Of Their Bones Are Coral Made

Full fathom five, or deeper still,
At rest within the ocean’s chill
The ocean currents may create
A home for fish and tiny krill
Where war machines have met their fate
The seascape changes, day by day
As predators now follow prey
To chase them into turret caves
And places they can hide away
In ships and tanks beneath the waves
A month goes by; the wreck conceals
Now, groupers, triggerfish, and eels
In every crevice, cave, and hole;
A shadow from above reveals
A shark or tuna on patrol
The algae fronds and coral fans
Have overgrown what once was Man’s,
Re-writing all his grand designs
And following their separate plans
They soften all the human lines.
Will corals act as Sandburg’s grass
As months and years and decades pass,
To cover death, and loss and grief
Until, through seas as clear as glass
We only view a coral reef?














Photos: David Doubilet/National Geographic (click to embiggen; you’ll be glad you did)

These gorgeous photos may be found in the February 2011 issue of National Geographic magazine, on newsstands January 25 (you can tell from the fact that Jan 25th has already passed, that this phrase is part of the contractual agreement with Nat Geo to use these wonderful pictures), in a photo-essay on a variety of artificial reefs—from deliberately sunken ships and tanks, to the supports of oil and gas rigs, to a cemetery where cremated remains, mixed into concrete, allow those who desire to spend their eternity sleeping with the fishes.  Over time, each artificial reef is transformed–“nothing of him that doth fade / but doth suffer a sea-change / into something rich and strange.”  There are more photos, and the accompanying essay, here: http://ngm.nationalgeographic.com/2011/02/artificial-reefs/doubilet-photography

Parenthetically… I have been a National Geographic fan for as long as I can remember.  When I mentioned this fact to my fellow travelers two years ago in Greece & Bulgaria, it turns out that the vast majority of them, in their secret heart of hearts, had fantasized about taking the same amazing trip we did, seeing the same sights, talking to the same people… but with a NatGeo press pass.  So when the NatGeo rep contacted me with the offer to use some of their pictures for a blog post, there was no possible way I would turn that down.  And even if it were not part of the agreement, the idea that I could legitimately close my post with an official National Geographic magazine cover is just soooo coooool.  I know I’m not actually writing for National Geographic.  But I can dream.

Ride The “Headless Monk” Haunted Water Slide!

While laying out the water slide
Behind the roller coaster,
Some workers felt an icy gaze
And so they called a ghoster.
If they had called the Scooby Gang
(in fact, I think they tried)
They’d see it was the guys who ran
The haunted water slide
They’re honest as the day is long
(at night, there’s some duplicity—
They started silly rumors for
A bit of free publicity!)
But no, they called a different man—
A paranormal whiz—
Who used, in part, a Ouija Board
To tell us what it is!
And Orbs showed up in photographs!
(I’ll tell you, if I must—
They’re just a well-known artifact
Of camera-flash and dust!)
It seems that this anomaly
While living, was a monk,
Who, having somehow lost his head
Was rather in a funk.
He wandered ‘round Thorpe Park at night
And sometimes in the day
Though having no more mouth, of course
There’s nothing he would say.
But workers felt his icy gaze,
I note (with some surprise—
It seems to me, a headless monk
Is also missing eyes)
There are, of course, some skeptics
Who deride this as a trick…
And we could not get a comment
Out of Nearly Headless Nick.
There’s a lot going on in the world today.  Tough for a fluff story like “New Water Ride At Amusement Park” to, er, make a splash.  Unless… didn’t I see this on Scooby Doo?  (Even Tim Minchin’s “Storm” remembers this!)  It’s a haunted water slide–and not just that, but one duly investigated by a paranormal expert!  Who used the ideomotor effect a Ouija Board, and photos of lens flare and dust motes caught in the camera flash anomalous photos and orbs to verify, there really is something strange in your neighborhood!  
The Southwest London Paranormal Team, though, are unashamed to use these long-debunked methods, and based on their testimony (and additional evidence of underground anomalies, found by a geophysicist), the ride was moved.  Some months ago, it appears, given the progress on the ride in its new location.  My, my, it wouldn’t surprise me a bit if it was up and running by the time the summer season opens.  If only there were a way to get this park a bit of publicity…

Ride The “Headless Monk” Haunted Water Slide!

