0 The Invention of Air

It isn't often that I wind up able to talk about a book, science, a scientist, and my genealogy in the same post, but Steven Johnson's The Invention of Air manages that feat.

The book is a pleasure to read.  Johnson's linchpin is Joseph Priestley's life and science.  I'd always thought of him as an English scientist, which turns out to be only partly true.  He finished his life in the USA, corresponding particularly with Thomas Jefferson both in revolutionary and post revolutionary days.  The Jefferson connection (and before that, Franklin) make for some interesting reading and historical insight outside of science as well as inside.

In his writing on Priestley's science, Johnson captures some of my themes about scientists being people, having lives, and those having some influence on what work they do and how they do it.   Also nice to see was that Johnson did not take the oversimple telling of 'good guy / bad guy' for Priestley's advancing the phlogiston theory and holding on to it longer than most.

To back up, as not everybody already knows, Joseph Priestley was one of the major chemists of the 1700s, most known perhaps for 'discovering' oxygen, but also (and Johnson makes a good case that this was the more significant) that plants release oxygen and consume carbon dioxide.  His approach to his research, though, was not the stereotypical one step leading to the next with some ultimate conclusion drawing ever closer.  It was more the 'try many things and see a) what happens or b) what works'.  And he then was active in describing how it is he did his experiments, as often the method itself was the important aspect of the work.

If you know a young scientist, I'll suggest you get this for them as well and not just yourself.

The genealogy I'll put below the fold.  For here, it suffices that I'm not a descendant of Priestley's.

As I got late in to the book, I found that when Priestley came to the USA, he moved to Northumberland County, Pennsylvania.  This is about 100 miles, as the crow flies, outside Philadelphia.  Being that far away from an intellectual center, Johnson noted, greatly slowed Priestley's communications and discussions.  Which, given how Priestley worked, was a great barrier.  His reason for being so inconveniently far away was the Yellow Fever and Smallpox that were rife in Philadelphia.

At that time (call it 1800, he arrived before and died after, and shows up in the 1800 census) I have several ancestors in Pennsylvania.  One particular family is Peter White and Elizabeth Brittain, who lived in what was then Northumberland County (now Columbia).  As I make it by Google earth, about 20 miles from Priestley's location in Pilot township.

Elizabeth's father, Zeboeth Brittain (or Zeboath) died in 1790, in Northampton county -- about 50 miles outside Philadelphia -- of smallpox.  I'd have thought 50 miles was enough to be safe, but Priestley had some fair reason to be even farther away.

Alas, no prospect that Peter and Elizabeth, or Peter's father John, who also lived in Northumberland, ever met up with Priestley.  Peter and John were farmers.  John was about Priestley's age.  But 20 miles in 1800 was a 2 day trip, possibly more then due to the roads versus mountains problem (i.e. roads tended not to cross mountains, and Priestley and the Whites were in different valleys).

Still, I find it helpful to think about the notable figures, such as Priestley, versus ancestry.  Saying that he was contemporary with my 5 times great grandfather (John White/Johann Weisz) helps bring things in to a perspective better than observing that 1800 was 210 years ago.

Detail: The Invention of Air

0 Coping with Math

I confess that for the most part, math has been something that I enjoy and have fun with.  'Coping' hasn't so much been my experience; but I have known plenty of people for whom it was more difficult, and even highly unpleasant, activity.  Since it sometimes turns in to an obstacle that scares people away from doing science, and I like science as well as the math, I do keep an eye out for books that might help people past that obstacle.

My favorite book in that realm is Sheila Tobias' Overcoming Math Anxiety.  Her story was being one of those people who had been scared out of math and science.  Later, she decided that she liked physics and would slog through the math she had to, that was preventing her from doing the science she liked.  Along the way, she discovered many myths that she had bought in to, things that produced anxiety in her when math was mentioned.  Hence the title. 

