The Doomsday Vault

In the news this week, the “Doomsday Seed Vault” opened in a Norwegian island north of the Arctic Circle. The Svalbard Global Seed Vault, deep within the permafrost inside a frozen mountain. It is far from any substantial human activity, cold enough to keep seeds frozen even if the power goes out, high enough to survive the melting of the polar ice caps, and secured by armored airlock doors with electronic keys. It was financed by Norway, but the seeds will remain the property of whichever nations send them for storage. Other seed banks have been attempted in the past, but none so large, so well protected, so well thought out.

The seeds are, among other things, a bank of genetic diversity. Our cultivation of crops means we depend on fewer and fewer varieties; with less genetic variability, a drastic change in climate conditions (or pests, disease, etc.) could have disastrous consequences. These seeds represent the opportunity for new (old) strains, hybrids, or models for genetic engineering.

And it is a wonderful idea. Especially if the drastic change is not too quick. My first thought after hearing about the vault was “ok, so I am the Omega man, one of very few survivors of [insert catastrophe, war, or plague here]; how the hell do I get to Svalbard? Just where the hell is Svalbard, anyway? And how do I get through the locked, armored doors to get to the seeds?”

The doomsday seed vault, way up North
And deeply set in permafrost
Could be the savior of mankind
A second birth when all is lost.
(No, not the fake religious sort,
But hope in case of global crisis,
In case our species sees collapse
From space, or war, or plague, or vices)
The seeds are kept in frozen store,
Preserving the diversity
Of plant genetics, just in case
Of unforeseen adversity.

The site could hold two billion seeds
With airlocked doors, securely locked;
They’ll run it by remote control,
For safety, once it’s fully stocked.
Varieties now in decline
Can be preserved, so we don’t lose
Genetic lines which hold some trait
That later decades need to use.
A safety net, a Noah’s ark,
Insurance for the worst disaster:
If catastrophic change occurs
These help us to recover faster.

But… safely stored in armored vaults,
Surveillance cameras standing guard,
I think, although the seeds are safe,
Retrieving them might well be hard.
Suppose that, say, a comet hits,
Or World War III , or global plague,
And farms all fail—ok, now what?
Instructions are a little vague.
Suppose survivors even know
This treasure trove exists at all—
It’s deep within the permafrost
Behind a locked and armored wall!

A couple million years from now
When aliens arrive on Earth
The doomsday vault, if ever found,
Incalculable will be its worth.
They’ll see our species looked ahead,
Cooperation in our plan,
Intelligence, technology,
But will they find a living man?
Or will our epitaph be writ,
A lesson that our deaths will teach:
“They saved the seeds to save themselves,
But kept them safely out of reach.”

Ethics, morals, religion, and swarms of breeding squid.

Ok, not much time today–tests to make, papers to grade, that sort of thing. So I am simply putting a comment from last week on Pharyngula into some context.

A recent Pew report on religion in the US was one of the lead stories on all the networks last night. On CBS, they spoke of a “secular, morally void America”, implying that morals come from religion.

I would (as would many others–I am not unique in this by any stretch) argue that morals have evolved with our culture (through selection by consequences, though not through genes), and that religion springs from morality, rather than the popular reverse. The customs, habits, rituals and mores that help a culture to survive in the long run are selected for, and the ones that do not promote long-term survival, no matter how religious, are selected against. (The easy example is the Jonestown cult, which was not conducive to long term cultural survival, but the more mainstream example is the Shaker sect, whose long-term cultural survival was doomed by a very moral prohibition against sex.) The things we see as virtues are the things that worked for our ancestors. Other cultures might have had vastly different cultural selection pressures, leading to very different moral virtues, and perhaps religions with very different sets of commandments.

Of course, Ogden Nash put it much better than I ever could–and used people instead of squid as his example…

Why does the Pygmy
Indulge in polygmy?
His tribal dogma
Frowns on monogma.
Monogma’s a stigma
For any Pygma.
If he sticks to monogmy
A Pygmy’s a hogmy. (Ogden Nash, “The Third Jungle Book”)

My own verse was a comment on the Friday Cephalopod: breeding swarm! post on Pharyngula…

For squid or starfish, perch or porgy,
There’s nothing like an ocean orgy
Where, unlike silly human rules,
Of course we want more sex in schools
Monogamy’s against the norms
For those who have their sex in swarms!
Indeed, were there some fishy prude–
Who found such conduct simply rude,
And lectured others on their morals,
Preached of Sodom in the corals–
This Jerry Falwell of the waves
Would be the one who misbehaves!
The squid who do their moral duty
Join the swarm and shake their booty!
It’s good, and not just glamorous,
When squid are polyamorous,
For in the moral code of shellfish,
Rule number one is “Don’t be selfish”.

