One Fish, Two Fish

One fish
Two fish
Cleaning-
Crew fish
Wonder who fish?
Yellow-blue fish!
Little fish, as bright as lights
Who love to munch on parasites!
Some are yellow; some are blue
Some very few, some other hue
Why are they colored just like this?
Go ask an ichthyologist!
Some are happy; some may gripe
The nice one has a vivid stripe!
From here to there, from there to here,
There’s fishes in our hydrosphere!
Here are some who like to learn
They love to learn for food they earn
Oh me! Oh my!
Oh my! Oh me!
What funny things live in the sea!
Some have two fins, and some have four
Some have eight legs, and some have more!
Where did they come from?
Ooze or slime?
They’ve co-evolved for a long, long time
We see them live
We see them die
Beneath the sea
Beneath the sky
Too many times
We say good-bye
Each one unique; each one distinct
Sometimes we’re why
They go extinct.

The New York Times has a really nice article about learning in fish, with both laboratory and reef studies examining different aspects of a single larger question, but with an irritating, very basic mistake that happens to be one of my pet peeves.

On the reef, the article reports on two different teams out of the University of Queensland, one looking at the effect of the cleaner wrasse (reefs without cleaner wrasses had about 5 times as many parasites as those with cleaners), and the other examining the role of color and pattern in the recognition of cleaner wrasses (color and stripe are both important, in case you wondered). In the lab, the ability of fish to recognize and differentially respond to visual stimuli was examined by yet more of those busy Queenslanders; damselfish demonstrated they could learn to recognize various patterns (in one experiment) and colors (in another) in both two and three dimensional targets.

Remarkably, the fish also learned when the food reward was delayed and delivered far from the stimulus. The damselfish exhibited what is called anticipatory behavior, in that they would tap the image and then swim quickly to the other end of their tank in anticipation of their food reward. This response is much like Pavlov’s dogs who learned to anticipate food at the sound of a bell.

No, it’s not. Not like Pavlov’s dogs, that is. The task the fish were presented with was clearly an operant chamber–a Skinner box (or Skinner tank, as it were)–the elegant device B. F. Skinner invented in order to examine operant behavior. Not respondent behavior, which is what Pavlov looked at.

In an otherwise excellent article (including a description of the procedure clear enough to easily see this error), does one sentence really make such a difference?

Well… yes. I don’t know whether the mistake is the fault of the reporter or of the research team; sadly, either is possible. Behaviorism has been subject to steady misrepresentation for decades. It’s as if the creationists got to control what the majority of Americans knew about evolution… Like that could ever happen.

And this one is so incredibly easy, too.

Basic.

Like, oh… Dr. Seuss.

*sigh*

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Plato, Linnaeus, Darwin, and Atheism

Barbara Bradley Hagerty’s NPR piece, “A Bitter Rift Divides Atheists“, put two thoughts in my head. The briefer first: Taking a look at religious sectarian violence the world over, isn’t BBH impressed at how atheists handle alleged disagreements?

The second will take some time. You might want to pour yourself a drink first.

Plato’s view of reality proposed that there were ideal forms (platonic ideals) which we mere humans could not perceive—our abilities limited to seeing only imperfect copies of these ideals. We did, however, recognize kinds, as approximations to those ideals. We saw and recognized triangles because of their similarity to the ideal triangle, cats because of their similarity to the ideal cat, and so forth.

Linnaeus, in categorizing species, followed the platonic tradition. A species was defined by a representative of that species, a prototype, and by limited variation from that ideal. There was an ideal cat, but of course some are larger or smaller, striped or solid or tortoise-shell mottled or calico, with longer or shorter tails, faster or slower, more or fewer toes. This view of life made it very difficult to conceive of one species becoming another, or splitting into two.

Darwin rocked the world when, in his “Origin of Species”, he essentially rendered the word “species” obsolete, at least as it had previously been known. The average or ideal cat was no longer of any great interest; rather, the population of cats, individuals varying from one another, was what was important. There is, if I may abuse a metaphor, a spectrum of cats, a spectrum of pigeons, a spectrum of finches on each island of the Galapagos. The spectra vary for each species, but we could no more treat one individual as “the ideal” than we could suggest that any one wavelength represents sunlight, or fluorescent light, or incandescent.

