I had a little phone interview today, and as most interviews do, it made me wonder “what the heck have I been doing with my life?” My career trajectory seems plausible - until I have to articulate it. Then I wonder how I got here.
In honor of that strange feeling of 30-something disorientation, here’s a dryly amusing video summarizing life as a series of graphs, arrows, and Venn diagrams. The format’s gotta be just as valid as a resume.
There is a common denominator that links all these artists. It is the profound joy that all feel who observe the natural world with a sustained and devoted intensity.
- Sir David Attenborough
I was tickled to see this charming Telegraph article on a natural illustration exhibition entitled “Amazing, Rare Things” (beginning March 2 at the Queen’s Gallery, Holyroodhouse, Edinburgh). I was even more tickled to realize it was written by Sir David Attenborough. His nature documentary series, like The Living Planet (1984), had a huge impact on me as a child. Even now, if I visualize the concept “ecosystem,” I see not empty savanna, but David Attenborough in the savanna, wearing his genteel exploratory khakis, whispering or shouting depending on what sort of fascinating creature he was stalking.
Even when he was being sandblasted or frozen or heckled by lyrebirds, Attenborough always seemed genuinely delighted to be there. That’s why his words above, about nature artists, ring so true. The late Crocodile Hunter, Steve Irwin, gave me the same impression; it’s tragic that his career was only a fraction of Attenborough’s long tenure. It seems fitting that Terri Irwin introduced this touching, often hilarious 2006 NTA tribute to Attenborough (Part 1; Part 2). It includes some wonderful black and white footage of the naturalist as a young man. I never even realized how much I loved Attenborough, until I watched this.
The Nature Conservancy ran a photography contest until the end of December and just announced the winners last week. The “Best Nature Photo” winner was Joseph Napolitano with this technicolor invertebrate. Wow, biology is cool.
Ok, so the science entries on Conservapedia are easy targets - finding mistakes is like shooting fish in a barrel. And quite a few of my fellow science bloggers have engaged in targetpracticelately. But not all the entries are grossly biased. Some probably sound quite plausible to the layperson. Like this one:
Mutations are changes in the genetic code caused by copying errors, or by external factors such as solar radiation or exposure to mutagenic chemicals. Mutations are sometimes the cause of disease, such as cancer or Down’s Syndrome (which is the result of an extreme mutation which causes an extra chromosome to be present). Evolutionists claim that heritable mutations produce genetic variety, upon which natural selection acts. However, mutations can only decrease information, never increase it.
(Accessed Feb 26, 2007 - nothing over there is stable, it kinda. . . mutates).
In my opinion, it’s entries like these that are most insidious, because there are no obvious red flags. They seem unbiased, simple, factual. And increasingly, students accept whatever they find on the internet as fact. (I don’t care if it’s Wikipedia or Conservapedia: it’s not ok to cite a site, especially those that change as often as wikis do!) Few of my college biology students would have picked up on the problems in this entry. I’m going to walk through it; this information will be nothing new for those readers who are biologists, but I think it’s an eye-opening exercise to see how easily the misinformation slips through and how hard it is to explain why it’s grossly oversimplified, if not wrong.
First off, it’s properly Down syndrome, although the s is frequently blurred in pronunciation, so many people think it’s Down’s. I can understand that - I spent several days in Edinburgh and never figured out I was on Princes Street, rather than Princess Street. Not a huge issue - although a reference like an encyclopedia should weed out such trifling errors.
A more misleading statement is categorizing trisomy 21, which causes 95% of Down syndrome cases, as a mutation (which has just been defined as a change in the genetic code). “Trisomy” is the presence of an extra, unaltered copy of a chromosome, which has not undergone changes in its base pair code. There is nothing “mutant” about this extra chromosome. Trisomy is a simple sorting error, as if you did your laundry and started grouping your socks by threes instead of two. The individual socks are normal, it’s the grouping that’s the problem.
Only about 5% of Down syndrome cases involve actual changes to the genetic code: translocations or duplications of various parts of chromosome 21. Only these atypical cases of “familial” Down syndrome should really be considered mutations. Citing Down syndrome as a representative example of a disease caused by mutation is a bizarre choice, especially given the plethora of diseases caused by single-base changes in a gene. Sickle cell, cystic fibrosis, Tay-Sachs. . . the list goes on.
On the other hand, in order to associate these diseases with mutations, you need to accept that the disease-causing alleles of each gene arose as mutations of the original, functional allele. In other words, the genes evolved. It gets worse: the alleles were selected over time according to the principles of population genetics, such that the diseases mentioned above now occur in well-known geographic or ethnic patterns. In other words, natural selection acted on heritable genetic variety created by mutation - just as those darn evolutionists claim.
But Conservapedia denies that mutation can produce heritable genetic variety. At least at its current level of dialogue, it does - I’ve actually seen single-gene disorders erroneously cited as evidence that mutations can only be destructive (disease-causing), never constructive (evolution-causing). Speaking of which, let’s look at the final line:
However, mutations can only decrease information, never increase it.