In talking with people, anxiety stands out as a major barrier.  One of the myths I'll mention here is that some people just have some magical 'math gene' that makes it easy for them, and nobody else can do any math.  But it's only math that needs this magical gene.  Nobody says "I can't play basketball, I don't have the magic gene for it."  Basketball, we all know, you can play regardless.  If you practice more, you'll get better.  If you want to play professionally, then, yes, you need good genes.  And that's probably also true for mathematics.  But you don't need to be a professional level basketball player to enjoy playing the game.  And you don't need to be a professional level mathematician to do science.

If you had to be professional level at math to do science, I couldn't be doing science.  I'm pretty good with math.  But, to continue the basketball analogy, I'm more the level of a very good high school player or decent college player.  I did earn a bachelor's degree in applied mathematics.  But only that much.  And that puts me with more math than most scientists -- folks who are doing quite good science. 



More specific to pre-teen and early teen age girls is Danica McKellar's Math Doesn't Suck.  I mentioned this book before in holding place, and surprised quasarpulse (my daughter) by mentioning it favorably.  See her comments there in full.

My pro- comments stand.  But quasarpulse's objections also do.  Summarizing a little:
Pro:

• The mathematics is explained correctly, and conversationally.  
• Beyond the mathematics, there is a strong positive 'you can do it' message.
• For the target audience of middle school to junior high (call it 10-15 years old) girls who are reading or watching stereotypical (and stereotyping) magazines or shows aimed at the same age group, it includes enough references to that culture (personality 'quizzes', for instance) that the book is not alien.

Con:

• Too much following the stereotype.  To quote quasarpulse ... they seek to feminize math not just by making it look pretty, but by making its content and application appropriately feminine.

The question is, how strong is that con?  The concern is, if the math is presented in too 'girly' a fashion now (middle school math for Math Doesn't Suck, pre-algebra for Kiss My Math), then at a later date, whether geometry, calculus, statistics, ..., when the topics aren't 'girly' in the way presented in these books, the girls might well be toast.  Able only to work with the math as long as all examples are from shopping for cute shoes and the like.

My take is that for the level of McKellar's books, most math examples from any book are functionally equivalent to that shopping.  In quasarpulse's terms, I think it is merely a matter of painting the power tools pink.  In these books, the girls are shopping for cute shoes.  In older math books, the examples were shopping for baseball gloves.  You understand as much mathematics either way.  And if, after going through your math class (or math book), you can't figure what a 12% discount on a $23 pair of shoes is, but only if it were a $23 baseball glove (or vice versa), you haven't really learned the math.  But that isn't the fault of the examples.

There's a different matter quasarpulse raised, and on that we're in complete agreement.  I just don't think it's an issue to be addressed best by math books.  That is the experience gap.  People who never do any things like throw balls, run around, play with rockets, build bridges from toothpicks, and so on, find it difficult to learn physics.  Usually it's girls who don't have that experience.  Best way to address it, I think, is for kids to do and try as many different things as possible whether at school or at home.  My ideal math book would also pull its examples widely.

All that said, of the two of us, only quasarpulse has been a girl age 10-15.  And she is heading towards her math/science/engineering degree, because of, and in spite of, her experiences along the way.  So I weight her opinion highly.

Detail: Coping with Math

0 Science humor

No, I won't inflict any mathematician/engineer/scientist jokes on you.  (Not that I couldn't ....)  I've been reminded recently of some good science humor cartooning.

Online, you might enjoy:
PHD Comics
XKCD

A science cartoonist I've enjoyed for years and recently reread his collections Einstein Simplified and Einstein Atomized is Sidney Harris.  You can get an online taste here. 

And, though it was never really a science cartoon, Gary Larson's Far Side is a favorite of mine, and was quite popular among scientists.

Detail: Science humor

0 Experimental reading

I've been reading more general audience science books lately, which is part of the reason for relative quiet here.  But it makes for ideas later.

