What’s my pre-Cambrian rabbit? What’s YOUR pre-Cambrian rabbit?

I try to be honest with myself in how I think about things.  It is hard to be aware of one’s blind spots, and it is tiring to be suspicious of ideas that make one feel better.  I may have picked up the habit of self-skepticism from an early exposure to Karl Popper, or a lot of training by curmudgeonly old-school molecular geneticists, but however I got it, I’m stuck with it.  Popper taught us all about falsifiability, and my post-doc advisor taught me to have an adversarial relationship with my own ideas, but my favorite formulation is from the evolutionary biologist J.B.S. Haldane.  

Evolution is a big, big concept, with ramifications that permeate the entire world of biology, geology, and astronomy, and more.  But, to be honest about how one thinks, one must be aware that it’s still only an idea, a view of the world that may be wrong.  Haldane was (according to the story) asked what would cause him to change his mind about evolution as an explanation for life on earth.  “A fossil rabbit in the pre-Cambrian” was his reply.  Pre-Cambrian rocks are over 500 million years old.  There are pre-Cambrian fossils, but only of simple invertebrates and mysterious life forms long extinct.  But, significantly, there are fossils; if there were rabbits 500 million years ago, they could have been fossilized, so it is in principle possible that Haldane’s reliance upon evolution could have been shaken.  

Any responsible thinker should have a pre-Cambrian rabbit for their beliefs.  The people who study climate change, if they were honest, would reconsider everything if it were found that carbon dioxide did not in fact help to trap heat, and that hundreds of years of data were in fact due to an easily overlooked artifact.  Cancer researchers, if they were honest, would re-evaluate a lot of their beliefs if the apparent connection between smoking and lung cancer were shown to be the result of some chemical in the packaging of cigarette boxes.  Furthermore, for an honest thinker, it’s not a matter of simply recognizing falsifying evidence when it appears.  Rather, like Haldane, the honest thinker must be aware enough of their thinking that they can imagine and define things that would falsify their beliefs before encountering them.  

The news recently has really been getting me down.  I have become convinced of a theory that our president is a racist, and that his presidency will be severely detrimental to this country.  This theory is based on observation of facts and informed by historical parallels.  But, while it is consistent with all facts, it is a theory.  It is, and must be, falsifiable.  The president could decide to fire his Jeff Sessions and Stephen Miller and General Kelly and all the other people who have pushed him in the direction of racism, and renounce many of the claims he’s made; despite rigorous fact-checking, many of the claims he’s made about immigrants could be shown to be true (somehow); he could actually do things to promote racial harmony—these would all be possible but unlikely.  They would falsify my theory, and elevate my mood.  

But, I have noticed something more disturbing in the mirror world inhabited by those whose sympathies lie with the president.  For them (and those who insist that anthropogenic climate change, vaccines, and evolution are bunk), there simply is no pre-Cambrian rabbit.  There is no possible fact or observation that will change their position, and whether this is bad faith or just simple-mindedness, it makes rational argument impossible.  When a Trump supporter at one of his tinpot “Triumph of the Will” rallies was asked about some of the images and recordings of children torn from their parents, they admitted that they were disturbing, but ultimately opined that they were probably faked.  I’ve also heard dodges about how Trump is accomplishing great (but unspecified) things and how everybody is out to get him; and, finally, fake news, fake news, fake news.  Even the most reliable, scrupulously reported pre-Cambrian rabbit is fake.  

I don’t know a way beyond this impasse to civil discourse, although I’m pretty sure it doesn’t involve Facebook memes or using InfoWars as a reliable source.  Perhaps any real attempt at discussion must be made one-on-one.  Before attempting conversation, we have to tell each other about our pre-Cambrian rabbits.  Acknowledging that our beliefs are falsifiable is the opposite of a sign of weakness; rather, it is a sign of honesty, like duelists of old showing each other that they are only using the prescribed weapons.  Also, if you showed me a rabbit skull and told me it came from, say, the Laurentian Shield, I’d want to see some acceptable proof—and, like the rabbit itself, proof that I would be willing name as acceptable before it is produced.  

I really doubt that a fossilized rabbit will ever be discovered in pre-Cambrian rocks.  But, to be absolutely sure, I would be thrilled and excited to hear that a truly, completely verified rabbit fossil had been found in the basement sediments of the Grand Canyon.  It would show me that I was working under an erroneous view of the world, and it would be fascinating to try to understand this newly illuminated world.  And, while I would love to be wrong, I think that rabbit is more likely than finding that our president is not a racist.

Like Clockwork

Anybody who has the slightest connection to the world of lutherie knows that every year, some engineer* in some corner of the world will discover the Secret of Stradivari--some odd treatment or technique that will allow any modern builder to replicate "the" sound** of the classic Cremonese instruments.  It's like those of us who follow biology know that every year--at least, if the popular press is to be believed--some researcher will discover "the" cure for cancer.  Really, if all the stories in the newspapers claiming that a cure for cancer is just around the corner were true, the dread disease would have been history long ago.