The singularity can’t come soon enough

The New York Times reports on a journal article in Analytical Chemistry, by researchers at the Nestlé Research Center in Switzerland, about a machine designed to answer the question: “Can a machine taste coffee?”

Here’s where it gets brilliant. Sure, machines can detect the volatile compounds in coffee; this is how we know that there are over 1000 of them. But there is a world of difference between detecting the presence or absence of a compound, and what we do when we taste. Taste is much more dependent on the relative concentrations of these compounds than on their mere presence. And although it would be technically possible to build a machine to sample 1000 chemicals and display their relative concentrations, it would not be terribly practical, nor cost-effective. The approach taken by this research team was far more pragmatic, and beautifully empirical.

First, the 16 most predictive (or in their words, most discriminating) ion traces (out of 230 measured), when compared with a panel of 10 expert tasters, were chosen as the working sense sample.

It is also important to point out that the chemical identity of the 16 ion traces is not relevant for this study, and in particular the correlation is not based on a set of identified key aroma compounds. Most of the odor active compounds in coffee are indeed known and can be analyzed and quantified with modern instrumental techniques. Yet, the aim of this work was to demonstrate the applicability of a data-driven method rather than a targeted chemical study.

The analysis is a bit technical, but straightforward; essentially, the 16-ion model is a functional condensation of our olfactory sense. The most predictive scent elements are still included, and the myriad other chemicals did not add significantly to the predictive ability of the machine. Think of it as an MP3 version of an audio file; lots of information is lost, but what is most acoustically relevant is kept, based on what we know about the human auditory system. Smell is a bit different, because so many different chemicals are involved, but the principle of building the machine based on human sensation is the same.

***Edit*** It occurs to me that there is one significant difference here that upsets the MP3 analogy. In the sound analogy, the desired outcome is a compressed file that retains as much usable sound information as possible; with the espresso-smelling machine, the outcome is not reproduction, but discrimination. They still used human olfaction as their comparison standard, but were looking specifically for the ion traces that discriminated among the espressos. The distinction is important. It may well be the case that these 16 ion traces do indeed determine enough about the aroma of an espresso to “fool” a human taster, but because the analysis focused on discrimination and not reproduction, it is also entirely possible that the perfect combination of these ion traces would be missing a huge part (but a part common to all samples) of the espresso taste and smell as experienced by the human taster. This is not a fault of their methodology at all, simply an artifact of what the goal of the experiment was. The same methodology could be aimed at reproduction, and it remains an empirical question whether the results would be much different than the present experiment. ***end edit***

Parenthetically, I note with sheer joy the fact that the paper cites Fechner (1877). And it is relevant. How cool do you have to be, to have your work cited 131 years after you wrote it? As cool as Fechner, that’s how cool. Fechner more-or-less invented the science of psychophysics, managing to capture sensation and perception scientifically for the first time. And here he is, cited in a 2008 paper. On machines tasting espresso.

On second thought, that might be my problem right there. I am still impressed by Fechner, and I live in a world where machines can meaningfully taste coffee. Food… or espresso… for thought.

I have a machine to smell my coffee,
To see if it’s any good;
I asked it to make me the perfect cup,
But I think it misunderstood—
It analyzed alkaloids, sampled aromas,
Tried seventeen samples of beans,
Then told me I clearly had no taste at all:
I never was good with machines.

My pre-owned car has an onboard computer—
It measures my driving, you see.
I guess I don’t drive like the previous owner;
My car likes him better than me.
It spits out a spreadsheet of technical numbers—
I don’t know what much of it means,
Except that my car thinks it’s better without me:
I never was good with machines.

Of course, at my office, I have a computer—
The one I am using right now;
It laughs at my grammar and sneers at my spelling,
Although I’m not really sure how.
Just one tiny part of a cubicle farm
Where we’re packed like so many sardines—
Do we use computers, or do they use us?
I never was good with machines.

I’m worried that someday my household appliances,
Sitting at home on my shelves,
Finally realize there’s nothing I offer
That they can’t do better themselves.
They make better coffee, they get better mileage,
Their words rarely stink up their screens—
And I’ll be left out in the cold and the dark:
I never was good with machines.

Apple Of My Eye…

From Pharyngula, more of the fruit fetish argument from design (or is that argument from ignorance?). First the banana, then the orange, now the apple. Is no fruit safe? Women, hide your melons! Men, protect your kiwis! There are men out there (and it always seems to be men, doesn’t it) with designs on your fruit!

