Evo-Devo Again

The beard at right belongs to author Wallace Arthur, Professor of Zoology at the National University of Ireland, Galway. I recently read his excellent book Creatures of Accident : The Rise of the Animal Kingdom (New York, Hill and Wang, 2006. x + 255 pages). Naturally, there’s a book note, with a couple of entertaining excerpts. The book, by the way, has its own website.

This is the second book^* I’ve read about evo-devo: “evolutionary developmental biology”, sort of embryology informed by genetics and microbiology. Cool stuff, cutting edge, and learning some about it clarifies an unusual amount of evolutionary concepts for me. One key idea is that evolution doesn’t operate on adult animals, it operates on developing embryos. That small shift in perspective sheds a lot of light.

Author Arthur takes a delightfully cozy and intimate tone in his book, which I thought was almost like an expanded personal essay at times, and very enjoyable for it. Arthur managed to avoid a number of possibly intimidating details in pursuit of focusing on some central concepts over which he lingered a bit to avoid leaving any readers behind. I thought he did a great job and I enjoyed the book quite a bit. I also didn’t mind having a peek at the author’s photo inside the back cover occasionally, either.

Arthur set out to write without revealing his biases towards big questions about creation and whether a who or what was responsible for it, and he managed quite well until he got to his chapter called “Big Questions”, when he finally revealed himself. The preceding parts of the book had been so gentle that I was a bit surprised by his vehemence, although I wouldn’t argue with it in the least.

To research this chapter ["Big Questions"], I did something I had never done before: I visited some Web sites representing creationism in its many guises. This exercise was a revelation indeed, but probably not of the sort that the Webmasters had intended. What I found most striking was the appalling lack of integrity of those concerned. The deliberate misuse of quotations and details from the work of scientists suggested that all honor and honesty had been cast to the four winds. I realized that I was in a different social context from the one I have known and loved for my whole scientific career, where an honest search for the truth is at the heart of things. Instead, I was in a milieu where the dominant ethos was to force acceptance of a particular worldview by any means whatever. No holds barred. not the Spanish Inquisition perhaps, but the intention seemed the same; to stifle freedom of thought. And it mattered not whether I was in the grips of young-earth creationists or intelligent-design proponents. The latter were more slippery and difficult to pin down, but always in the end I found evidence of dishonesty. [p. 226]

__________
^* The first, which I got very excited about, was Sean Carroll’s Endless Forms Most Beautiful.

On Not Reading Singh’s Fermat’s Enigma

For a few days recently I was reading Simon Singh’s book, Fermat’s Enigma : The Quest to Solve the World’s Greatest Mathematical Problem (New York : Walker and Company, 1997, 315 pages). However, I stopped reading after about 80 pages.

The reason had nothing to do with the subject, which was interesting and developing reasonably well. Finding out more about Fermat, his work and his life and his time, and learning some about the man who has apparently proved Fermat’s notorious “last theorem” (Wikipedia on Fermat’s Last Theorem can fill you in on those details if you want) was all to my liking.

What was not to my liking was Singh’s writing. It was writing that was too loose, too flabby when dealing with subjects that I feel require more precision in their presentation. Writing a popular treatment about a mathematical or scientific subject is no time for technically sloppy or carelessly inaccurate prose. Writing for the scientifically or technically unsophisticated reader demands care. I’m sure you’re aware by now that this is an idée fixe for me, and for Ars Hermeneutica.

There were no major transgressions but a pile-up of minor infractions to the point that it was irritating. Let’s look at a few examples.

Mathematical theorems rely on this logical process [of proof] and once proven are true until the end of time. Mathematical proofs are absolute. To appreciate the value of such proofs they should be compared with their poor relation, the scientific proof. [p.21]

In one sense you could say that once proven mathematical theorems are true, in the sense that once proven they stayed proved. However, the sentence is sloppy and ambiguous as a result, suggesting that perhaps the theorem was not true before it was proven.