While laying out the water slide
Behind the roller coaster,
Some workers felt an icy gaze
And so they called a ghoster.
If they had called the Scooby Gang
(in fact, I think they tried)
They’d see it was the guys who ran
The haunted water slide
They’re honest as the day is long
(at night, there’s some duplicity—
They started silly rumors for
A bit of free publicity!)
But no, they called a different man—
A paranormal whiz—
Who used, in part, a Ouija Board
To tell us what it is!
And Orbs showed up in photographs!
(I’ll tell you, if I must—
They’re just a well-known artifact
Of camera-flash and dust!)
It seems that this anomaly
While living, was a monk,
Who, having somehow lost his head
Was rather in a funk.
He wandered ‘round Thorpe Park at night
And sometimes in the day
Though having no more mouth, of course
There’s nothing he would say.
But workers felt his icy gaze,
I note (with some surprise—
It seems to me, a headless monk
Is also missing eyes)
There are, of course, some skeptics
Who deride this as a trick…
And we could not get a comment
Out of Nearly Headless Nick.
There’s a lot going on in the world today.  Tough for a fluff story like “New Water Ride At Amusement Park” to, er, make a splash.  Unless… didn’t I see this on Scooby Doo?  (Even Tim Minchin’s “Storm” remembers this!)  It’s a haunted water slide–and not just that, but one duly investigated by a paranormal expert!  Who used the ideomotor effect a Ouija Board, and photos of lens flare and dust motes caught in the camera flash anomalous photos and orbs to verify, there really is something strange in your neighborhood!  
The Southwest London Paranormal Team, though, are unashamed to use these long-debunked methods, and based on their testimony (and additional evidence of underground anomalies, found by a geophysicist), the ride was moved.  Some months ago, it appears, given the progress on the ride in its new location.  My, my, it wouldn’t surprise me a bit if it was up and running by the time the summer season opens.  If only there were a way to get this park a bit of publicity…

Size Matters: The Daphnia Genome

The Daphnia, or water flea,

Contains more genes than you or me;
Five thousand more at least, you see,
The most we’ve seen amass!
The Daphnia’s thirty-one thousand genes
Allow adaptiveness, which means
Its features change to match the scenes
As generations pass
The Daphnia is closely tracked;
As waters change, these fleas react,
Evolving spikes that once they lacked
Which make them tough to swallow
To predators, to day and night,
To changes from pollution’s blight,
To water change, however slight,
Mutations soon will follow
The genes of Daphnia create
New copies at a higher rate—
A rate perhaps three times as great
As similar crustaceans
Environmental pressures yield
A spear-like tail, or spiky shield
Which reproduction soon revealed
Were useful adaptations
Our egotistic human eyes
Dismiss these useless little guys
And focus on our larger size
Which demonstrates our worth
But as our chromosomes are mapped
We find the Daphnia more apt
To test the waters, then adapt
And populate the earth
NPR reports on the results of a recent genome analysis, of one of the most well-studied organisms around… one you may have accidentally swallowed while swimming in a lake, without realizing it.  Now, I don’t have access to Science, but a quick search found a press release from one of the many universities involved: 

Scientists have studied Daphnia for centuries because of its importance in aquatic food webs and for its transformational responses to environmental stress. Predators signal some of the animals to produce exaggerated spines, neck-teeth or helmets in self-defense. And like the virgin nymph of Greek mythology that shares its name, Daphnia thrives in the absence of males — by clonal reproduction, until harsh environmental conditions favor the benefits of sex.

Arguably, more is known about the ecology and stress biology of the water flea than any other animal. The genome project was conceived with an expectation that many new gene functions would be uncovered when studied in light of the animal’s natural environment — not necessarily expecting to discover many more genes.