That last sentence should be in quotes--I lifted it verbatim from an article in this week's Economist that discusses a paper about why science journalism sucks with such regularity.  The paper*** focuses on the ten journal articles about ADHD that garnered the most attention from the popular media, and what happens after the big splash.  It concludes that the findings in each of the "top ten" are novel, generate testable hypotheses, and in eight out of ten cases, are unsupported by subsequent research. The paper refrains from slamming the media, but points out that the popular press is easily impressed by high-impact journals, top-tier universities, and seems unwilling to follow up and look for confirmation of splashy results. 

The Economist cops to some blame for this state of affairs, but also apportions some blame to the scientists themselves, because the follow-up articles don't make it into the same high-impact journals.  (Nobody mentions one of my least favorite things, the University Press Release, which is often horrible and swallowed whole by the media.)  So, it admonishes itself, and then lets itself off the hook.

And, on the very same page, there is this article: "Magic Mushrooms--Violins constructed from infected wood sound like those of Stradivari," about how some engineer in Switzerland has discovered the Secret of Stradivari...



*I don't know why, but it's practically always an engineer

**a bogus goal in itself; for one thing, there is no unified sound of Cremona, or even of any single maker, and for another, one of the things that makes these fiddles so prized is their protean sound.

***Gonon F, Konsman J-P, Cohen D, Boraud T (2012) Why Most Biomedical Findings Echoed by Newspapers Turn Out to be False: The Case of Attention Deficit Hyperactivity Disorder. PLoS ONE 7(9): e44275. doi:10.1371/journal.pone.0044275.  It's PLOS, so it's open access, and it's an amusing paper, so go read it.  

 

Views may differ

Nobody sees the same thing the same way. I see the quail sitting in the morning sun on our pile of scrap metal, and I think about a bird that makes my life richer with its plumage and charmingly dorky quiff. The foundation contractor, seeing the same bird, notes "them's good eatin'."

I subscribe to a handful of magazines, and it can be amusing how differently they see the same thing. As a tree-hugger, I get the official organ of the Sierra Club. Nerd that I am, I get Science, official organ of the AAAS. I recently started getting The Economist, which I like for good writing and its acknowledgement of the existence of countries other than the US and the EU, but seems to be the official organ of people with a deal of money who want to make damn sure that they will always get more. Needless to say, how these rags see the same thing often differs.

What sets me off on this observation is the latter magazine's special feature on the Arctic in an era of climate change. You might view the Arctic as being kind of like a distant uncle--almost a stranger, partly because he's so damn hostile that he tries to kill you when you visit, but really interesting and exotic. We are in a situation where we are just starting to find out some amazing things about this uncle--but at the same time, we know that he's dying. All three magazines acknowledge that the Arctic that humanity has known for all of recorded history is toast, and own that it is due to human activity*. It's their views of the basic facts that vary.

Sierra's is boringly predictable, if justified--their hair is on fire. Science is more interesting. They remind me of a dispassionate doctor, attentively monitoring the pulse of the dying uncle, reporting the ebb and flow (actually, just the ebb) of arctic ice, the disappearance of habitat, the relentless northward creep of ecosystems, pointing out calmly exactly what is going on and how and why. Occasionally there will be an editorial suggesting that, while the uncle is dying, we really ought to at least slow the rate of decay. These editorial outbursts are rare, and as striking as Star Trek's Spock breaking down in tears.

And then there's The Economist, far and away the most interesting in how it views the matter--in the way that sociopaths are interesting. The entire thrust of the special feature on the Arctic was this: Our rich, fascinating uncle, who has been affecting our lives for as long as we have lived, and has so much to tell us, is dying. Whoohoo! I hear he has a gold watch--we can cash that in! He's got property that we can liquidate for profit, profit, PROFIT! We can actually hasten his demise by trying to get at this stuff--but he won't care if he's dead, and it will get us the stuff quicker! Hell, he's going to die anyway, so it's practically a moral obligation to hurry up! What? Oh, yeah, I suppose it's sad he's dying, but hey, PROFIT!!!

Oh well. I suppose I should give The Economist some credit for being arch-conservative and actually acknowledging anthropogenic climate change as a solid, undisputed fact. It's how you can tell The Economist is not an American magazine.

The Flame Challenge

There was an editorial in Science magazine that really caught my attention; instead of being from the editor in chief or some other notable scientist, it was from Alan Alda, who seems to be enjoying a career as a science popularizer. The letter is a challenge that resonated with me, since it stems from an experience that both Mr. Alda and I shared--a youthful question that was not satisfactorily answered.

"What is a flame?"

I clearly remember asking my dad this very question, and (like Mr. Alda) not getting an answer that made me feel any closer to understanding. I don't know why, but I remember exactly where we were and what time of day it was, walking to the grocery store after dinner one evening. Maybe it's so clear in my mind because the event made me realize my dad couldn't necessarily answer all my questions.

