.9 million in Poland (Simona Frank: R&D expenditure and personnel in the candidate countries in 2000, Statistics in focus, Science and technology, Theme 9-1/2003).

But my main concern here is not science policies, R&D expenditure, or the quantity and quality of research in Romania. What I wanted to and started to talk about is the lack of a culture of science in the mass media and among intellectuals in general, including even many of those who are employed by universities or research institutes.
Science has become much more popular and fashionable in the West during recent decades. Numerous science books written for the general public in a simple and easy-to-understand language - but without too much dumbing down - are bestsellers; it is possible now to make a succesful Hollywood movie about the life of a mathematician (I am talking about 'A Beautiful Mind'); most large bookstores have an impressive collection of popular science books. Some of these books are much more than popular science: they are frequently cited in the real scientific literature and have a strong influence on the field; many represent an inspired - and inspiring - mix of scholarship in the natural sciences, philosophy, and good writing. Authors like Richard Dawkins, Stephen Jay Gould, Steven Pinker, Daniel Dennett, Steven Weinberg have become a lot more popular than numerous highly regarded names in postmodern literary criticism and philosophy. [Frankly, I am not surprised. Try reading an essay or a book by one of the science guys and compare it to a representative writing of the of the postmodernist camp.] Museums of science, technology and natural history in the United States are larger, richer, and more interactive than ever. Whenever a famous scientist gives a public presentation, lecture halls are quickly filled and tickets are sold out in advance. A few months ago Stephen Hawking gave a lecture in Houston. All of the almost 5000 tickets that went on sale were gone by the time of the presentation.

It seems like the two cultures of C. P. Snow are antagonistic or lack real communication only in the eyes of those who still see the arts and the social sciences entirely independent of the natural sciences. The best and some of the most influential thinkers of our time are scientists who are also good writers – or writers/artists who know quite a bit about science. This ‘culture of science’ has been given the name “third culture” by literary agent and science writer John Brockman and is promoted on his website “The Edge” (http://www.edge.org), a discussion forum for a distinguished group of scientists and ‘new humanists’. Twelve years after introducing the idea of the ‘third culture’, Brockman suggests that “the third culture now includes scholars in the humanities who think the way the scientists do. Like their colleagues in the sciences, they believe there is a real world and their job is to understand it and explain it. They test their ideas in terms of logical coherence, explanatory power, conformity with empirical facts. (…) They are not reducing the humanities to biological and physical principles, but they do believe that art, literature, history, politics – a whole panoply of humanist concerns – need to take the sciences into account.”

As I already suggested, I do not think that the ‘third culture’ and the ‘new humanists’ have a strong presence in Romania. Most people base their worldviews entirely on tradition and authority or embrace either the numerous new waves of mysticism and pseudoscience or a nihilistic and relativistic postmodernism. Although not everything is going well in this regard in the Western world either, I still hope that getting closer politically and economically to the European Union will increase not only the quantity and quality of research in Romania, but will also improve science education and the acceptance and understanding of science.

Like in other, more western parts of the world, most people in Romania seem to have an overall positive attitude toward science. They just don’t know what exactly it is. Those few who know better have the responsibility of educating the general public. For example, by speaking out when pseudeoscientific or antiscientific nonsense hits the media; explaining in simple terms but with convincing logic why pseudoscience is not science or why darwinism and evolutionary theory cannot and should not be blamed for the horrors of fascism and communism. It is unlikely that a country will have its Silicon Valleys and a greatly succesful economy as long as its political leaders and influential intellectuals do not recognize the importance and value of both scientific research and science education. In the long term, they should also realize that the social sciences and humanities cannot ignore the natural sciences anymore. As evolutionary biologist Edward O. Wilson put it, “most of the issues that vex humanity daily – ethnic conflict, arms escalation, overpopulation, abortion, environment, endemic poverty, (…) cannot be solved without integrating knowledge from the natural sciences with that of the social sciences and humanities. Only fluency across the boundaries will provide a clear view of the world as it really is, not as seen through the lens of ideologies and religious dogmas or commanded by myopic response to immediate need.”