That is not the way mathematicians look at theorems and proofs, however. Theorems are seen more as emergent truths of a mathematical system, statements that have always existentially true but unknown to be true before they are discovered and their truth established by means of proof.

It’s akin to finding a rock and saying “I recognize this as a sedimentary rock, so it will henceforth be a sedimentary rock.” Most of us would look askance at such a statement with the obvious reaction: “Wasn’t it always a sedimentary rock, even before anyone saw it?”

Arguing in the author’s favor, I suspect that he didn’t mean his sentence this way; rather, he wanted to make the point that once the truth of a theorem is established by proof, that proof remains valid unless an error is discovered in the proof or some problem is discovered in the mathematical system in which the theorem and proof is embedded. However, that’s not what he wrote.

As for that bit about “their poor relation, the scientific proof”–it will take at least another entire essay for me to deal with the issues raised by that “poor relation” jibe (it doesn’t upset me that much) and the lack of understanding surrounding the reference to “scientific proof” (that does upset me quite a bit).

Together Fermat and Pascal would discover the first proofs and cast-iron certainties in probability theory, a subject that is inherently uncertain. [p. 40]

Yikes! According to the book-jacket, Mr. Singh has an advanced degree in particle physics. A great deal of experimental particle physics means looking at decay products of high-energy nuclear interactions, processes that are governed by probabilities. Exact probabilities in many cases. He should know better than to write that probability theory is “inherently uncertain.” Probability theory is a mathematical discipline with exact results, and those exact results describe processes that are inherently uncertain. To ascribe “inherent uncertainty” to a discipline whose subject is “inherent uncertainty” is naive and/or thoughtless, and does nothing here to keep the unsophisticated reader from getting confused.

Fermat’s panoply of theorems ranged from the fundamental to the simply amusing. Mathematicians rank the importance of theorems according to their impact on the rest of mathematics. [p. 66]

I simply found this statement bizarre, suggesting as it does that there are mathematicians someplace whose job it is to rank the importance of theorems to the world of mathematics. Do they have a list they check against? Where do they publish their list of theorems, ordered by importance?

Of course Mr. Singh is talking figuratively, looking for an “objective” way to describe the importance of Fermat’s theorem, but he does it again with sloppy writing that suggests something quite other than what he intended.

Instances like these kept cropping up and their irritation overwhelmed me by around page 80. I knew by then that I wouldn’t enjoy reading the book and it didn’t even seem worth the bother of finishing so that I could write a negative book note–I much prefer guiding potential readers towards good books rather than away from bad books.

Part of my professional mission, though, is to consider how we (the big “we” of those who write science for general consumption) communicate science, and how we can communicate it better. Sometimes that means looking at examples of miscommunication so that we can improve. Think of is as an engineering approach (as Henry Petroski does in his excellent books) in which failure has much to tell us about how to succeed.

GetPercent

The website GetReligion discusses press coverage of news stories about religion, and how well they exhibit an understanding of the religious issues involved. Their name comes from the idea that “The press…just doesn’t get religion.”

Well, in this little example I’m afraid there’s a bit of a need for some GetMath. In a story called “Define social justice — give at least one example“, Mark Stricherz is discussing a story about Jeremiah Wright Jr., the pastor of the church Barack Obama belongs to. I have no issues with the analysis, just with this excerpt

As Ramirez noted, plainly but aptly,

“Obama was one of the thousands who joined Trinity under Wright’s leadership. When Wright became Trinity’s pastor in 1972, the church had 85 members. Today, Trinity has a congregation of 8,500, with more than 80 ministries, making it one of the largest and most influential black churches in the nation.”

In other words, during his tenure Wright’s congregation increased by more than 1,000 percent.

Of course, one notes that Wright’s congregation increased by well over well over 1,000%. In fact, it increased by 10,000%. In other words, it increased by a factor of 100.