Mr. Alda's challenge (which you should try; if you do, feel free to put it in comments or link to it) is to come up with an answer that will satisfy an 11-year old. So, here's my go--this is off the cuff, in the spirit of me springing the question on my dad, so no editing:

What is a flame? It's kind of hard to define, because it's two things at once--it's a thing and a process, the same way a dance is a thing and a process. I could say a dance is a thing, a set of steps that a group of people do, but it's also a process, where the people are doing a set of steps and moving around from start to finish.

So, a flame's like that--it's a thing, a chemical reaction involving some atoms changing partners. But it's also a process, that starts with some wood and some air and ends up with some ash and some smoke. The process is really neat.

If you're burning wood, it's got a bunch of atoms of carbon that are all bound to each other. Those atoms are OK with their situation, but they'd much rather be bound to oxygen to make carbon dioxide. But if they're in wood, it's really hard for them to do that. The first thing that's got to happen is that you have to give those carbon atoms in the wood the chance to react--get them on the dance floor, like--and the way you do that is with a lot of heat, like from a match. That actually makes wood vapor, kind of like the way that water makes water vapor or steam when you heat it up. Word! Wood--as a gas!

Anyway, wood gas is on the dance floor and now it can bump into oxygen and react with it. That reaction releases a bunch of energy--energy that used to be needed to hold carbon atoms together but isn't needed any more--and we see some of that energy as light, feel some of it as heat, and some more of that energy is used to vaporize more wood. So, the "thing" of a flame is that chemical reaction, but the "process" of a flame is wood or wax getting heated up, vaporizing so it can react with oxygen, reacting with oxygen, giving up a lot of energy, and using some of that energy to keep the process going. You're left with some carbon dioxide, and some ash, which is the bit of wood that can't get vaporized to burn.

I love looking at fire--I mean, it's toasty warm and makes neat patterns, but it's so cool to think about those carbon atoms getting heated up to get on the dance floor, join with oxygen, and keep the dance going.

-----

Well, there it is, no editing. It's definitely not perfect, and a couple of bits make me cringe. Not sure if I should enter, edit and enter, or just give it a miss. I wonder if 11-year old me would be satisfied. As I recall, when I asked my dad this question, I had just finished reading a YA-science book about plasma and how wonderful the world would be when we have fusion power, and my dad was a professor of biochemistry. There's no doubt I wouldn't be able to deliver the above explanation to 11-year old me--I doubt I'd be able to refrain from interrupting with a question.

Darmok and Jalad at Tanagra

As you might infer from the Friday Flora, I’ve been visiting my parents. Unlike me, they have a TV, so I spent some time ambling through Newton Minnow’s “vast wasteland” of network entertainment. I caught an episode of “Star Trek: The Next Generation,” which reminded me that, once in a while, the vast wasteland produces something of note. This was a science fiction show that occasionally did what science fiction does best: take a big idea, and see how it applies to human life in the laboratory of fantasy.

Further events at my parents’ house reminded me of another episode of this show. The big idea was that communication with different cultures might be complicated by a lack of agreement on what exactly is meant by “communication”. The intrepid space explorers encountered a culture that communicated entirely by metaphor, rather than plain language. Rather than saying “we should go over there and do such-and-so,” they would name a relevant story. The clever captain eventually figured this out, leading to a satisfactory ending.

My parents had an alien visitor as well, their friend Dr. C. from Australia. My father worked with Dr. C. in 1979-80, and since then Dr. C. has made quite a name for himself in the study of inflammatory responses. He wanted to fill me in on the state of research, and especially how his studies might cast light on my father’s Alzheimer’s disease. Now, the certain way to make time disappear is to ask a scientist “tell me about your research,” and Dr. C. had just finished writing a review with about 600 references, so he had a lot to talk about.

Scientists are sometimes regarded as being members of a unique culture, and often regarded as being unintelligible. As Dr. C. was discussing his work, I realized that he was, like the aliens in the TV show, communicating differently. Rather than saying “TNF has this effect on this class of cells, probably by this mechanism,” he would simply name a relevant paper and flash the abstract up on his laptop. It took me a while to figure this out—it’s actually a standard form of communication among researchers, but I’ve been focused on teaching for a while, and trying to communicate like a normal human. Now I’ve got a stack of reading to do and a growing appreciation of some interesting biology--and an appreciation of how alien scientists can seem.

This about says it all...

And it even mentions one of my favorite eukaryotes, Fuligo!

From the ever-wonderful XKCD. (Click on it to make it legible.)

Science-speak gem of the day

Science writing occasionally barfs up pithy nuggets, worthy of Basho or Rumsfeld:

"An unexpected residual excess of teleological thinking has influenced the evolution of biological sciences during the last few decades."

J. F. Linares, I. Gustafsson, F. Baquero, and J. L. Martinez (2006). Antibiotics as intermicrobial signaling agents instead of weapons. Proc. Natl. Acad. Sci. USA 103:51, 19484-19489.