References

1. L. Giosan and T. Oprea. Science in post-communist Romania. Ad Astra, 1 (2) 2002.
2. Candidate countries Eurobarometer. Public opinion in the countries applying for European Union membership. CC-EB 2002.3 on science an technology. European Commission, January 2003.
3. S. Frank. R&D expenditure and personnel in the candidate countries, in 2000, Statistics in focus, Science and technology, Theme 9-1/2003.
4. C. P. Snow. The two cultures. Cambridge University Press, 1993.
5. E. O. Wilson. Consilience: the unity of knowledge. Vintage Books, 1999.

Global warming does not cause earthquakes

According to Wired magazine's "Biggest Discoveries of 2005", the most important discovery of 2005 is that

Thanks to the Asian tsunami and Hurricane Katrina, global warming can no longer be ignored.

I agree that global warming can no longer be ignored, but you don't need to know too much about earth science to realize that the Asian tsunami has absolutely nothing to do with it.

The truth about the Enlightenment

An excellent article by philosopher Simon Blackburn. It is great to hear somebody talk like this after all the noise about the coming apocalypse, the anti-humanism of science, the dangers of technology, and so on:

"The west, it is sadly said, has lost confidence in the Enlightenment. It is quite common to see intellectuals state as a fact that the Enlightenment project has been tried and failed. This is a lie. There never was one single Enlightenment project, and of the Enlightenment projects that there were, many have succeeded beyond the wildest hopes of their proponents. The Enlightenment provided the matrix I have talked of, in which scientific enterprises could flourish. Now, our understanding of the world is better because of physical science. Our understanding of ourselves is better because of biological science. We live longer, and we feed ourselves better, and ‘we’ here includes not only people in first world countries, but countless people in the third world. We look after the environment better, and in time we will manage our own numbers better. Outside the theocracies of the east more people have more freedoms and enjoy more education, more opportunities and may even have more rights than ever before. We owe this progress entirely to the culture forged, in the west, by Bacon and Locke, Hume and Voltaire, Newton and Darwin. Humanism is the belief that humanity need not be ashamed of itself, and these are its great examples. They show us that we need not regard knowledge as impious, or ignorance as desirable, and we need not see blind faith as anything other than blind."

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.

My talk on bed thicknesses and power laws

At the end of April I am going to give a talk on power-law and lognormal distributions and how they apply to turbidite bed thickness data. Here is the abstract. And here are some previous thoughts and links on the subject of log-log plots, power-laws and bed-thickness distributions.

U.S. science supremacy threatened by competition

Number 67 in the 'top science stories of the year' in Discover Magazine is entitled 'U.S. Science Supremacy Threatened by Competition'. Some interesting facts: according to the National Science Board, an independent policy group that advises the president and the congress,

the drop in foreign applications - down 28 percent at the graduate level - is (...) certain to affect the future of science. Many who come here to study do not return to their native countries. A survey by the National Science Foundation in 2000 reported that 38 percent of U.S. scientists with doctorates were born abroad.

Also:

the number of research articles by Americans has been stagnant compared with an increasing number written by Western Europeans in the last decade.

The importance of numbers

Bought the third edition of "Statistics and Data Analysis in Geology" by John C. Davis - a lot of it looks familiar, but it's good to have this on the shelf. I like the good old citation at the beginning from Lord Kelvin -- I have seen it several times before, but it still sounds important:

"...when you can measure what you are speaking about and express it in numbers, you know something about it; but when you cannot express it in numbers, your knowledge is of a meagre and unsatisfactory kind; it may be the beginning of knowledge, but you have scarcely in your thoughts advanced to the state of science, whatever the matter may be."

Power laws and log-log plots II.

