Science

When I was a little kid, I asked some adults the following question.

If hot things cool, and cool things warm up, could something hot cool down and warm back up?

The people I asked didn’t understand my question and just laughed. I have no idea how old I was, but I wasn’t old enough to articulate what I was thinking.

Here’s what I had in mind. I knew that hot things like a cup of coffee grew cold. And I knew that cold things, say a glass of milk, get warm. Well, could the coffee get so cold that it becomes a cold thing and start to warm back up?

Could the coffee become as cold as the glass of milk? Common sense suggests that can’t happen. When we say coffee grows cold, we mean that it becomes relatively colder, closer to room temperature. And when we say the milk is getting warm, we also mean it is getting closer to room temperature. We’ve never left a hot cup of coffee on a table and come back later to find that it has cooled off so much that it is colder than room temperature. But could there be small fluctuations?

As the coffee and milk head toward room temperature, could they overshoot the target, just by a little bit? Say room temperature is 70 °F, the coffee starts out at 150 °F, and the milk starts out at 40 °F. We don’t expect the coffee to cool down to 40 °F or the milk to warm up to 150 °F. But could the coffee cool down to 69.5 °F and then go back up to 70 °F? Could the milk warm up to 70.5 °F and then cool back down to 70 °F?

I didn’t get a satisfactory answer to my childhood question until I was in college. Then I found out about Newton’s law of cooling. It says that the rate at which a warm body cools is proportional to the difference between its current temperature and the ambient temperature. This law can be written as a differential equation whose solution shows that the temperature of a warm body decreases exponentially to the ambient temperature. The temperature curve always slopes downward. It doesn’t wiggle even a little on its journey to room temperature. Cold bodies warm up the opposite way, exponentially approaching room temperature but never exceeding it.

In case it this seems obvious, think about thermostats. They don’t work this way. Say the temperature in a room is 85 °F and you’d like it to be 72 °F, so you turn on the air conditioning. Will the temperature steadily lower to 72 °F? Not exactly. If you were to plot the temperature in the room over time and look at the graph from far enough away, it would look like it is steadily going down to the desired temperature. But if you look at the graph more closely, you’ll see wiggles. The AC may cool the room to a little below 72 °F, maybe to 70 °F. The AC would cut off and the temperature would rise to 72 °F. Unlike the cup of hot coffee, the AC will often overshoot its target, though not by too much. The temperature may feel constant, but it is not. It oscillates around the desired temperature.

The video below features a demonstration that lightning is as likely to strike wood as metal.

I want to focus on one line from the video. After showing simulated lightning strikes that hit a wooden rod five times and a copper rod five times, the narrator says

It’s five all, proof that metal does not attract lightning.

No, such an experiment would prove no such thing. I imagine the researchers conducted a much larger experiment and selected a representative sample. And I’m willing to accept their conclusion that metal does not attract lightning. But I would not accept such a conclusion from an experiment with 10 samples. What the experiment proves is that, under their experimental conditions, lightning will sometimes strike wood even a metal rod is nearby.

I have two complementary criticisms of this made-for-video science.

1. The results could easily happen if their conclusion were not true.
2. The results could easily not have happened if there conclusion were true.

Suppose in reality, lightning will not always strike the metal rod, but will prefer the metal. Suppose in the long run, lightning will strike the metal rod 60% of the time. It would not be unusual in that case to do an experiment with 10 strikes and find that half or more of the strikes hit wood.

Now suppose the researchers are exactly correct. In the long run, lightning has no preference for one rod or the other. What would viewers have thought if they showed a clip of 10 strikes, of which 6 hit metal and 4 hit wood? Many would have howled in protest. If lightning really had no preference for metal, the result should have been an even split, right? This is an example of the Law of Small Numbers. People underestimate the variability of small samples.

If the probability of lightning striking each rod is 50%, then in a sequence of experiments each containing 10 strikes, most will not have an exact 5-5 split. If you flip 10 fair coins, the most likely outcome is a 5-5 split, but this will happen only about 1/4 of the time. It’s more likely that you’ll get near a 5-5 split, sometimes with more heads and sometimes with more tails.

The exact 5-5 split in the video is good showmanship, but it’s misleading science.

Related posts:

Law of small numbers
Example of the law of small numbers
Law of medium numbers

There’s a law of large numbers, a law of small numbers, and a law of medium numbers in between.

The law of large numbers is a mathematical theorem. It describes what happens as you average more and more random variables.

