Science Is A Cephalopod

Hey, my first chance to show off some of the new artwork (for the upcoming revised, updated and improved book)! Mike McRae, the artist behind my banner art (thanks, Podblack, for suggesting him!), has drawn a few illustrations for the chapters. He asked me what I had in mind for each, listened carefully to my rambling suggestions, then wisely ignored a great many of them in order to produce something much much better.

And sometimes, his choices were very very different from mine. For instance, rather than sticking with a cuttlefish for each illustration, he has used octopus, squid, and even nautilus! At first, the notion of the nautilus grabbing the prize gig of representing science rather galled me… but then, it suddenly could not be more perfect. Science, after all, grows by testing hypotheses, and discarding ideas that cannot be supported. If science has grown to the point where an old idea no longer fits, we abandon it, and sort of wall it off (there is no reason to reconsider geocentrism as being worth another look at this point, after all). And with every rejection, science grows.

I guess what I am trying to say is…

Science is a nautilus; it builds upon its past,
By discarding what it clearly has outgrown;
Empirically assessing views that will or will not last,
And adding to the sum of what is known

Our ancient view of nature was ridiculously small,
From the universe itself, to our place in it—
But our knowledge grew, until that view could never hold it all,
And it’s growing more with every passing minute

A new and better theory soon replaced the old and weak;
This may also be abandoned as we grow;
If a theory is found wanting, then a better one we seek,
Which is how we keep increasing what we know

The nautilus will build a wall, to permanently close
Any cell for which it has no further use;
When you find a static charge can heat the air up till it glows,
You’ve got lightning with no need to call in Zeus

Should a scientist today concede the Earth is really flat?
That phlogiston is the reason fires burn?
That demons are the cause of plagues (and never mind that rat)?
That is not the way to grow from what we learn!

An open mind is willing, if it must, to close a door,
If the evidence is clear that’s what to do;
We must never mourn the tiny room we occupied before—
There is so much more amazement in the new!

Good News On The Parasitic Worm Front!

The Beeb is reporting on an article in the current edition of the journal Nature, reporting a draft genomic sequence for the Schistosoma flatworms (the nasty little buggers responsible for schistosomiasis, which kills hundreds of thousands of people each year. The Nature paper is fascinating; sequencing the gene has allowed the researchers to identify a great deal about the critter’s physiology and behavior, and has led to many promising avenues toward combatting the parasite in humans and other mammals.

Readily, steadily,
Diligent scientists
Studying parasites,
Sequencing genes,

Target the worm that brings
Schistosomiasis,
Finding new treatments, and
Maybe vaccines!

Killingly, chillingly,
Deadly S. mansoni
Lives in your liver, your
Bloodstream, your guts;

Suddenly, somehow my
Scoleciphobia
No longer seems like I’m
Totally nuts.

Crawlingly, gallingly,
Snail-hosted parasites
Work their way into their
Humans as well;

Now, these advances in
Parasitology
May save their hosts from a
Miserable hell.

Cuttlefish!

Ah… XKCD has done it again!
(and of course my formatting screws it up–click image for the full comic!)

A cuttlefish learns, so amazing quickly,
And oh so incredibly much—
We’ve figured out chemistry, quantum mechanics,
Biology, Physics, and such;
We could, if we chose to, go traipsing through wormholes
To galaxies light-years away;
But frankly, there’s something more baffling to study,
And that’s why we’ve chosen to stay.

These rather unusual featherless bipeds,
So noisy, so smelly, so strange—
It seems they can learn, or at least they respond
To contingencies which we arrange.
They learn rather slowly, it must be admitted;
It could be their brains are quite small.
And given their habits, the evidence tells us
Some probably don’t learn at all.

They somehow invented some horrible weapons
Which all thinking beings should fear
They constantly threaten complete devastation—
I’m rather surprised they’re still here!
They keep dumping poison in lakes or in rivers
Where others get water to drink—
Although this is senseless, and foolish, and stupid,
I still believe some of them think.

They’ve hit upon something that multiplies thinking,
A process they like to call “science”,
Where each person builds on the other ones’ progress
Like standing on shoulders of giants.
Some say these “humans” are smarter than cuttlefish;
I won’t be taking that bet!
But maybe—just maybe—with science to help them,
These humans… they might make it yet.

A Blood-Curdling Cautionary Tale Of Science Run Amok

Genetically, of course, a spork
Is half a spoon, and half a fork
A laboratory in New York
Created them, then popped the cork.

Please, gentle reader, do not swoon,
But there was also, once, a foon
(That’s half a fork, and half a spoon)
Created, sadly, all too soon.

In cutlery, one tempts the Fates
When artificially, one mates
Utensils from across the plates
Regardless of recessive traits.

A careless thought: “let’s cross F-1
Again with forks, and have some fun.”
The simple plan was soon begun,
Then all too soon: “What have we done?”

With thirst for blood and killing drives
Such meddling ends in loss of lives
I only hope someone survives
To tell—the sporks have found the knives!

From xkcd, of course.

A Lizard Is A Lizard Is A Lizard

A lizard will remain a lizard
Even if it grows a gizzard.

Even if it grows some fur,
A lizard’s what it always were;

A lizard will be of that ilk
Despite evolving glands for milk;

A lizard with an upright stance–
Could that be different? Not a chance!

A lizard standing on two legs,
Who bears live young instead of eggs,

No matter what, you’ll always find
It still belongs to lizardkind.

Hmmm….

At last I think I understand
Some crazy things about this land:

The audience for Bill O’Reilly?
Lizards prob’ly rate him highly.

The changing views of John McCain?
The answer’s simple: Lizard Brain.

Paris? Brittney? Cher? Madonna?
Must look hot to some Iguana.

I think I’ll stop here, if you wish–
It’s time to feed my inner fish.

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!)