Back again to power laws. After some more googling, I found an even more important piece of blogging by Cosma Shalizi: Speaking Truth to Power About Weblogs, or, How Not to Draw a Straight Line. The title says it all: just don't play with power law distributions by fitting straight lines to log-log plots, because chances are that you will get a reasonably looking line and R squared will be relatively large, but that still does not mean that there is a power law distribution. Shalizi is complaining about papers in statistical physics and complexity theory that do such things -- well, he should see what is going on in sedimentary geology, where somebody invented the 'segmented power-law distributions' and now everybody who is measuring bed thicknesses is fitting not one, but two or even more straight lines to log-log plots of cumulative distributions. It's utter nonsense, even more so than with a single straight line, but it looks very sophisticated and regular, and people keep doing these plots and all kinds of fancy interpretations based on them (earthquakes, self-organizing criticality, confinement, erosion, etc.). If it plots as a straight line - fine, it's a power law, we explained everything. If it does not plot as a straight line -- well, just fit two straight lines and talk about two populations, and how the original power-law distribution has been modified by erosion, confinement, etc. - and we explained everything again. I know I am also guilty of some of this in my thesis, but at least I have never done the segmented power law plots.

Just for the records: here is a link to my paper in Sedimentology. Overall I am fairly happy with it, I haven't changed my mind about most of the things I have written about in this paper, unlike with many other subjects I have done some work on.

Power laws and log-log plots I.

Did a bit of reading today on power law distributions, just to refresh my memories from three years ago when I was writing my thesis. And found some interesting papers and notes on the web, e.g., this one. I think we are still far from being able to use bed thickness distributions in a useful, predictive way, even though this has become a popular subject among turbidite experts. One of the problems is that it is easy to play with the distributions (e.g., take an initial power-law distribution and modify it by amalgamation), but things are probably a lot more complicated and cannot be explained just with amlagamation and basin topography. The other problem is that power-law distributions and their exponents cannot be assessed by fitting a straight line to an exceedence probability plot, as it is explained here. This method is bound to give erroneous estimates when dealing with a single distribution, but it is close to meaningless when people want to break out two different populations by fitting not one, but two lines to the exceedence probability plot.

Well, I guess that is enough about power laws for today.

Richard Dawkins is the first on the list of the top 100 public intellectuals of Britain, as voted by readers of Prospect Magazine. Yess!

Found a good quotation from philosopher Simon Blackburn on "Butterflies and Wheels". Originally it appeared in the Oxford Dictionary of Philosophy, in the "Postmodernism" entry:

While the dismantling of objectivity seems to some to be the way towards a liberating political radicalism, to others it allows such unliberating views as the denial that there was (objectively) such an event as the Second World War or the Holocaust...The postmodernist frame of mind...may seem to depend on a cavalier dismissal of the success of science in generating human improvement, an exaggeration of the admitted fallibility of any attempt to gain knowledge in the humane disciplines, and an ignoring of the quite ordinary truth that while human history and law admit of no one final description, they certainly admit of more or less accurate ones...

Going back to Freud (see the last entry): here is some supporting material for the claim that Freud

belongs more in a museum of errors, with studies of the four humours, the benefits of blood-letting, pre-Copernican astronomy, the forensics of witchcraft, alchemy, phrenology and phlogiston.

Finished reading two books by Steven Johnson: Emergence and Mind Wide Open. The latter is fresher. Quite liked it overall, although it does not feel as enlightening as Richard Dawkins or Steven Pinker often do. But then, this might be too high of a measuring stick.

In the final chapter of Mind Wide Open, S. Johnson paints a bit too positive picture of Freud. Maybe it is a great insight indeed that the mind is divided, but it looks to me that there are a lot more misses than hits in the freudian view of the mind. It is a little bit like saying that the geosynclinal theory is very important because it got a few things right: sediments often do accumulate in big piles several miles thick and then become parts of folded mountain ranges. Well, that's true, but there is no explanatory power to it -- for that, you need modern plate tectonics and basin analysis. So, isn't it easier to just forget old and wrong concepts like id, superego, and miogeoclines?

Richard Dawkins writes about science writing here. A couple of noteworthy comments:

"Prick your reader’s imagination with a stunning fact, or a fresh metaphor, or by turning a familiar fact dizzyingly upside down, or by filtering it through the alien lens of a Martian eye. However useful science may be, and however relevant to everyday life, that is the least important thing about it. Science is, above all, wonderful. You may write to inform. You should write to inspire.