The first book in the experimental line is geared for middle school to junior high students.  It's perfectly useful for older folks as well.  And it will probably be a good idea to have one at hand for some of the experiments if performed by the younger.  101 Incredible Experiments for the Weekend Scientist by Rob Beattie.  The experiments cover a range of things, from making slime to making a cloud.  Some weather and climate examples, but not especially aimed to that.  The experiment descriptions do also contain a 'how it works' section, which I take to be very important.

The second is geared to an older audience, college age, but I think most experiments and observations can be done by middle school to jr. high students.  They just might want someone else to do the translation to more familiar language.  That's Clouds in a Glass of Beer: Simple Experiments in Atmospheric Physics by Craig F. Bohren.  This is the book (chapter 10) that prompted my Tuesday note.  Its 22 chapters include much more by way of explanation of the science behind what you're observing in doing the experiments, and how this ties in to the atmosphere. 

In both cases, the authors mention some things that the experimenter can use for proceeding to further experiments.  They usually aren't laying it out exactly this way, so keep your eye open for comments like 'best results are for doing X' (using a small tube, for instance, to see surface tension).  That's a sign that you can get different results if you use a larger tube, and it can be informative to see just how much the result depends on the size of the tube.

Detail: Experimental reading

0 A challenge to the computer folks

Something I'd like to be able to do is to track the citation history backwards from a given paper.  But I want a couple of things that it looks like typical bibliographic sources don't do.  As matters of computer or library science, I don't think they're terribly difficult.  I've seen things done which strike me as much more complex.

Let's start with some paper, call it paper A.  It cites, say, 15 papers (papers B, second generation).  Each of those cites another, say 15, which at least temporarily means a list of 225 papers (C, third generation).  Easy to get the list of papers cited by paper A (the 15 papers B1..B15), but significant manual effort, it seems, to get the collected list of papers C1..C225.  One thing I would like, however, and which seems completely unsupported, is that I'd like a count of how many times each paper shows up in this tree.  Some of the papers in the second generation probably cite others in the second generation.  And it's near certainty that many of the third generation papers are cited by several of the second, and probably a good number of third generation cite each other.  This is pretty much just a simple social network kind of analysis -- some papers have lots of friends, and some not so much.  I'd like to see which papers are highly connected, and which aren't, working within the group established by papers cited by a paper of my interest (actually won't be one of my own in practice) and lines of reference descent from there.


The second sort of thing I'd like to see is for the chart to be continued through enough generations that sources like Newton's Principia start appearing on the list.  I'm curious how many generations, in terms of citation history, modern work is removed from some of the landmark sources.  Unfortunately, it seems that the bibliographic databases I have access to die out in the mid 1980s, which is a long time from when I want to be getting to.

Detail: A challenge to the computer folks

0 Title decoding

Title of a recent paper in Science: Motile Cilia of Human Airway Epithelia are Chemosensory (Shah and others, vol 325, pp. 1131-1134, 2009.)

Time to apply the Science Jabberwocky approach, as I'm unfamiliar with many of those terms:

Mimsy borogoves of Human Airway Bandersnatches are Frumious.
(motile) (cilia) of Human Airway (epithelia) are (chemosensory)

4 terms we need to get definition of (those of we who don't already know them, that is).

Cilia, whatever they are, can apparently be motile or non-motile. By the writing, that doesn't seem to be the new observation. But that they can be frumious, er, chemosensory, is apparently news.

The abstract itself tells us what the cilia are -- microscopic projections that extend from eukaryotic cells. (If we know what a eukaryotic cell is, we're set. Otherwise, we have to do a little more research, and discover that eukaryotic cells are those with separate parts to them, including a nucleus -- that covers all animals, plants, and fungi).

We also have to go look up 'epithelial'. We're ahead of the game if we know that epi- tends to have something to do with 'on the surface'. Epithelial cells are those that are on the surface of our body cavities -- lungs, digestive system, etc..