If you accept that single-base changes (mutations) occur in genes at all, then you have to accept that these alterations will change the information coded in the gene. But “decrease the information”? I don’t think that wording makes any sense, unless you’re talking about a deletion of part of the gene. If you lose three base pairs, then yeah, I guess you’ve decreased the information by three base pairs. You could also increase the information by adding in three base pairs. Neither “increasing information” or “decreasing information” accurately describes how the gene works. A mutation that alters a gene so it no longer works does not “decrease information.” It alters the information, such that the gene’s functionality is decreased. That’s a heritable variation right there: a nonfunctional copy of a gene can produce a phenotype like colorblindness that is inherited.
This “information” wording is probably chosen to exploit our intuitive preconceptions about information as the creation of an intelligent author. It’s difficult to imagine how random changes to a gene could improve its function, just as it’s hard to envision how random changes in a book would improve the story. An better way of stating the Conservapedia position would be “mutations only decrease functionality, never improve it.” That’s a common impression among my students, because it is intuitive. Generally, when you make a typo, it’s a mistake, not a new word (I think it’s still information, though). You expect a typo to be a mistake. And if you’re using Microsoft Word, they get cleaned up, or at least flagged so you can go back and fix them.
But sometimes Word doesn’t catch a typo. Why not? Because you’ve accidentally typed an unintended, but valid, word. You’ve changed the information in the sentence. The sentence may still make sense. It could even be better than what you originally intended. This might be a rare outcome, but it’s certainly not impossible; I know it’s happened to me before. And it’s just as possible for a mutation in DNA to improve the functionality of a gene, or change it to something new.
As every teacher knows, it’s quite difficult to explain complex biological concepts at a novice level. And it’s hard to pin down how this Conservapedia entry gives the wrong impression. But it does. A reader could well be left with the idea that a mother who gets a sunburn risks both skin cancer and having a baby with Down syndrome. That makes no sense.
Unfortunately, I don’t think we should acknowledge that Conservapedia has largely been written by students, and just let it go, like New Scientist did. The creators have chosen to present the site as an equally authoritative alternative to Wikipedia, not a student project. And the most troubling thing is, it’s more accessible than Wikipedia. I love Wikipedia, but in the quest to be comprehensive yet precise, its contributors have done what I just did (on a smaller scale): add information and clarification until entries are long and full of jargon. Plus, hyperlinks are used to the fullest. This keeps individual entries nonredundant, but on the other hand, reading an entry outside your comfort zone often demands dipping into ten or twenty other entries to learn the unfamiliar terms used in the original entry. This even happens when, we suspect, vandals infiltrate Conservapedia and mess up the content - those entries become more conceptually difficult than the unvandalized ones. Oh, those nutty, naughty scientists, with their big words.
At this point poor Conservapedia has been pretty well scrambled - not only are its entries being fiddled with, it’s down much of the time. But even so, as a put-upon student writing a much-procrastinated paper, would you rather encounter the Conservapedia paragraph above, or Wikipedia’s entry on mutation? Here’s a brief taste of Wikipedia:
Gene mutations have varying effects on health depending on where they occur and whether they alter the function of essential proteins. Structurally, mutations can be classified as:
Small-scale mutations affecting one or a few nucleotides, including: Point mutations, often caused by chemicals or malfunction of DNA replication, exchange a single nucleotide for another. Most common is the transition that exchanges a purine for a purine (A ↔ G) or a pyrimidine for a pyrimidine, (C ↔ T). A transition can be caused by nitrous acid, base mispairing, or mutagenic base analogs such as 5-bromo-2-deoxyuridine (BrdU). Less common is a transversion, which exchanges a purine for a pyrimidine or a pyrimidine for a purine (C/T ↔ A/G). A point mutation can be reversed by another point mutation, in which the nucleotide is changed back to its original state (true reversion) or by second-site reversion (a complementary mutation elsewhere that results in regained gene functionality). These changes are classified as transitions or transversions. An example of a transversion is adenine (A) being converted into a cytosine (C).
Obviously, no reference can be equally accessible to readers at every level of education. But I think we should probably acknowledge that while we laugh at Conservapedia, it’s got its target audience pegged. And that could be a real headache for educators down the line.
Jesse Peper’s surreal paintings mix totemic animals like fish, birds, and snakes with religious iconography and the dark bloom of decay. He’s also the featured artist at Juxtapoz this week.
Janet Stemwedel at AES has collected a LOT of perspectives on the scientific process and interpreted them as flowcharts. Not only are they geek-chic, they give me nostalgic fuzzies of teaching 100-level Introduction to Science (before I switched over to powerpoint).
Janet’s post centers on whether “belief” should be in this flowchart, or not. Is a scientist obligated to “believe” the results of the scientific process? Or is “belief” nonessential to good science? I tend to believe (ahem) that belief can be left out entirely, but if you disagree, there’s a flowchart for you, too.