Religions, arguably, may be described platonically. Using Linnaeus as our guide, we could arrive at Homo catholicus, “catholic man”; H. orthojudaicus, “orthodox jewish man”; H. australobapticus, southern baptist man, and so forth. We may do this because there does exist a set of beliefs that defines each religion (whether or not its followers adhere to those beliefs). There is no requirement for H. orthojudaicus to believe in the divinity of Christ, nor of H. australobapticus to follow the ex cathedra pronouncements of the pope. Each species religion has its own defining dogma, so a positive definition is quite appropriate. Many individuals fall short of that defining dogma, so variation (or “error”) is also expected.

Note, though, that these positive definitions are quite limited. To know that someone is H. catholicus tells us a few things to expect about this person. Knowing only that someone is not a member of this species tells us very nearly nothing at all. The non-catholic may be Christian, Muslim, Jew, Hindu, Pantheist, Wiccan, Polytheist, Deist, any of thousands of other belief systems… or may be atheist. The non-Sunni may be Muslim, Christian, Jew, Hindu… or atheist. The non Orthodox Jew may be Jew, Christian, Muslim… or atheist. A negative definition (non-X) tells us almost nothing at all about someone.

Atheism is, and must be, negatively defined. It is the “none of the above” alternative to the list of thousands of religions and sects. There is no creed to which all atheists must cling, even in theory. There is no defining characteristic shared by all atheists—even “they don’t believe in god” is incomplete, as the majority of religious believers also do not believe in the other religions’ god(s). (Recall that the first people to be called “atheist” were early Christians, because they did not believe in the Greek pantheon!)

As a privative category (defined by what it is not), there is no ideal atheism from which to have schisms. There is, instead, a spectrum of beliefs. To the extent that we take this spectrum and attempt to split it into black and white (or any segments, even ROY G. BIV) , we are artificially imposing boundaries where there are none naturally. The “hard atheism” and “soft atheism” dichotomy is not about atheism, but rather about the presence or absence of a completely different and orthogonal set of beliefs—after all, the people most likely to positively affirm the statement “there is no Zeus” are people who also positively affirm that there is a Yahweh. “Hard” atheism can only be defined one deity at a time, which makes it something other than “none of the above”. It is an attempt to use the vocabulary of religion to describe the absence of same.

A Darwinian, population-centered approach, is more accurate. Atheists are bigger or smaller, smarter or stupider, louder or quieter… pretty much like the rest of H. sapiens is. And, in truth, H. catholicus varies pretty widely from its alleged ideal form, so much so that the term “cafeteria catholic” is commonplace. The entire Order Religiosa will, in fact, contain tremendous variability, both within and between species. We should not expect all catholics to behave alike, nor all jews, nor all muslims, nor all protestants (let alone all denominations within these broader groups).

The truth is, no matter where we look, we see spectra. We see variability. It is not unexpected; it is not diagnostic; it is not evidence of schism. It is nature.

Writingly, Bitingly,
B. Bradley Hagerty
Writes about Atheists,
Finding a schism;

Godlessness, organized
Quasi-religiously:
All of humanity
Seen through her prism.

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Shakespeare’s “Linguistic Fingerprint” Solves Mystery

We crave to know: Did Shakespeare write this play?
The academic types love to dispute
This work or that; the tool they ply today,
A software program, used in the pursuit
Of plagiarism in college papers. Now
It serves to tally up the phrases seen
In this and Shakespeare’s plays, and thus allow
Comparisons made, among them and between.
Two Hundred matches found, of phrases three
Words or more in length. (In truth, they did
Find as many for another—thus, we see
That Shakespeare shared the task with Thomas Kyd)
“Linguistic fingerprints”, it seems, have shown
He wrote the play, but did not work alone.

The software program “Pl@giarizm” was intended to catch cheating students. It may have caught an entirely different fish. Scholars have disagreed as to the authorship of The Reign of King Edward III, although at least some Shakespeare anthologies include it. Much of it seemed… just not Shakespeare.

We may have an answer:

Sir Brian Vickers, an authority on Shakespeare at the Institute of English Studies at the University of London, believes that a comparison of phrases used in The Reign of King Edward III with Shakespeare’s early works proves conclusively that the Bard wrote the play in collaboration with Thomas Kyd, one of the most popular playwrights of his day.