No scientist has won the Nobel Prize for Literature. Why not? I suspect that it simply hasn’t occurred to the judges. “Literature” automatically conjures “novelist”, or “poet”. Yet, could there be a better subject for great literature than the spacetime fabric of the universe? Or than the evolution of life?"

Kingdoms of Either and Or

Something really worth taking note of, from Jonathan Weiner's The Beak of the Finch (p. 231-232):

Currently most evolutionists regard the possibility of speciation among neighbors as unorthodox, even though Darwin himself proposed it. The standard model of speciation requires geographic isolation. That has been the canonical pattern for half a century, and many evolutionists belive it is the universal pattern. But evolutionists are forever dividing and subdividing into schismatic sects, kingdoms of Either and Or. Do new species arise in archipelagoes, like Darwin's finches, or do they arise among neighbors? Is the origin of species fast or slow? Is the mechanism natural selection or sexual selection? And so on. None of these questions really have ot be framed either-or. It is almost a law of science: the more indirect the evidence, the more polarized the debate. Evolutionists sometimes catch themselves sounding like the Little-Endians and Big-Endians in Gulliver's Travels, fighting tooth and nail over the proper way to crack an egg. Meanwhile, the more direct the evidence, the less the answers look either-or.

This 'law' of indirect - or poor - evidence resulting in more polarized debates seems to work in other areas of science as well. For example, in sedimentary geology, there is (was?) a strong debate about whether most thick-bedded sands deposited in the deep sea are due to deposition from turbidity currents or debris flows. Probably the only positive outcome of the debate is that some people are paying more attention to the evidence and they are starting to realize exactly that "the more direct the evidence, the less the answers look either-or". Debris flows can easily become turbulent flows - and the other way around: in their final, depositional stages, turbidity currents can transform into predominantly laminar flows. To claim that 99% of deep-water sands result from debris flows rather than turbidity currents just because many depositional features suggest laminar behaviour is a perfect example of thinking in terms of black-and-white or kingdoms of 'Either and Or'. It is analogous to calling cars 'frictional machines' because they use friction to stop.

Going back to the last subject: of course, the other side of the coin is that our inborn moral intuitions can only serve as safe guidance in situations that were not uncommon in times when our brains formed -- that is, a long time ago. To rely on these intuitions in issues as complicated as bioethics is a big mistake, as it is more than convincingly pointed out on Carl Zimmer's weblog.

Hardwired morality

Carl Zimmer has an article in the April issue of Discover Magazine about how neuroscience is providing more and more evidence that morality is hardwired into the human brain. For example, there are two variants of a famous moral dilemma about saving the lives of five people who are about to be hit by a train. In the first version, you can throw a switch and thus kill one person (he or she would be hit by the redirected train; in the second, you can push a fat guy off a footbridge, who would fall on the tracks and thus stop the train. Most people tend to say they would throw the switch, but they would not push the guy to his death. It just does not feel right. The two versions of the dilemma also light up different areas of the brain, as shown by MRI imaging: we tend to use logic to reach a conclusion in the first case, but emotions play an important role when it comes to killing somebody without the indirectness of some intervening machinery. The reason for this probably is that evolution has hardwired our brains for the latter case, but there are no hardcoded, visceral responses to throwing a switch, even if we know that it leads to the death of another human being.

Such findings should be serious food for thought for those who argue that morality can only originate in the brains or souls or hearts (whatever, pick your favorite) of true believers, and you must be an immoral animal if you do not believe in some supernatural power. But I guess somebody who rarely thinks does not like too much food for thought.

A couple of books

I went today to a Borders bookstore where Steven Johnson was talking about his new book, Mind Wide Open. I wrote here not long ago that popular science has become indeed popular in the US. However, this venue could not count as supporting evidence: in a city as large and as diverse as Houston only about a dozen people gathered to see a guy who is probably one of the best science writers around. He is certainly one of the best 'science speakers'. I haven't read yet any of his books, but bought now two of them (Emergence and Mind Wide Open), and hardly can wait to start going through them. Emergence must have some similarities to 'Linked', written by my fellow Transylvanian Albert-László Barabási.