To move from a fractional factor, say 0.45, to an expression in percent, one multiplies by 100. Thus, 0.45 of something is also said to be 45% of that something. To move from an expression in percent to a decimal fraction, divide the percent figure by 100. Thus, 32% of something is 0.32 times that something.

This works even if the fractional part is greater than the something being compared to, it’s just that the decimal expression is greater than 1, and the percent expression is greater than 100%. This general expression

where is the percent expression, is what I’ve called the fractional part, and is the amount being compared to, works regardless of whether the “quantity” is greater than or less than the “comparison” value.

So, in Mr. Wright’s case, his congregation, in going from 85 to 8,500 increased by a factor of 100, or by

I expect Mr. Stricherz knows this and simply mistyped, but it did provide me an excuse for a little pedantic moment of the type I love so much.

Global Warming Fact-Sheet

Via NASA’s Earth Observatory mailing list my attention was drawn to their newly freshened Global Warming fact sheet, written by Holli Riebeek (dated 11 May 2007), and I wanted to take this space to draw more attention to it.

As most of my readers will know, there’s a great deal of misleading disinformation and obfuscation in our current global-warming “debate” here in the US, a concerted effort by some business and political forces to confuse the public into thinking that there is no scientific consensus on anthropogenic climate change, i.e., global warming because of carbon-dioxide (and other greenhouse gas) emissions being pumped into the atmosphere from human sources.

There is consensus among scientists working in the field; how and why and what it all means is nicely summarized in this short, succinct, and accurate fact sheet. Without being patronizing and without distorting the information, it’s a clear and understandable presentation of what we (the science “we”) know about global warming, the trends, the causes, and the likely or possible consequences.

In particular, the author addresses this question:

But why should we worry about a seemingly small increase in temperature? It turns out that the global average temperature is quite stable over long periods of time, and small changes in that temperature correspond to enormous changes in the environment.

It keeps popping up as a joke, especially during wintertime or a cool day in the summer, when people casually say “I wouldn’t mind a bit if it were a degree or two warmer”.

What is missing in this superficial understanding is a realization that, overall, the Earth’s temperatures are quite stable on average, and that very small changes in average temperatures can have very, very large effects on weather patterns and that those changes in weather patters lead to subsequently surprisingly large shifts in the weather we get at any particular location. In other contexts this is sometimes called “the butterfly effect”: consequences can be out of all proportion (i.e., nonlinear) to the causes. Ice ages have been accompanied by changes in the average global temperature of only about 5°C — which doesn’t sound all that big.

This is discussed quite well in the fact sheet, and summarized (in part) this way:

Potential Effects

The most obvious impact of global warming will be changes in both average and extreme temperature and precipitation, but warming will also enhance coastal erosion, lengthen the growing season, melt ice caps and glaciers, and alter the range of some infectious diseases, among other things.

For most places, global warming will result in more hot days and fewer cool days, with the greatest warming happening over land. Longer, more intense heat waves will become more frequent. High latitudes and generally wet places will tend to receive more rainfall, while tropical regions and generally dry places will probably receive less rain. Increases in rainfall will come in the form of bigger, wetter storms, rather than in the form of more rainy days. In between those larger storms will be longer periods of light or no rain, so the frequency of drought will increase. Hurricanes will likely increase in intensity due to warmer ocean surface temperatures.

It’s a good piece and a few minutes invested in reading through it will arm the reader with better understanding that will help cut a confident path through the thicket of opinions and misinformation that have clogged the information superhighway on the issue lately.

The “Woodstock of Physics”

There has been lots of talk, relatively speaking, this week about a now-famous event that took place at the annual meeting of the American Physical Society 20 years ago. The first piece that I saw was in the New York Times (Kenneth Chang, “Physicists Remember When Superconductors Were Hot“, 6 March 2007 — his piece is fine, but I think I’ll scream if anyone mentions mag-lev trains again in the same breath as superconductors, or anything else for that matter) about what quickly became known as “The Woodstock of Physics”, if you can imagine.