The program found about 200 matches between Shakespeare and the play, and about 200 between Kyd and the play:

The Shakespeare matches came from four scenes, about 40 per cent of the play. The remaining scenes had about 200 matches with works by Kyd, best known for The Spanish Tragedy, a play known to have influenced Shakespeare, indicating that he wrote the other 60 per cent of the play.

Nice work.

But according to the software, some of my students must have collaborated with some pretty impressive researchers! I should show them a bit more respect!
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NPR’s Brain On God


Image (and story), NPR

Part 1: The God Chemical

Serotonin, in the human, is found mostly in the gut;
It helps peristaltic motion not to quit.
Serotonin—“the God chemical?”—If true, I’ll tell you what:
In both processes, the end result is shit.

Neurotransmitters will regulate the way we think and feel,
Or hallucinate or daydream, just the same.
We may feel a holy presence, but that doesn’t make it real;
It’s just serotonin, playing at its game.

Part 2: The God Spot

Teasingly, seizingly,
Neural activity,
Mostly confined to the
Temporal lobe,

Looks diagnostic to
Epileptologists,
Pointing to Abraham,
Moses, or Job.

Part 3: Spiritual Virtuosos

The brains of those who meditate (or speak in tongues, or pray)
Exhibit odd activity, or so researchers say.
It shouldn’t be surprising that their brains are acting odd—
That’s quite a lot of work for them to do… creating God.

Part 4: The Biology Of Belief

Can I influence things with my mind?
In experiments, run double-blind,
The clear answer is “no”;
But the money will go
To the studies more poorly designed.

The data, so far, have been clear;
Your mind won’t, when you’re gone, persevere.
Once you draw your last breath,
There’s no life after death,
Though that isn’t what some want to hear.

And the numbers are clear about prayer:
No effect (maybe God isn’t there?).
And I don’t find it funny
To hear that my money
Is spent on this sordid affair.

Part 5: Near-Death Experiences

The cases all vary, as well you might guess—
There cannot be “standard conditions”
The end of a life is a terrible mess—
Too bad for the researchers’ missions.

Reports of a “near death experience” may
Involve seeing a light, or may not.
Did your life flash before you, as some people say?
(I guess sometimes, they simply forgot.)

Was your heart being monitored? How ‘bout your brain?
You may guess that such cases are rare.
The claims may be many, but sometimes we strain
To find something reliable there.

But always the stories will grow in the telling
To tales we can hardly conceive!
(Especially so, when there’s books to be selling)
Some people just want to believe.

A couple of comments… I really really really found this article annoying. In what appears to be “showing both sides to the story”, weasel-like language is used again and again. “Scientists are looking at…” um… how many scientists? What percentage of the people looking at this topic are looking at it from this perspective? “[A] small but increasing number of scientists…” increasing from what to what? Again, what percentage of relevant researchers fit your description?

In this case, I have taught courses in relevant subject areas, and I know that they are presenting a very highly distorted view of the picture. But you don’t have to believe me; there are libraries and databases you could check. Libraries and databases that NPR must have studiously ignored.

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The Worth Of Science

Ok, I never do this–it is tough enough to come up with one post a day (I usually can’t, so you get a few a week, but rarely as many as seven!), let alone more than that. But the NPR comment thread includes people asking what tangible value we get from the amazing discovery of the new (ok, newly found) ring around Saturn. And other commenters are taking the bait, giving answers framed in terms of dollars or other pragmatic criteria.

It is in times like this that I am thankful to both History and Winston Churchill. History, because scientific discoveries so often prove practically useful–sometimes long after they are found (the recent Nobel prizes show that practical applications certainly can come from pure research), and Churchill for one quote. Asked if he would suspend Arts subsidies in order to help the war effort, Churchill replied “What the hell do you think we’re fighting for?”

If Churchill can use that reasoning, so can I.

What use is this discovery?
How many will it feed?
How many will it rescue from their poverty and need?
How many of my dollars went
To see this plan succeed,
While all around the globe, the people starve, the people bleed?