For now, I still have to work on Jonathan Weiner's 'The beak of the finch'. It is a great book, with a somewhat different perspective from what I got used to in writings by Dawkins or Pinker. Apart from learning quite a bit about how evolution works (not in theory, but in practice, in the field), it also gives good insight into the research process. Reading about how the Grants and their graduate students were essentially tracking evolution on a small island, sometimes I think about how nice it would have been if I knew exactly what questions I wanted to answer when I started my PhD :) ...

Neural nets and arbitrary classification

I have been reading a bit about neural nets and - I must admit - most of the stuff that you find in books or on the web is not easy reading for me. Kevin Gurney's book (An Introduction to Neural Networks; its web version is available here) is an exception to a certain degree -- at least I could follow it pretty well until I got kind of tired and confused when he started discussing Hopfield nets. Kohonen maps or self-organizing maps were a bit easier to swallow, but I actually had to start playing with them myself before it started to make sense. And then I realized that thinking of Kohonen maps in terms of neural nets is much more difficult than their geometric interpretation -- that is, a two-dimenisional lattice with a certain number of nodes that moves and stretches in the data space until it fits or describes relatively well the data cloud. In other words, it is quite like nonlinear principal component analysis, which is still easier to grasp than input layers, winning neurons, etc.

I have stolen the animated gif above from a superb website on neural nets that has several java applets showing how these things work. I especially recommend the demo of the 3D Kohonen map.

It took me a while to realize that it is wrong to assume that a Kohonen map is picking out real clusters in the data. That could be true if, on one hand, there is good clustering in the data in a statistical sense, and, on the other hand, there are only a few nodes in the map - that is, about as many as in the data. However, often there are no real, well-defined clusters in the data, but Kohonen's classification method is still applied - and should be applied. What Kohonen's group recommend is a two-step classification: start out with a large number of nodes in the SOM (self-organizing map) and reduce the number of nodes or clusters in a second step, with k-means clustering (see details here) applied to the map itself.

I think however that the second step is not very useful if the data does not have clusters. It is still definitely worth applying the Kohonen classifier to reduce dimensionality and visualize multidimensional data, but applying the k-means clustering as well only results in an image with less resolution and more arbitrary boundaries. It is a little bit like posterizing a color photograph, that is, reducing the number colors to only a few, although there were a lot more information and no well-defined classes in the original image (I know this latter assumption is usually not valid, but put that aside for now). Why would one do that?

This type of classification (probably real nerds would say that 'quantization' is a better word), when there are no well-defined classes, is comparable in many ways to the classification systems used in the more descriptive natural sciences. For example, in sedimentary geology, sediments or rocks are often divided into facies A, B, C, and so on; and, in most cases, the boundaries between these facies are not very clear and it would be difficult to show any statistical siginificance for the existence of clustering. So, strictly speaking, this classification is incorrect, but it still can be useful (e.g., you can write long journal articles :) ).

Of course, once you leave these somewhat subjective territories of science and think about how 'clustering' is done in everyday life, you realize that this simple-minded 'quantization' is even more questionable. People like to and tend to think dichotomically: us vs. them, black vs. white, liberal vs. conservative, christian vs. muslim, and so on -- this is not news. The result is that, to use the Kohonen terminology, the quantization errors are huge, and the cluster boundaries are essentially arbitrary. The sad part is that sometimes - many times - people kill each other because of these errors.

In light of this, isn't it reassuring that two-dimensional Kohonen maps can use lots of nodes or clusters, thus describe reality better, and still be useful in making things more visible and intelligible?

Understanding evolution

I stumbled upon a new website on evolution, created as a teaching resource by the by the University of California Museum of Paleontology. Among its many authors are Eugenie C. Scott (director of the National Center for Science Education) and Carl Zimmer (who wrote Evolution: The Triumph of an Idea). Excellent website, there is material that could fill a book (or more), including subjects like the nature of science, evolution 101, history of evolutionary thought, etc. It is websites like these that increase exponentially the value of the internet and make it worthwile to pay the monthly fee for a high-speed connection...