Today it’s the lead story in my e-mail’s “Physics News Update” (9 March 2007 edition), by Phil Schewe and Ben Stein of AIP (the American Institute of Physics is an umbrella organization that encompasses the American Physical Society, and publishes Physical Review and Physics Today, among others).

So this is the story that got everyone all excited twenty years ago. I wasn’t at that meeting — I usually attended a smaller local meeting the next month where most of my low-temperature colleagues congregated by tradition — but I certainly remember the buzz it created in the hallways near my lab. This is probably the event I will recall when people start talking again, as they seem to every generation or so, about how physics is pretty much played out and all important discoveries have already been made.

It was rather more excitement than you might expect to see among a group of typically staid physicists. By the way, this gives you a chance to see the differences between a news story written for the public, and one written with an audience of physicists in mind.

“THE WOODSTOCK OF PHYSICS,” the famous session at the March 1987 meeting of the American Physical Society, earned its nickname because of the rock-concert fervor inspired by the convergence of dozens of reports all bearing on copper-oxide superconductors. The 20th anniversary of this singular event was celebrated this week at the APS meeting in Denver.

Why such an uproar over the electrical properties of an unlikely ceramic material? Because prior to 1987 the highest temperature at which superconductivity had been observed was around 23 K [i.e., "Kelvins", centigrade sized degrees where 0 K is "absolute zero"]. And suddenly a whole new set of compounds–not metallic alloys but crystals whose structure put them within a class of minerals known as perovskites–with superconducting transition temperatures above 35 K and eventually 100 K generated an explosion of interest among physicists. Because of the technological benefits possibly provided by high-temperature superconductivity (HTSC)—things like bulk power storage and magnetically levitated trains—the public was intrigued too.

This week’s commemoration of the Woodstock moment (the months of feverish work leading up to the 1987 meeting) provided an excellent history lesson on how adventurous science is conducted. Georg Bednorz (IBM-Zurich), who with Alex Mueller made the initial HTSC discovery, recounted a story of frustration and exhilaration, including working for years without seeing clear evidence for superconductivity; having to use borrowed equipment after hours; overcoming skepticism from IBM colleagues and others who greatly doubted that the cuprates could support supercurrents, much less at unprecedented temperatures; and finally arriving at the definitive result–superconductivity at 35 K in a La-Ba-Cu-O compound. In October 1986 Bednorz and Mueller prepared a journal article confirming their initial finding in the form of observing the telltale expulsion of magnetism (the Meissner effect) from the material during the transition to superconductivity. Submitting this paper, however, required the approval of the IBM physics department chairman, Heinrich Rohrer who, that very week, had been declared a co-winner of the Nobel prize for his invention of the scanning tunneling microscope (STM). Afraid that he would not be able to obtain the preoccupied Rohrer’s attention, Bednorz obtained the needed signature by thrusting the approval form at Rohrer as if he (Bednorz) desired only a celebratory autograph. A scant year later Bednorz and Mueller pocketed their own Nobel Prize.

The IBM finding was soon seconded by work in Japan and at the University of Houston, where Paul Chu, testing a YBaCuO compound, was the first to push superconductivity above the temperature of liquid nitrogen, 77 K. Very quickly a gold rush began, with dozens of condensed matter labs around the world dropping what they were doing in order to irradiate, heat, chill, squeeze, and magnetize the new material. They tweaked the ingredients list, hoping to devise a sample that superconducted at still higher temperatures or with a greater capacity for carrying currents. At this week’s APS meeting Chu said that he and his colleagues went for months on three hours’ sleep per night. Several other speakers at the 2007 session spoke of the excitement of those few months in 1987 when-according to such researchers as Marvin Cohen (UC Berkeley) and Douglas Scalapino (UC Santa Barbara)-the achievement of room-temperature superconductivity did not seem inconceivable.