Chemosensory ... well, sensory is nicely obvious. Chemo- as a prefix means that the cells are sensing chemicals.


So with a little decoding work, and perhaps using google search for definitions (enter define:epithelial as your search and you'll get links to the definition of epithelial), we arrive at our understanding of the title. -- There are cells lining the surface of our airways that have little extensions. The authors show that the extensions are sensitive to chemicals.

In reading the paper itself, we find that it is particular kinds of chemicals that these cilia are sensitive to -- 'bitter'. When they detect such compounds in the air, they start getting active and try to flush out the bad stuff they've detected.


The conclusion is not especially a surprise to me. I've long been confident that my airways were sensitive to certain chemicals (though I didn't know which). Walking past a perfume counter has always been a problem for me, as my lungs shut down or at least try to. Folks have said that it's just my imagination, and all that is happening that I'm smelling the perfume and causing the rest. That doesn't work well as a hypothesis because I have an exceptionally bad sense of smell. Usually the way I know the perfume is present is because I start having more difficulty breathing. The paper also corresponds to a different experience of mine. Namely, I don't have such reactions to flowers, even flowers in large masses as we get in spring with the honeysuckle, or lilac bush. The cilia are reactive to bitter compounds (known from the paper) and probably (a point that's very testable) perfumes have more such compounds than flowers do.

Per my usual, I've written the corresponding author about this post. Also, if the sample donation process is quick, easy, painless, harmless, I'm willing to donate a sample of my highly-reactive (I think) epithelial cells for their further research.

Detail: Title decoding

0 Science Jabberwocky

Twas brillig and the slithy toves
did gyre and gimble in the wabe.
All mimsy were the borogoves
and the mome raths, outgrabe.

Beware the Jabberwock, my son!
The jaws that bite, the claws that catch!
Beware the Jubjub bird, and shun
The frumious Bandersnatch!


... The start of Jabberwocky by Lewis Carroll. No, I'm not going to try to persuade you that there are some deep underlying scientific meanings behind it.

Rather, it provides some suggestions on how to read science in areas that you're not familiar with. I have to confess that in areas outside mine, there seems to be a terrible array of words no more obvious than 'brillig' and 'slithy'. And words that look familiar, like 'gyre and gimble', but which don't look like they are supposed to mean what I'm used to them meaning.

Still, even with most of the words being unfamiliar, we can read this can know quite a lot. That's part, after all, of what makes Jabberwocky readable at all. So, let's take line by line, work our way through, and see what we can extract even from intentional nonsense.

1) Twas brillig and the slithy toves
a) Brillig probably means something about the weather. We might expect 'twas sunny' (or cloudy, etc.) in a poetic start.
b) toves are things that can be slithy. We don't know what either of the terms is, but we can get that far. Probably there are also non-slithy toves. Poetry doesn't follow the rules of scientific writing, but usually you won't see a modifier (slithy) unless it's possible for the thing to not be that way.

2) did gyre and gimble in the wabe.
a) normally gyre and gimble would mean something about spinning. A gyre is a rotating mass of fluid, a gimble is a sort of bearing that permits pivoting -- but both would be nouns, and in this case they're clearly verbs. The toves are gyring and gimbling, or at least they did gyre and gimble. Pretty often when a noun is turned to a verb, it doesn't mean exactly what it used to. And, when it's applied to something that we don't know, we should tread cautiously about it having acquired a different meaning than we're used to. English is nothing if not free with having multiple meanings for words.
b) wabe ... probably some kind of place. We might be unsurprised with 'field' 'park' or the like here. On the other hand, it could also be more of an event -- a party, ballgame. Or could even be abstract ('the ether', 'the astral plane').

3)All mimsy were the borogoves
a) Borogoves are things that can be mimsy
b) Mimsiness occupies some kind of range, from not mimsy at all, to all mimsy. These particular borogoves are all mimsy. I can just see the scientific writing here: "We examined a sample (N = 30) of borgoves, and found their average mimsiness to be 45% with a range of 30 to 95% mimsy." Replace borogove with 'meteorological station' and mimsiness with 'completeness' and there's many a paper on the subject.