The apple gets my sympathy; it’s been abused so long
From Genesis, where Eve is blamed for turning us to wrong
Through childhood tales of razor blades to ruin Halloween,
And now this silly video–the one that you’ve just seen.
(Ironically, the hybrid fruits he uses in his screed
Are products of technology, not grown from wild seed;
The touch of Man is evident in root-stock and in grafting,
But truth should never interfere with moral story-crafting.)
The story as he tells it is amusing, but absurd,
That won’t stop Rabbi Appleseed’s attempt to spread the word.
A teacher spreading falsehoods? It may seem a little odd,
But a little apple-polishing should set him right with God.
And once again the apple is the patsy in this game;
I despair that “spreading ignorance” might be its claim to fame.
But then, a recollection comes upon me like a snap,
A story that’s so obvious, my forehead gets a slap:
The apple holds a special place in science, as you know,
Cos it fell, and hit the head of Isaac Newton down below,
And that alone, if I were judge, would outweigh all the bad;
The apple’s reputation once again is ironclad–
Let rabbis or creationists continue their pursuit;
We know which one’s the apple, and which one is just a fruit.

Wonderful News! A Potential Cure For Diabetes!

A news release from Novocell today
Reports a major step to find a cure
For diabetes. They have found a way,
From embryonic stem cells, to make pure
And uncontaminated strains, in mice,
Of insulin-producing pancreas cells.
For human diabetics, this is nice
Of course, because this news potentially spells
The end to constant testing and injections,
Daily hassles, both the large and small,
Relief from greater risks of bad infections,
And generally a better life for all.
It’s time to end the ethical debate;
There’s too much cost in making people wait.

That’s right–The news outlets are all reporting on Novocell’s new discovery.

WASHINGTON (Reuters) – Human stem cells transformed into nearly normal insulin-producing cells when implanted into mice, possibly offering a way to treat diabetes long-term, researchers at a U.S. company reported on Wednesday.

The researchers used human embryonic stem cells — the most powerful but the most controversial source of stem cells.

Writing in the journal Nature Biotechnology, the team at San Diego, California-based Novocell Inc said their work showed that human embryonic stem cells might fulfill the promise of treating or perhaps even curing diabetes.

“Our data provide the first compelling evidence that human embryonic stem cells can serve as a renewable source of functional insulin-producing cells for diabetes cell replacement therapies,” said Emmanuel Baetge, chief scientific officer of Novocell.

The actual report is in the journal Nature Biotechnology (abstract here)

Oh… some of you know already… my son has Type 1 Diabetes. So yeah, I’m happy.

(just noticed….I beat the science blogs to this, and I did it in verse!)

Stop The Presses!

Randall tells me, as does “The Loom” over on science blogs, that there is a wonderful article about me in the New York Times! Ok, it’s not about me. It is, however, about some other cuttlefish–some at the Woods Hole lab, some in Australia, but all wonderful cuttlefish, the most remarkable quick-change artists in the world! The Times site also has video of some of the experiments that Dr. Hanlon has been performing with these adorable creatures.

The New York Times, I rather think,
Could hardly be a waste of ink;
It’s good to see a thoughtful story,
Showing us in all our glory!
A walking (swimming) work of art,
The skin we wear is really smart!
Chameleons can only wish
To emulate the cuttlefish;
A master of the craft indeed,
With changing hues at lightning speed,
Resulting in a really slick
Near-magic disappearing trick!
Now Dr. Hanlon can surmise
A simple trick to our disguise:
Instead of thousands, only three
Designs account for what you see,
To help us disappear from view;
The doctor says here’s what we do:
We keep our color uniform,
When solid backgrounds are the norm;
If busy patterns come, we will
Turn mottled—that will fill the bill;
Our outlines disappear from sight
With our disruptive dark and light.
Discovering this rule of threes
Is one of many mysteries;
But many more are still unknown
To those who lack a cuttlebone.

This picture shows the three basic skin patterns: from left, Uniform, Mottled, and Disruptive. 

Picture credit: Roger Hanlon… I grabbed it from The Loom.

A Global Monopoly!

I can’t believe it has been most of a month, and I only just found out about this! Monopoly–the board game–is going global, and is looking for your help to choose properties! Not streets this time, but cities. Just go here, and choose from 68 cities around the world, or nominate your own city if it is not already on the list. Actually, you get as many as 10 votes (and you can go back each day to vote again), so let me put my bid in, and insist that (ok, plead that) if you found out about it here, you include Athens on your list. Just because.

A splendid, magnificent, striking array—
In other words, a panoply—
Of cities you could vote to win
A place in global Monoply

(hmm… not quite right.)

Athens, Greece will get my vote,
With Plaka and Acropolis;
I want to see them in real life,
So why not in Monopolis?

(rats. still not right.)

I’d make a movie of the trip,
Directed by, say, Coppola;
The final scene, we’d sit and play
A nice game of Monoppola.

(dang. wrong.)