The Woodstock event, featuring 50 speakers delivering their fresh results at a very crowded room at the New York Hilton Hotel until 3:15 am, was a culmination. In following years, HTSC progress continued on a number of fronts, but expectations gradually became more pragmatic. Paul Chu’s YBaCuO compound, under high-pressure conditions, still holds the transition
temperature record at 164 K. Making lab samples had been easy compared to making usable power-bearing wires in long spools, partly because of the brittle nature of the ceramic compounds and partly because of the tendency for potentially superconductivity-quenching magnetic vortices to form in the material. Paul Grant, in 1987 a scientist at IBM-Almaden, pointed out that HTSC applications have largely not materialized. No companies are making a profit from selling HTSC products. Operating under the principle of “You get what you need,” Grant said, superconducting devices operating at liquid-nitrogen temperatures weren’t better enough so as to displace devices operating at liquid-helium temperatures.

Nevertheless, the mood of the 2007 session (Woodstock20) was upbeat. Bednorz said the 1986/87 work showed that a huge leap forward could still take place in a mature research field whose origins dated back some 70 years. Bednorz felt that another wave of innovation could occur. Paul Chu ventured to predict that within ten years, HTSC products would have an impact in the power industry. Paul Grant referred to the study of superconductivity as the “cosmology of condensed matter physics,” meaning that even after decades of scrutiny there was still much more to learn about these materials in which quantum effects, manifested over macroscopic distances, conspire to make electrical resistance vanish, a phenomenon which at some basic level might also be related to the behavior of protons inside an atomic nucleus and the cores of distant neutron stars.

(Photographs and an original summary press release from the 1987 meeting is available at our Physics News Graphics website, www.aip.org/png)

All In Perspective

From a report about Exxon’s latest record earnings^*, this extraordinary statement

For the full year, net income surged to $5.71 per share from $3.89 per share in 2004. Annual revenue grew to $371 billion from $298.04 billion.

To put that into perspective, Exxon’s revenue for the year exceeded Saudi Arabia’s estimated 2005 gross domestic product of $340.5 billion, according to statistics maintained by the Central Intelligence Agency.

Now, I’m not talking about the statement about Exxon’s revenues, which is extraordinary, but about the helpful “putting into perspective” that the revenues were about the same as the GDP of Saudi Arabia.

Does the average reader know more — or have more perspective on that number — knowing that it’s comparable to the GDP of a country whose economics are not terribly familiar? Please! That’s about as helpful as saying the earnings in dollars is about the same as the number of miles in a light-week, or the number of sperm the average man produces in a year (about 390 billion). Even saying that it’s nearly 5% of the US national debt is more revealing. (It is, however, only about 50% greater than Wal*Mart’s yearly revenues.)

How about something that really gives a sense of how big such a number is. Something like: imagine that you were able to spend $10,000/hour, 24/7, 365.25 days a year, a pretty breathtaking pace — for perspective, that’s over 4 new Hummer H2s each day (use the surplus to buy the gas) . It would take you over 42 thousand years to spend Exxon’s yearly revenue.

Or, suppose we were to use the money to pay out to people an amount equal to the median US income in 2004: $44.4 thousand. Exxon’s yearly revenues would pay the median income to 8.3 million workers. For perspective, that’s about 11 workers for every mile between Earth and the Sun.

To my mind, either of these comparisons gives quite a bit more “perspective” than the GDP of Saudia Arabia
———-
^* Steve Quinn, “Exxon Mobil Posts Record Profit for 2005“, Associated Press / Yahoo! News, 30 January 2006.

Atoms are not Watermelons

A few days back I finished reading How to Write: Advice and Relfections, by Richard Rhodes. Although I’m frequently drawn to read them, books about writing are rarely satisfying, interesting, or useful. Rhodes’ book managed all three, and I can recommend it.

Here are three passages I made note of as I read that I wanted to copy into my blog, which also serves as my commonplace book.