This money could be better used—
We could have gotten more!
Let’s fix the problems here at home, before we go explore!
The piles of money spent on this
We cannot just ignore—
A tenth of a percent* of what we spent on Iraq’s war!

Let’s question all the cost, of course,
And effort that we’re spending,
Against the gains in science, and the knowledge we’re extending.
It may not help to win a war,
If that’s what we’re pretending,
But stuff like this can make our culture one that’s worth defending**.

*ok, slightly less. Poetic license. Total cost of Spitzer telescope: 720 million dollars, according to Caltech. Total cost of Iraq war so far: 860 Billion as of February of this year, according to the NYTimes.

**not my idea—Winston Churchill’s.

Oh, I forgot! This and the last post were also posted as comments on an NPR story here.

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New Bling For Saturn! (Galileo’s Revenge)


When Galileo told the Pope
“Here, look into my telescope—
You’ll see much beauty there, I hope.”
His Holiness, the Pope, said “Nope.”

“Now kiss my ring, instead, and swear
That nothing of the sort is there—
I know you think it is not fair,
But I’m the Pope, as you’re aware.”

The Pope’s command was quite absurd,
But Galileo gave his word,
(Though some report him undeterred:
“E pur si muove” overheard.)

In hindsight now, with great delight,
We know, despite his Papal might,
That evidence would come to light
To prove the heretic was right.

With Urban’s ring already kissed,
The chance to get it right was missed,
Just one more error on the list—
But now, we find another twist!

What wonders will the cosmos bring?
Now Saturn sports another ring!
Much bigger than the Pope’s, this thing
Is interplanetary bling!

Four centuries have come to pass
Since Galileo ground his glass;
Far too much time for him, alas,
To tell the Pope to kiss his ass.

But now, the kids will learn in school:
That Saturn sports another jewel;
That telescopes are really cool;
One may be Pope, but still a fool.

I hope you will all, by now, have heard the very cool news: a new ring has been discovered around Saturn–a very different ring than any of the others; thicker, wider, in a different orientation than the other rings. The infrared imager on the Spitzer Space Telescope detected the faint image; the density of this ring equates to about 20 grains of material per cubic kilometer. You would not see it if you were standing in the middle of it; as Gertrude Stein said about Oakland, “when you get there, there isn’t any there there.” Once again, science and technology stretch the limits of what humankind can perceive… when we are willing to look through the eyepiece.

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Ardi, You Gorgeous Creature!

If my blog is the first you have heard of Ardi, you need to get out more. Ardipithecus ramidus is her species, “Ardi” is her nickname, and I love her. She is, I will admit, a bit old for me, and a bit dead. Four point four million years dead. So it is a bit of a Platonic love, even if she predated Plato by more years than the gent could have imagined were possible. She made the front page of the New York Times today (that’s the link above), with a photo spread online and everything, and I knew exactly what I was getting into when I clicked to look at the comments. I swear, the experimental studies on cognitive dissonance prove that creationists know they are liars: Festinger knew that we tend to look for confirming evidence–things that support what we already believe–and tend to avoid discomfirming evidence… but creationists are all over this story like stupid on Ken Ham, making excuses for what seems like the millionth nail in their pathetic coffin.

For those of you who love the archaeology/anthropology bit, have fun with all the wonderful articles and commentary. For those of you who also enjoy watching a nice train wreck… don’t forget to read the comment threads.

It’s predictable as sunrise; it’s predicable as tide;
As the evidence is published, it is just as soon denied.
“It’s the fossil of a monkey!” “Hey, my brother’s also short!”
“There is nothing in the Bible that’s denied by this report!”
“Evolutionist conspiracy!” I cannot list them all,
As if Ardi acts as proof there was Creation, and then Fall.
There will never be a fossil found to calm the silly storm,
That’s accepted as example that’s transitional in form.
The specimens were numerous, but never quite enough—
Unless you’ve found “the missing link”, they’re gonna call your bluff.

Our family tree has changed again, as many times before;
Each fossil was disputed in its turn, so what’s one more?
How comforting—there’s one thing that’s consistent from the start:
Creationists and ignorance will never, ever part.