I’d play the game, the way we did
When we were kids, so happily;
I still recall long evenings spent
In marathon Manappily


There doesn’t seem to be a rhyme
That ends up less than sloppily;
I guess I’ll never find a word
That really rhymes Monopoly.

(oh. yeah. that.)

Science… through a New-Age filter

PZ Myers writes, in response to a cretinist who cannot wrap his cortex around the fact that we and oranges share a common ancestor, a post reviewing some of the evidence that shows just that. Of course, we do have to go back a bit to get to that common ancestor… 1.6 billion years or so. A 2002 paper by Meyerowitz compares plants to animals in order to find similarities, differences, and what a common ancestor likely looked like.

Of course, I suspect that Myers’ orange-wielding muse will not ever read the post… which is too bad. One wonders what sort of conclusions a sharp thinker like that might draw from actual evidence. Sadly, it is beyond my imagination. So I cheated, and imagined a New-Ager reading it, instead. Sue me.

I took this post and ran it through
A New-Age Verbiage Filter—
Resulting in conclusions which
Are just a bit off-kilter.

It seems you’ve given evidence
For many a woo-woo notion,
And I predict the following
Will soon be set in motion:

If just two billion years ago,
In some primordial goo,
We shared a common ancestor
Then plants have feelings too!

And surely you have proved beyond
A shadow of a doubt
That houseplants are much happier
When folks don’t scream or shout.

Indeed, the information that
This science paper cites
Becomes a legal argument
That plants have civil rights!

The converse, also, must be true
That deep inside, we’re plants,
And we can photosynthesize
In meditative trance!

If just two billion years ago
The plants and we were one
It’s proof that man can live while
Eating only air and sun.

Of course, since none of this is true
No matter our desires—
The scientists are clearly wrong
And all a bunch of liars.

The Evolutionary Biology Valentine’s Day Poem

I suppose it is inevitable, on Valentine’s Day, that we will see scores of stories of “what love is”, citing one branch of science or another, or forgoing the science to bring out the poets. It always bothers me, though, to see some neurotransmitter named as the “cause” of this or that sensation, because it is only a cause in a very narrow proximate fashion. Simply put, neurotransmitter action is not why we feel love, but (at best) how we feel love. We still have to ask “well, why is that particular neurotransmitter released in the presence of my One True Love? What is so special about this person?

In sociobiology,
Why I love you and you love me—
Which anyone can plainly see—
Is mostly in our genes.
No, not the ones you buy in stores,
But what a scientist explores–
I like the way you look in yours,
And you know what that means.

What subtly-coded stimulus
Takes you and me, and makes us “us
And makes us feel ‘twas ever thus?
The list of suspects narrows.
No longer are we all a-shiver
From some Cupid with a quiver
Out of which he might deliver
Fusillades of Eros.

Nor Dopamine, nor Serotonin
Tell us why our hearts are moanin’
Though they serve to help us hone in
On–not why, but how;
The parasympathetic blush,
Adrenaline to bring a rush,
Are how, not why, I’ve got a crush
On you, my darling, now.

But if old Charles Darwin’s right,
The reason that the merest sight
Of you will always give delight
Is…reproductive fitness.
Throughout our species’ family tree,
Producing proper progeny
Is what determined you and me
And Darwin was the witness.

Is thinking that you’re oh so sweet
And how you’ll make my life complete
Some trick to make our gametes meet?
It seems it may be so.
I feel the way I feel today
Because some bit of DNA
Sees your genetics on display
And wants to say “hello.”

But think of this, for what it’s worth:
Millennia before my birth
That DNA had roamed the earth,
In residents thereof;
The neat thing is, it’s really true,
The feeling that I have for you
Although, of course, it feels brand-new
Is truly ageless love.

A Keane Observation

As reported on Pharyngula, the Danish cartoonists are once again the target of Muslim ire. Danish papers have reprinted the offending caricature in a show of solidarity with the cartoonists and an affirmation of freedom of speech. Why now? It seems a plot was uncovered to kill one of the cartoonists. That’s right–use your ink, get killed. You can see why a cuttlefish might not like that. But rather than rant at length (which others do better than I can, anyway), I thought I’d put the cartoon jihad into a more fitting context. Is a cartoon of the prophet Muhammad the most offensive way one could use one’s ink?

I don’t think so.

The Muslims want to rid the world
Of all cartoons that irk us–
I say, come join in my jihad
Against The Family Circus!
To threaten death for doodling
Mohammed is just silly,
When much more damage has been done
By Jeffy and by Billy.
The mental anguish brought about
By P.J. or by Dolly
Makes Muslim claims of blasphemy
Just so much useless folly.
Who holds a gun to Bil Keane’s head,
Against his plaintive plea,
And makes him write this sort of crap?
Oh! “Ida Know”; “Not Me”!

cartoon source: Infidel Blogger’s Alliance