Yet, Daphnia’s genome is no ordinary genome.

“Daphnia’s high gene number is largely because its genes are multiplying, by creating copies at a higher rate than other species,” said project leader and CGB genomics director John Colbourne. “We estimate a rate that is three times greater than those of other invertebrates and 30 percent greater than that of human.”

“One theory is that Daphnia is so good at adapting to so many environments because it has this huge catalog of genes to call upon,” says Thomas. The researchers note that more than one-third of Daphnia’s genes are undocumented in any other organism – they are completely new to science.

Daphnia, as I understand it, have been used as a barometer of lake condition, because they are so sensitive to conditions, and so quick to adapt (across generations, not within).  The combination of an environmentally sensitive species well studied as an ecoresponsive indicator, and a thorough understanding of the underlying genetics, will allow an unprecedented depth of understanding in examining epigenetic processes.

Or, maybe I misunderstood everything.

An update, of sorts.  I just saw this really nice pdf file of my verse.  Apparently, I’m listed on the Daphnia Genomics Consortium Collaboration Wiki… and apparently, somebody made a really nice pdf of my verse without asking (tsk, tsk!).

Size Matters: The Daphnia Genome

The Daphnia, or water flea,

Contains more genes than you or me;
Five thousand more at least, you see,
The most we’ve seen amass!
The Daphnia’s thirty-one thousand genes
Allow adaptiveness, which means
Its features change to match the scenes
As generations pass
The Daphnia is closely tracked;
As waters change, these fleas react,
Evolving spikes that once they lacked
Which make them tough to swallow
To predators, to day and night,
To changes from pollution’s blight,
To water change, however slight,
Mutations soon will follow
The genes of Daphnia create
New copies at a higher rate—
A rate perhaps three times as great
As similar crustaceans
Environmental pressures yield
A spear-like tail, or spiky shield
Which reproduction soon revealed
Were useful adaptations
Our egotistic human eyes
Dismiss these useless little guys
And focus on our larger size
Which demonstrates our worth
But as our chromosomes are mapped
We find the Daphnia more apt
To test the waters, then adapt
And populate the earth
NPR reports on the results of a recent genome analysis, of one of the most well-studied organisms around… one you may have accidentally swallowed while swimming in a lake, without realizing it.  Now, I don’t have access to Science, but a quick search found a press release from one of the many universities involved: 

Scientists have studied Daphnia for centuries because of its importance in aquatic food webs and for its transformational responses to environmental stress. Predators signal some of the animals to produce exaggerated spines, neck-teeth or helmets in self-defense. And like the virgin nymph of Greek mythology that shares its name, Daphnia thrives in the absence of males — by clonal reproduction, until harsh environmental conditions favor the benefits of sex.

Arguably, more is known about the ecology and stress biology of the water flea than any other animal. The genome project was conceived with an expectation that many new gene functions would be uncovered when studied in light of the animal’s natural environment — not necessarily expecting to discover many more genes.

Yet, Daphnia’s genome is no ordinary genome.

“Daphnia’s high gene number is largely because its genes are multiplying, by creating copies at a higher rate than other species,” said project leader and CGB genomics director John Colbourne. “We estimate a rate that is three times greater than those of other invertebrates and 30 percent greater than that of human.”

“One theory is that Daphnia is so good at adapting to so many environments because it has this huge catalog of genes to call upon,” says Thomas. The researchers note that more than one-third of Daphnia’s genes are undocumented in any other organism – they are completely new to science.

Daphnia, as I understand it, have been used as a barometer of lake condition, because they are so sensitive to conditions, and so quick to adapt (across generations, not within).  The combination of an environmentally sensitive species well studied as an ecoresponsive indicator, and a thorough understanding of the underlying genetics, will allow an unprecedented depth of understanding in examining epigenetic processes.

Or, maybe I misunderstood everything.