As an aside… The NYTimes article, in part, states

The Ardipithecus specimen, an adult female, probably stood four feet tall and weighed about 120 pounds, almost a foot taller and twice the weight of Lucy. Its brain was no larger than a modern chimp’s. It retained an agility for tree-climbing but already walked upright on two legs, a transforming innovation in hominids, though not as efficiently as Lucy’s kin.

In one sentence, they identify Ardi as female; in the next and following, her pronoun is “it”. Wha? My pets have the privilege of gendered pronouns, but not my great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-…. great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-great-grandmother? (bonus points for whoever can fill in the ellipses within an order of magnitude) This is just not fair!

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Grand-Dad!


I have a small bottle of sepia ink
Which I use for particular writing.
The feel of a quill-pen is special, I think,
And I find the whole process exciting.

I read in the news, of an interesting find,
Of a well-preserved cephalo-fossil
(The paleontologists gladly remind,
What we learn may be truly colossal!

See, soft-tissue fossils are rare, as a rule,
So an ink-sac was quite unexpected—
This cephalofind was the coolest of cool,
As a rock that can still be dissected!)

The scientists ground up the fossilized sac
To make ink for its own illustration—
Some see this as fitting, while others attack
It as cruel (in unique presentation!*)

Myself, as his great-great-great-great-great-great-great
Great-great-grandson, I want his return.
His repatriation to Cuttle-Estate,
To his burial inkwell—er, urn.

*Anyone who does not follow this link and read the whole thing is a complete gooberhead. Just sayin’.

Cuttlecap tip to Karen–Thanks!

A Verse On The Echidna’s Four-Headed Penis

Ok, in truth, this was inspired by this post on Pharyngula, but that was not the whole point of PZ’s post, so I was going to use some other source… but frankly, if you google “echidna penis” you get more than, perhaps, you were looking for. Anyway, go ahead and do an image search for an echidna’s penis, and you will see that it has four heads. A little more looking into the available information about female echidnas, and you may understand why.

I count myself very grateful indeed that I am not an Echidna.

Two heads are better than one, so they say,
So four heads are better by far;
It took evolution to build this array,
And to humans, it still seems bizarre.

It never would work for a human male, though,
(Is it blessing, or is it a pity?)
See, men tend to think with their dicks, and we know
That nothing gets done by committee.

Selection Favors The Prepared Cephalopod

So I had read the news release, and thought “Ah! Finally, a chance to beat Myers to a post about cephalopods!” Silly me. You don’t tug on Superman’s cape; you don’t spit into the wind; you don’t pull the mask off the ol’ Lone Ranger, and you never try to beat PZ Myers to a story involving cephalopods. But I do have a cooler illustration (which I will put at the bottom, just for suspense; the first illustration is the same one PZ used), again from Mike McRae. I was not planning to post it yet, but this story is just too perfect.


The first illustration, from Science magazine; on the left is a fossil ammonoid; on the right, the vampire squid Vampyroteuthis infernalis. The vampire squid lives in water with very little dissolved oxygen; the ability to live in such conditions may be the reason for an explosion of cephalopods following the Permian Extinction. For more information, see PZ’s post, or the New York Times article, or even the Science article, if you have access.

The Permian Extinction wiped out ninety-plus percent
Of the creatures that had, by that time, evolved.
A rapid rise in atmospheric CO2 had meant
That the water had less oxygen dissolved.
(I know, I know, the animals on land were also hit,
But the news today is focused on the sea;
And you may call me biased—which I’ll readily admit—
So this story is more interesting to me!)
The ammonoids—the ancestors to octopus and squid,
And to cuttlefish (their greatest claim to fame)—
Were badly hurt, like all the rest; their population slid,
Ah, but from those few survivors, see what came!
The ammonoids exploded (metaphorically, of course),
Filling niches left by species that had died;
The few remaining species were selection’s vital source
For diversity to fill the planet wide.
Their secret to survival? One scenario is this:
They’d adapted to the cold, anoxic deep,
And the new conditions everywhere were like their old abyss,
So selection said: “I think, this one I’ll keep.”
When catastrophe sweeps multitudes from off the planet’s face,
Evolution makes the best of what’s still there;
This story shows that, sometimes, if you want to win the race,
Be a metabolic tortoise, not a hare!

Now, the beautiful illustration–a cephalopod version of Darwin’s “Tree of Life”!