4) and the mome raths, outgrabe.
a) likewise, raths can be mome. There are some non-mome raths out there probably.
b) further, raths, or at least mome raths, can be outgrabe.
c) We might also guess that raths and borogoves have some tendency to be near each other.

5) Beware the Jabberwock, my son!
The jaws that bite, the claws that catch!
a) Beware the Jabberwock. Easy enough; if you see a jabberwock, beware.
b) Jabberwocks are things that have jaws and claws. These are probably either why you should beware of a jabberwock, or how it is that you'll identify one. (They could also spit venom, but you won't know that until it's too late. The jaws and claws should be obvious much earlier.)

6) Beware the Jubjub bird, and shun
The frumious Bandersnatch!
a) Ok, there's a Jubjub, which is some kind of bird. It'd be nice to know what one looks like, so that we can properly beware.
b) More interesting, and helpful, is 'shun the frumious Bandersnatch'
i) Bandersnatches are things than can be frumious, and generally are (compare 'shun the poisonous rattlesnake' -- all rattlesnakes are poisonous, but in giving a warning, we do much more often use the redundant modifiers)
ii) we should shun them. Now this is interesting. Jabberwocks and Jubjubs, we should beware, but Bandersnatches we should shun. Shun is a social word, meaning we should not socialize with Bandersnatches. We would not say 'shun the poisonous rattlesnake', it'd be 'beware', 'flee', and the like. Shunning, we'd do with someone who was socially unacceptable 'shun the bore', 'shun the self-involved', and so on. Bandersnatches, apparently, are some kind of social creature that one could interact with, but you shouldn't. The reason we should not socialize with them is probably that they're frumious -- that's why the redundant modifier got used. So now we know that frumious describes some socially unacceptable behavior (at least to the person speaking).

I won't go through the whole thing. It's a piece of Through the Looking Glass, and you can find the whole Jabberwocky here.

Even with a torrent of unknown words, we can infer quite a lot about the things being discussed. In reading scientific work, unknown words will be common, so getting used to inferring what you can (couldn't make much headway on the Jubjub bird, but a fair amount on those frumious Bandersnatches) is a very good idea. Then keep reading and see how things get elaborated on. In Jabberwocky we never do hear more about the Jubjubs, so we're stuck at they're some kind of bird to beware. In a scientific paper, you'll usually see the same terms come up repeatedly, in different forms and contexts, so that it is often possible to build up a pretty good image by the time you slog through it. I confess it's a slog, since I've read papers outside my fields, and they're much more work to read than papers in my fields. Still, I get there.

Detail: Science Jabberwocky

0 New Book on the way

Species: A history of the idea, by John Wilkins, is now available. I've ordered my copy.

I've known John over the net for several eons as time counts on the net, including seeing him write about species and the idea. For this central concept of biology, there turn out to be many different definitions that get used in practice, and probably all of them have changed through time as we learned more. Here, you get it all from the very earliest thoughts to the present. Likely not a middle-school or jr. high level read. John's a good writer, but his audience here is mostly the highly educated and knowledgeable. Still, I'll be giving it a go myself. Those who seriously interested in biology should definitely get a copy.

Detail: New Book on the way

0 Scientific Specificity

Reading science is a bit different from what we're accustomed to in the rest of our lives. No, not that scientists use inscrutable jargon or math; plenty of other groups have their own jargons and uses or abuses of math. The challenge is that scientists, in writing and speaking science, are usually much more precise in what they say.

I was reminded of this in the comments to my note about the correlation between CO2 and temperature. Still thinking about how to write so as to avoid the problem. Since, even if I do complete the rewriting, there are many other scientists who won't be revising, I figure it's not a bad thing to write this general note.