The law of small numbers is a semi-serious statement about about how people underestimate the variability of the average of a small number of random variables.

The law of medium numbers is a term coined by Gerald Weinberg in his book An Introduction to General Systems Thinking. He states the law as follows.

For medium number systems, we can expect that large fluctuations, irregularities, and discrepancy with any theory will occur more or less regularly.

The law of medium numbers applies to systems too large to study exactly and too small to study statistically. For example, it may be easier to understand the behavior of an individual or a nation than the dynamics of a small community. Atoms are simple, and so are stars, but medium-sized things like birds are complicated. Medium-sized systems are where you see chaos.

Weinberg warns that medium-sized systems challenge science because scientific disciplines define their boundaries by the set of problems they can handle. He says, for example, that

Mechanics, then, is the study of those systems for which the approximations of mechanics work successfully.

He warns that we should not be mislead by a discipline’s “success with systems of its own choosing.”

Weinberg’s book was written in 1975. Since that time there has been much more interest in the emergent properties of medium-sized systems that are not explained by more basic sciences. We may not understand these systems well, but we may appreciate the limits of our understanding better than we did a few decades ago.

Related posts:

Laws of large numbers and small numbers
Gerald Weinberg’s law of twins
Subnatural and supernatural

The more active a research area is, the less reliable its results are.

John Ioannidis suggested popular areas of research publish a greater proportion of false results in his paper Why most published research findings are false. Of course popular areas produce more results, and so they will naturally produce more false results. But Ioannidis is saying that they also produce a greater proportion of false results.

Now Thomas Pfeiffer and Robert Hoffmann have produced empirical support for Ioannidis’s theory in the paper Large-Scale Assessment of the Effect of Popularity on the Reliability of Research. Pfeiffer and Hoffmann review two reasons why popular areas have more false results.

First, in highly competitive fields there might be stronger incentives to ‘‘manufacture’’ positive results by, for example, modifying data or statistical tests until formal statistical significance is obtained. This leads to inflated error rates for individual findings: actual error probabilities are larger than those given in the publications. … The second effect results from multiple independent testing of the same hypotheses by competing research groups. The more often a hypothesis is tested, the more likely a positive result is obtained and published even if the hypothesis is false.

In other words,

1. In a popular area there’s more temptation to fiddle with the data or analysis until you get what you expect.
2. The more people who test an idea, the more likely someone is going to find data in support of it by chance.

The authors produce evidence of the two effects above in the context of papers written about protein interactions in yeast. They conclude that “The second effect is about 10 times larger than the first one.”

Related posts:

Why microarray conclusions are so often wrong
Using Photoshop on experimental results
Irreproducible analysis
Make up your own rules of probability

My family loves the Little House on the Prairie books. We read them aloud to our three oldest children and we’re in the process of reading them with our fourth child. We just read the chapter describing when the entire Ingalls family came down with malaria, or “fever ‘n’ ague” as they called it.

The family had settled near a creek that was infested with mosquitoes. All the settlers around the creek bottoms came down with malaria, though at the time (circa 1870) they did not know the disease was transmitted by mosquitoes. One of the settlers, Mrs. Scott, believed that malaria was caused by eating the watermelons that grew in the creek bottoms. She had empirical evidence: everyone who had eaten the melons contracted malaria. Charles Ingalls thought that was ridiculous. After he recovered from his attack of malaria, he went down to the creek and brought back a huge watermelon and ate it. His reasoning was that “Everybody knows that fever ‘n’ ague comes from breathing the night air.”

It’s easy to laugh at Mrs. Scott and Mr. Ingalls. What ignorant, superstitious people. But they were no more ignorant than their contemporaries, and both had good reasons for their beliefs. Mrs. Scott had observational data on her side. Ingalls was relying on the accepted wisdom of his day. (After all, “malaria” means “bad air.”)

People used to believe all kinds of things that are absurd now, particularly in regard to medicine. But they were also right about many things that are hard to enumerate now because we take them for granted. Stories of conventional wisdom being correct are not interesting, unless there was some challenge to that wisdom. The easiest examples of folk wisdom to recall may be the instances in which science initially contradicted folk wisdom but later confirmed it. For example, we have come back to believing that breast milk is best for babies and that a moderate amount of sunshine is good for you.