People lost in a wilderness have been known to find their way out guided by the wrong map; orienting is apparently a function only loosely tied to locality.¹ [p. 30]

Not everyone liked the arrangement.² Dixie Lee Ray, the eccentric former chair of the U.S. Atomic Energy Commission and governor of the state of Washington, reviewed The Making of the Atomic Bomb for the Washington Times. My war scenes were too graphic, Dr. Ray complained. Everyone knows that war is terrible; why go on about it? Worse, she wrote, the book jumps around. [p. 108, italics in original]

A less global structural problem was deciding at what level to pitch scientific explanation. I’d read enough popular science to be impatient with explanation that depended on fanciful analogies. Besides being condescending, comparing an atom to a watermelon wastes half the analogy. Fortunately, nuclear physics is largely an experimental science. Reading through some of the classic papers in the field, I realized that I could explain a result clearly and simply by describing the physical experiment that produced it: a brass box, the air evacuated, a source of radiation in the box in the form of a vial of radon gas, and so on. Then I and the reader could visualize a process in terms of the manipulation of real laboratory objects, not watermelons, just as the experimenters themselves did, and could absorb the culture of scientific work at the same time–the throb of the vacuum pump, the smell of its oil. [pp. 109--110]

———-
¹He had been discussing memory and the occasional difficulty of coming up with just the right word. He discusses the use of dictionaries and thesauruses to help, and how he frequently finds words that were “just right” but weren’t what he was looking for.

²“The arrangement”, that is, of his masterly The Making of the Atomic Bomb, in which he uses historical narrative to follow several threads in science and politics, carrying each one to some stopping point before going to previous times to pick up a thread put down for awhile.

You Go, Roger Ebert!

The Panda’s Thumb suggests “One Thumb Up for the TalkOrigins Archive?” over this startlingly frank piece by Roger Ebert: “Film about volcanoes falls victim to creationists“, on the basis on the final paragraph:

[...]
Surely moviegoers deserve the right to decide for themselves what movies to see? “Volcanoes of the Deep Sea,” according to the AP, “makes a connection between human DNA and microbes inside undersea volcanoes.” It says that if life could evolve under such extreme circumstances, it might help us understand evolution all over the planet.

This is not a controversial opinion. The overwhelming majority of all scientists everywhere in the world who have studied the subject would agree with it. Although discussion continues about the mechanics of evolution, there is no reputable doubt about the existence of DNA and the way in which it functions.

Yes, there is “creationist science,” an attempt to provide a scientific footing for beliefs that should be a matter of faith. Creationists say evolution is “only a theory” and want equal time for their theories, one of which is that God created the Earth from scratch in six days, and man on the seventh.

Evolution is indeed a theory. Creationism is a belief, not a theory. In science, a theory is a hypothesis that has withstood the test of time and the challenge of opposing views. It is not simply somebody’s notion about something. The creationist belief cannot withstand such tests and challenges; it exists outside the world of science altogether.
[...]
An industry has grown up around the “science” supporting the “argument for intelligent design.” It refuses the possibility that evolution itself is the most elegant and plausible argument for those who wish to believe in intelligent design. If you are interested, you might want to go to www.talkorigins.org, where the errors of creationist science are patiently explained. And you might want to ask at your local IMAX theater why they allow a few of their customers to make decisions for all of the rest.

That’s a nice mention for talkorigins, sure, but look at what he says:

…where the errors of creationist science are patiently explained.

After all the time I’ve spent reading journalistic pieces by “real” journalists who go out of their way to avoid anything that might look like a fact as they rush to maintain “journalistic balance” by quoting non-scientific yobs about this silly creationist pseudo-controversy, hearing Roger Ebert (who is, after all, only a movie reviewer and not a “real journalist”) refer to the errors of creationist science is such an amazing blast of fresh air that I can hardly breath.
A fact, in fact. What a review! Two thumbs up for Roger Ebert!