Over in that note, I documented that there is indeed a correlation between CO2 levels and temperature. Quite a surprisingly large one, in fact. I also noted that merely running this correlation is not how the science is being done. (In fact, the science on temperature rising because of CO2 increase, if there were enough of one, predated there being observations of the CO2 increase or temperature rising. Conservation of energy is a powerful law.) Still, where there are people saying that there's no correlation between CO2 and temperature, there's the elementary disproof.

A catchphrase that I'd thought was very widely known (and correct, which is rarer) is "correlation is not causation". But that's particular to correlation. The more general point is, if you've supported a particular claim (CO2 correlates with temperature), that's all that has been supported. One thing we try to do in science is to find things which are true to work with. Some things that are true aren't very useful. But you can't reach a good scientific conclusion with things that are not true. These elementary truths are the building blocks for constructing larger true structures.

This is why the difference in reading for science vs. many other things. In many other areas, you can predict an entire argument from a short part of it (not least, because the author is arguing rather than trying to understand -- see my note discussion vs. debate for why this is such a difference). To read science, you need to keep this in mind. Examine that one tiny building block that's being presented at the moment very carefully, by all means. But avoid rejecting the whole thing because you think it might be used to build something that you don't like. If the block holds up to scrutiny, then it holds up and work with it.

Detail: Scientific Specificity

0 Read original sources

I've mention it here and there before, but was reminded recently of the importance of reading the original sources. The recent round was a document which said the IPCC had not discussed some points about sea surface temperature. I thought that was odd, so I looked up the IPCC section that talks about sea surface temperature (SST) and in truth, they do talk about those issues. If somebody is lying about what someone else says in such an easily identified way, time to pitch that original source and go looking for someone honest to learn from. So that's one reason to read the original sources -- to see who's lying and weed them out.

There are also more pleasant reasons to follow up to original sources. One is, often the source is being cited for something that's a minor part of what they were talking about -- and the major part is even more interesting. In oceanography, one of the things often mentioned in classes is the Ekman Layer. Don't worry about what it is exactly. Usually, a reference says that Ekman (1905) studied the formation of what we now call the Ekman layer for conditions of an infinitely deep ocean, infinitely steady winds, with absolutely constant friction through the depth of the ocean. Well, it turns out that, although he did examine that highly idealized case, this was a small part of the paper. In fact he also examined varying winds and varying friction. And the results of doing so were much more interesting than what he's normally cited for.

A second reason can be particularly important in science. In the original papers on an idea, the author is explaining something new to the audience. He can't assume nearly as much as later papers on the idea will. You'll also get to see the first matchups of the idea against observations. So I usually learn more by reading the original than by reading the textbook description. (For the geophysical fluid dynamicists out there -- Charney's paper on baroclinic instability is the one exception I've found. There also turn out to be reasons why it came out that way.)

Part three is that you'll get to see much more discussion of why the approximation can be made, and where it can be expected to fail. So, for example, a modern paper talking about the color of the sky -- perhaps for a planet orbiting some other star -- will merely mention 'We apply Rayleigh scattering law and arrive at ...'. It's only when you read Rayleigh's papers that you find out that the 'law' is an approximation, and it will fail under certain, predictable, conditions.

It can be difficult to get hold of the original sources when you start going after Reynolds 1895, Ekman 1905, etc. So the ideal can't always be met. Still, the whole IPCC working group 1 (physical science) 4th report is readily available online or you can order a print copy (also groups 2 and 3, but I'm a physical science guy, so look more to that one). So, when you encounter someone making claims about what the IPCC says, go take a look yourself. And if the point isn't clear, or it is interesting to you, start following up the citations they give. (Unfortunately, I think that after the first report, the writing declined in terms of readability by nonprofessionals. Any more, once you're past deciding if someone lied about the IPCC, I think you'll have an easier time reading by hitting the cited sources rather than the IPCC reports.)

Detail: Read original sources