Related posts:

A little coffee on the prairie
Galen and clinical trials
Randomized trials of parachute use

Jon Udell’s latest Interviews with Innovators podcast features Randall Julian of Indigo BioSystems. I found this episode particularly interesting because it deals with issues I have some experience with.

The problems in managing biological data begin with how to store the raw experiment data. As Julian says

… without buying into all the hype around semantic web and so on, you would argue that a flexible schema makes more sense in a knowledge gathering or knowledge generation context than a fixed schema does.

So you need something less rigid than a relational database and something with more structure than a set of Excel spreadsheets. That’s not easy, and I don’t know whether anyone has come up with an optimal solution yet. Julian said that he has seen many attempts to put vast amounts of biological data into a rigid relational database schema but hasn’t seen this approach succeed yet. My experience has been similar.

Representing raw experimental data isn’t enough. In fact, that’s the easy part. As Jon Udell comments during the interview

It’s easy to represent data. It’s hard to represent the experiment.

That is, the data must come with ample context to make sense of the data. Julian comments that without this context, the data may as well be a list of zip codes. And not only must you capture experimental context, you must describe the analysis done to the data. (See, for example, this post about researchers making up their own rules of probability.)

Julian comments on how electronic data management is not nearly as common as someone unfamiliar with medical informatics might expect.

So right now maybe 50% of the clinical trials in the world are done using electronic data capture technology. … that’s the thing that maybe people don’t understand about health care and the life sciences in general is that there is still a huge amount of paper out there.

Part of the reason for so much paper goes back to the belief that one must choose between highly normalized relational data stores and unstructured files. Given a choice between inflexible bureaucracy and chaos, many people choose chaos. It may work about as well, and it’s much cheaper to implement. I’ve seen both extremes. I’ve also been part of a project using a flexible but structured approach that worked quite well.

Related posts:

Posts on reproducibility
Problems versus dilemmas
Blogging about reproducible research

From the article Proverbial new “Twist” in Breast Cancer Detection:

… scientists at Johns Hopkins … have shown that a protein made by a gene called “Twist” may be the proverbial red flag that can accurately distinguish stem cells that drive aggressive, metastatic breast cancer from other breast cancer cells.

Related posts:

Detecting breast cancer from a hair sample
Visualizing cancer DNA scrambling
Killing too much of a tumor

I recently ran across a discussion of quantum mechanics from C. S. Lewis.

The older scientists believed that the smallest particles of matter moved according to strict laws: in other words, that the movements of each particle were “interlocked” with the total system of Nature. Some modern scientists seem to think — if I understand them — that this is not so. They seem to think that the individual unit of matter … moves in an indeterminate or random fashion; moves, in fact, “on its own” or “of its own accord.”

He goes on to explain that the macroscopic behavior of matter appears deterministic because the average behavior of billions of particles is very regular. His explanation is remarkably cogent for a professor of medieval literature writing in the 1940’s. He then discusses the philosophical consequences of quantum mechanics.

Now it will be noticed that if this theory is true we have really admitted something other than Nature. If the movements of the individual units is “on their own,” … then those movements are not part of Nature. It would be, indeed, too great a shock to our habits to describe them as super-natural. I think we should call them sub-natural. But all our confidence that Nature has no doors, and no reality outside herself for doors to open on, would have disappeared. There is something outside her, the Subnatural. … And clearly if she thus has a back door opening on the Subnatural, it is quite on the cards that she may also have a front door opening on the Supernatural …

From Miracles by C. S. Lewis, chapter 3.

Related post:

The world looks more mathematical than it is

According to this article from National Geographic News, some experts now believe the number of dinosaur species has been overestimated. Some specimens that were previously believed to be distinct species are now believed to be juvenile specimens of other species. (Hat tip to Eric Geiger.)

Here are some of my favorite posts from the Reproducible Ideas blog.

Three reasons to distrust microarray results
Provenance in art and science
Forensic bioinformatics (continued)
Preserving (the memory of) documents
Programming is understanding
Musical chairs and reproducibility drills
Taking your code out for a walk

The most popular and most controversial was the first in the list, reasons to distrust microarray results.

The emphasis shifts from science to software development as you go down the list, though science and software are intertwined throughout the posts.

Bigger animals have more cells than smaller animals. More cells means more cellular metabolism and so more heat produced. How does the amount of heat an animal produces vary with its size? We clearly expect it to go up with size, but does it increase in proportion to volume? Surface area? Something in between?