An update, of sorts.  I just saw this really nice pdf file of my verse.  Apparently, I’m listed on the Daphnia Genomics Consortium Collaboration Wiki… and apparently, somebody made a really nice pdf of my verse without asking (tsk, tsk!).

The Digital Pack-Rat, Vol. 24

Wow!  Looking back over the archives, I see it has been over a year since my last Pack-Rat post.  I’m certain there are dozens of verses I’ve let fall through the cracks in that time, but now I have at least rescued the ones from January and early February of this year.  If I ever get motivated, I might go fishing through the previous months as well.  Probably not.  Anyway, the link below each verse will bring you to the post where I found it, should you desire any context.  
When Russia launched their satellite
I watched it from Wasilla
While keepin’ watch for freedom’s sake,
A patriot guerilla.
This “Sputnik moment” I recall
From element’ry school—
I didn’t listen, though, because
It wouldn’t have been cool.
But now, they ask me questions, cos
I want to run for POTUS;
I’ll make up something dumb instead—
My base will never notice.
http://scienceblogs.com/pharyngula/2011/01/speaking_of_wtf_moments_heeeee.php
Higglety-Pigglety
Kenneth the porcophile
Feels that Kentuckians
Don’t care for Ham–
Thinking so backwards it’s
Antediluvian;
Most of them probably
Don’t give a damn.
http://scienceblogs.com/pharyngula/2011/01/its_so_easy_to_make_him_mad.php
Believers offended? Well, pardon my shrug;
They’ll call me a wimp, or they’ll call me a thug;
They think it’s a feature–it’s really a bug,
So yes, I’m a little bit smug.
The arguments come and the arguments go
There’s always one hiding they promise to show
That will tear me asunder! They strut and they crow,
But does it arrive? Sadly, no.
The dusty old logic that’s polished anew
The same dead-end leads that they used to pursue;
It’s tough to defend such a bankrupt world view
When the truth is, it’s simply untrue.
http://scienceblogs.com/pharyngula/2011/01/why_isnt_anyone_talking_about.php
Rebecca had a heart of gold–
At least, she said, gold-clad
She promised it was mine alone
But now I’m feeling sad
I thought her quite a treasure then,
But now I’m filled with doubt:
It wasn’t worth a nickel
Once I cut the sucker out.
http://scienceblogs.com/pharyngula/2011/01/how_innumerate_are_americans_a.php
To the best of his ability,
The Pope, in his nobility
Affected a fragility
Through Papal force of will
So he (I’m feeling catty) can
Pretend the gilded Vatican
Is destitute and ratty, and
Have others foot the bill.
http://scienceblogs.com/pharyngula/2011/02/poor_vatican.php
It’s disgusting and immoral
But it isn’t sex–it’s oral,
Which, by presidential precedent, is perfectly ok
Though it’s true you spilt your semen
You can blame it on the demon
And we’ll tell the press it’s good you’re not a pedophile or gay.
An exorcist can exercise
Between her lips, but not her thighs
The sacrosanct vagina is off limits to a priest!
When the church’s inquisition
Finds abuse of your position,
Not a soul alive expects a penance greater than the least.
http://scienceblogs.com/pharyngula/2011/02/creepy_priest_and_a_church_wit.php