A first guess would be that metabolism (equivalently, heat produced) goes up in proportion to volume. If cells are all roughly the same size, then number of cells increases proportionately with volume. But heat is dissipated through the surface. Surface area increases in proportion to the square of length but volume increases in proportion to the cube of length. That means the ratio of surface area to volume decreases as overall size increases. The surface area to volume ratio for an elephant is much smaller than it is for a mouse. If an elephant’s metabolism per unit volume were the same as that of a mouse, the elephant’s skin would burn up.

So metabolism cannot be proportional to volume. What about surface area? Here we get into variety and controversy. Many people assume metabolism is proportional to surface area based on the argument above. This idea was first proposed by Max Rubner in 1883. Others emphasize data that supports the theory that suggests metabolism is proportional to surface area.

In the 1930’s, Max Kleiber proposed that metabolism increases according to body mass raised to the power ³/₄. (I’ve been a little sloppy here using body mass and volume interchangeably. Body mass is more accurate, though to first approximation animals have uniform density.) If metabolism were proportional to volume, the exponent would be 1. If it were proportional to surface area, the exponent would be ²/₃. But Kleiber’s law says it’s somewhere in between, namely ³/₄. The image below comes from a paper by Kleiber from 1947.

The graph shows that on a log-log plot, the metabolism rate versus body mass for a large variety of animals has slope approximately ³/₄.

So why the exponent ³/₄? There is a theoretical explanation called the metabolic scaling theory proposed by Geoffrey West, Brian Enquist, and James Brown. Metabolic scaling theory says that circulatory systems and other networks are fractal-like because this is the most efficient way to serve an animal’s physiological needs. To quote Enquist:

Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. … Fractal geometry has literally given life an added dimension.

The fractal theory would explain the power law exponent exponent ³/₄ simply: it’s the ratio of the volume dimension to the fractal dimension. However, as I suggested earlier, this theory is controversial. Some biologists dispute Kleiber’s law. Others accept Kleiber’s law as an empirical observation but dispute the theoretical explanation of West, Enquist, and Brown.

To read more about metabolism and power laws, see chapter 17 of Complexity: A Guided Tour.

Related posts:

Networks and power laws
Rate of regularizing English verbs

To first approximation, out planet is a sphere. But how accurate is that approximation? What’s a better approximation? How good is that? This post will answer these questions and some related questions.

How well does a sphere describe the Earth’s shape? The Earth’s polar diameter is about 43 kilometers shorter than its equatorial diameter, a difference of about 0.3%.This is due to the equatorial bulge caused by the Earth’s rotation.

What’s a more accurate description of the Earth’s shape? An oblate spheroid.

What is an oblate spheroid? It’s the shape you get by spinning an ellipse around it’s minor axis. That says if you were to take a cross-section of the Earth containing the polar axis, the shape you get would be an ellipse. The polar axis would be the minor axis and the equatorial axis would be the major axis. But if you were to take a cross-section through the equator, or any plane parallel to the equator, you’d get a circle.

What is a prolate spheroid? A prolate spheroid is what you get by spinning an ellipse around its major axis.

What is an ellipsoid? An ellipsoid satisfies the following equation.

A sphere is an ellipsoid with a = b = c. An oblate spheroid is an ellipsoid with a = b > c. A prolate spheroid is an ellipsoid with a = b < c. A scalene ellipsoid is an ellipsoid for which a, b, and c are all distinct.

How good is the oblate spheroid model? The error in approximating the Earth’s shape as an oblate spheroid is less than 100 meters, two orders of magnitude better than the spherical model.

How are other planets shaped? The other planets in our solar system are also oblate spheroids with Saturn being the most oblate: the polar diameter of Saturn is about 10% shorter than its equatorial diameter.

Related post: Finding distances using longitude and latitude

One of my daughters had the following assignment for science. First you boil a couple leaves of red cabbage and pour off the water. In our case the water was inky blue, but the results may vary according to your water chemistry and possibly by your cabbage. Next add a little diluted ammonia to the water and the color will change. Add the right amount of vinegar and it will change back to the original color. Add more vinegar and it will turn a new color. The liquid can turn a wide spectrum of colors. (Which colors? You’ll need to do the experiment to find out!)

Now we’ve got a jug of ammonia left over. What can you do with a jug of ammonia? Any practical uses? Fun uses? Any more science demonstrations?

According to the Science Podcast, a study shows elephants in captivity have about half the median life expectancy of elephants in the wild.

audio, transcript