The Digital Pack-Rat, Vol. 24

Wow!  Looking back over the archives, I see it has been over a year since my last Pack-Rat post.  I’m certain there are dozens of verses I’ve let fall through the cracks in that time, but now I have at least rescued the ones from January and early February of this year.  If I ever get motivated, I might go fishing through the previous months as well.  Probably not.  Anyway, the link below each verse will bring you to the post where I found it, should you desire any context.  
When Russia launched their satellite
I watched it from Wasilla
While keepin’ watch for freedom’s sake,
A patriot guerilla.
This “Sputnik moment” I recall
From element’ry school—
I didn’t listen, though, because
It wouldn’t have been cool.
But now, they ask me questions, cos
I want to run for POTUS;
I’ll make up something dumb instead—
My base will never notice.
http://scienceblogs.com/pharyngula/2011/01/speaking_of_wtf_moments_heeeee.php
Higglety-Pigglety
Kenneth the porcophile
Feels that Kentuckians
Don’t care for Ham–
Thinking so backwards it’s
Antediluvian;
Most of them probably
Don’t give a damn.
http://scienceblogs.com/pharyngula/2011/01/its_so_easy_to_make_him_mad.php
Believers offended? Well, pardon my shrug;
They’ll call me a wimp, or they’ll call me a thug;
They think it’s a feature–it’s really a bug,
So yes, I’m a little bit smug.
The arguments come and the arguments go
There’s always one hiding they promise to show
That will tear me asunder! They strut and they crow,
But does it arrive? Sadly, no.
The dusty old logic that’s polished anew
The same dead-end leads that they used to pursue;
It’s tough to defend such a bankrupt world view
When the truth is, it’s simply untrue.
http://scienceblogs.com/pharyngula/2011/01/why_isnt_anyone_talking_about.php
Rebecca had a heart of gold–
At least, she said, gold-clad
She promised it was mine alone
But now I’m feeling sad
I thought her quite a treasure then,
But now I’m filled with doubt:
It wasn’t worth a nickel
Once I cut the sucker out.
http://scienceblogs.com/pharyngula/2011/01/how_innumerate_are_americans_a.php
To the best of his ability,
The Pope, in his nobility
Affected a fragility
Through Papal force of will
So he (I’m feeling catty) can
Pretend the gilded Vatican
Is destitute and ratty, and
Have others foot the bill.
http://scienceblogs.com/pharyngula/2011/02/poor_vatican.php
It’s disgusting and immoral
But it isn’t sex–it’s oral,
Which, by presidential precedent, is perfectly ok
Though it’s true you spilt your semen
You can blame it on the demon
And we’ll tell the press it’s good you’re not a pedophile or gay.
An exorcist can exercise
Between her lips, but not her thighs
The sacrosanct vagina is off limits to a priest!
When the church’s inquisition
Finds abuse of your position,
Not a soul alive expects a penance greater than the least.
http://scienceblogs.com/pharyngula/2011/02/creepy_priest_and_a_church_wit.php

New Roots On The Family Tree

The salient features

Of human-ish creatures,
Our sisters and brothers and cousins,
Across generations
Shows slight variations
And species, it seems, by the dozens
The picture’s still muddy,
As scientists study,
Concerning our relatives’ species
The task is colossal
Inferring from fossils
Of footprints, or bones, teeth, and feces
The clues, though, are leading
To claims of cross breeding
In hominids once thought distinct
With two populations
In different locations
With whom we’re genetically linked
It’s really exciting—
You see, we’re re-writing,
As only hard evidence can,
The view, now outdated
That claimed that we mated
With only the sapiens clan
In NPR’s 13.7 blog, Ursula Goodenough writes of recent research on hominid genomes, and the increasingly varied story of our family tree.  To take just one tidbit, it appears that the locals of Papua New Guinea are “roughly 92.5% African, 2.5% Neanderthal, and 5% Denisovan”–that is, this population (with which the rest of us are interfertile, of course) has genetic material belonging to two extinct hominid species, whom we had previously believed were distinct from (read: non-interbreeding with) H. sapiens.  We knew we shared common ancestry with them, but the notion that they are among our direct ancestors (for some modern populations, at least) is new.
As I tell my students, Darwin’s Origin of Species was ironically titled, because evolution by natural selection makes obsolete the concept of “species” as it was used at the time (or as creationists still use it).  Rather, as populations vary across time and geography, black and white distinctions simply do not exist.  Take the example of ring species, for instance, where neighboring populations can interbreed just fine, but populations a bit further apart (geographically, or chronologically, it works both ways) cannot, despite a continuous line of interbreeding populations linking the two.  Where is the species line to be drawn?  Are these one species, or two?
Frankly, it’s a bit like Pluto.  Pluto is what it is, whether it is called a planet or a planetoid; our linguistic handle on it is for our sake, and simply allows us to talk about it.  The concept of “species” is a similar abstraction; tremendously useful in some cases, impossibly vague in others.  
H. sapiens, H. erectus, Neanderthal, Denisovan, and more… which are “us”?  It depends on the context.  
This, like Pluto, may take some getting used to.  Human exceptionalism (not to mention the historical influence of creationism) and ego (“what a piece of work is man…”) have expressed themselves in a history of dehumanizing our ancestors.  Neanderthals are still brutes in the public eye (so easy a caveman could do it), despite recent attempts to update their image.  It would be difficult to maintain our belief that we are the pinnacle of creation, the top of the evolutionary ladder (yes, I know the metaphor is wrong), the final product of nature, if we must also recognize that by some measures we are far more closely related to Neanderthals than we had thought.   

Whoopie For ME!

Another day
Another vote
Another issue
We’re taking note
We’re all a-waiting
While they’re debating
They’re talking Whoopie
Is this for real?
Are they insane?
What’s taken over
The state of Maine?
The new election
Of state confection
They’re talking Whoopie
Picture a crème-filled sandwich
It’s sugar mixed with lard
Something that fits your hand, which
Will make your arteries hard
From Madawaska
To southern Kittery
Seems this much sugar
Will make you jittery
This pressing issue
Will make you wish you
Were talking Whoopie
Picture a Down-East picnic
What’s on your plate to see?
You give your fork a quick lick
Blueberry pie, for me!
They need a budget
Or folks will hurt
They say, “let’s fudge it
And talk dessert
This legal action
Is mere distraction
They’re talking Whoopie
For those too lazy to click links… the state of Maine is debating the adoption of a State Dessert, the Whoopie Pie, which was invented in Pennsylvania.  Me, I’m in favor of Blueberry Pie as the state dessert; if a state dessert can’t turn your smile blue, what good is it?

The Dictionary Atheist Baby

I looked at my cute little atheist baby
(With wonderful new-baby smell!)
And thought that she might be more accurate, maybe
With other descriptors as well
The privative “atheist”, so I’ve been told
Is a measure of what she is not;
It’s clearly the case, if I might be so bold,
There are more words describing the tot:
My baby is flightless; my babe is unwed;
She’s not blonde, for there isn’t a hair on her head;
She’s scale-less, of course, for as much as I’d wish
She has no hint of Mermaid, or tidbit of fish;
She’s hatless, for now, till I give her a hat,
And cloudless as well, though I’m glad about that;
She’s treeless, which helps her to fit in her cot,
And windowless—windows, again, she has not.
She has plenty of cute—I shall not call her cuteless—
And she’s sweeter than Mom’s Apple Pie;
But listing her negatives clearly is fruitless
When privatives do not apply.
In case the verse wasn’t blatant enough… I come down on the side that babies are not “dictionary atheists”, nor are trees, rocks, fish, clouds, or galaxies.  They are undefined with regard to religious terms.  (Ok, they are undefined in my view; some (but not all) religions claim membership from babies, and it is not relevant that the baby actively believe.  This baby is (culturally) orthodox, that one is muslim, even though they have not chosen this membership.  Other religions wait–the anabaptist tradition requires the active choice on the part of an individual to join the church; prior to that, you may be unsaved or perhaps “innocent”.)
In my (privative) view, if there were no religious believers, there would of course be no atheists.  The label would have never been invented, and would have no meaning.  We are all, right now, aflargists, because none of us are flargists.  We are all amulxists, because none of us are mulxists.  I could make up dozens of undefined things we are not.  But I prefer it when words actually have meaning, and give useful information.  It makes no sense to call my baby flightless, although she is “dictionary flightless”.  Since no babies are (I have asked them) active believers in any particular religion, it makes no sense at all to call them atheists.  It is simply a dimension which is undefined with regard to babies.