In honor of Auden’s centenary, York cabbies will be reciting his verse to their passengers. I expect most of the passengers will at least know who Auden is; if New York cabbies did the same, maybe not!
Take this quiz to see how much you know about Auden.
If all a top physicist knows
About the Truth be true,
Then, for all the so-and-so’s,
Futility and grime,
Our common world contains,
We have a better time
Than the Greater Nebulae do,
Or the atoms in our brains.
Marriage is rarely bliss
But, surely it would be worse
As particles to pelt
At thousands of miles per sec
About a universe
Wherein a lover’s kiss
Would either not be felt
Or break the loved one’s neck.
Though the face at which I stare
While shaving it be cruel
For, year after year, it repels
An ageing suitor, it has,
Thank God, sufficient mass
To be altogether there,
Not an indeterminate gruel
Which is partly somewhere else.
Our eyes prefer to suppose
That a habitable place
Has a geocentric view,
That architects enclose
A quiet Euclidian space:
Exploded myths - but who
Could feel at home astraddle
An ever expanding saddle?
This passion of our kind
For the process of finding out
Is a fact one can hardly doubt,
But I would rejoice in it more
If I knew more clearly what
We wanted the knowledge for,
Felt certain still that the mind
Is free to know or not.
It has chosen once, it seems,
And whether our concern
For magnitude’s extremes
Really become a creature
Who comes in a median size,
Or politicizing Nature
Be altogether wise,
Is something we shall learn.
Ok, I thought I lived in hicksville, but I have never seen artificial testicles on a truck before. Yet according to this WaPo article, they’re so pervasive, legislation has been proposed to regulate them.
The example below the fold is/are the patriotic “yellow ribbon camo nutz” from YourNutz.com.
We’ve Respectfully placed the Yellow Ribbon designating Support the Troops on our Exclusive 8” Customized Desert Scheme Camo Nutz.
I sure can’t add a thing to that.
If truckers must accessorize with body parts, I suppose it’s best that they’re fake. But wouldn’t they prefer some nice plastic brain case casts instead of those controversial sexual organs? No, I suppose they wouldn’t.
As every American knows, our health care system is exasperating. I recently left a job; fortunately, I’m healthy and relatively young, so obtaining temporary insurance was not a problem. But for those who have been seriously ill - either physically or mentally - it can be difficult or impossible to find affordable insurance. Genetic information is becoming yet another reason to fear rejection, even if you’re healthy.
A recent study led by researchers at Johns Hopkins found that individuals with a history of genetic conditions (including sickle cell disease or cystic fibrosis) were twice as likely as individuals with other chronic illnesses (such as diabetes or AIDS) to report being denied insurance. Although asymptomatic individuals carrying disease-causing alleles cannot legally be singled out by insurers (according to HIPAA, the Health Insurance Portability and Accountability Act), individuals diagnosed with the disease itself have no such protection. The subjects of the Johns Hopkins study had already been diagnosed, which is likely the case for most people with known genetic diseases; there is rarely reason to test for particular gene aberrations in the absence of symptoms, unless a close family member is affected. So insurers were not breaking the law by denying the subjects coverage. Still, it is provocative that the subjects with genetic diseases were treated more poorly than those with non-genetic, but quite serious, conditions.
The umbrella of “genetic diseases” usually includes disorders caused by single aberrant genes, such as cystic fibrosis, PKU, hemophilia, and Huntingtons disease. But genetics also predispose people to diseases like breast cancer or colon cancer - conditions for which certain forms of genes are associated with significantly elevated (though not certain) risk. BRCA1 and BRCA2 mutations account for only about 5% of breast cancer cases - but a woman with one of these mutations is 3 to 7 times more likely to develop breast cancer than a woman without a BRCA mutation (reference). Still other genes, such as PALB2, are likely responsible for some non-BRCA breast cancers. It’s unclear how many cases of breast cancer are genetically triggered, because the genes responsible are still being identified. Recent studies have also found genetic risk factors for conditions as diverse as autism, schizophrenia, and Parkinson’s disease; although we know next to nothing about how aberrant genes contribute to these neurological conditions, we can say that individuals with certain alleles have elevated risk. Increasingly, these conditions are also considered “genetic.”
Basically, there is no clean line between a “genetic” and “non-genetic” condition. I’d have difficulty naming a disease with no genetic contribution. Skin cancer is caused by UV light exposure - but people with dark skin have much lower risk, because melanin is protective. Individual genetics impact blood chemistry, weight, and metabolism, influencing our risks for obesity, heart disease, diabetes, and stroke. Blame diet, lack of exercise, or stress if you wish, but our genes determine how we respond to those environmental factors. Even contagious viral or bacterial diseases are influenced by genetics. Individuals with certain alleles are more resistant (either to infection or to disease progression) than others. For example, a partially deleted form of the chemokine receptor CCR5 protects against HIV infection. We’d like to think everyone has a fair shot at good health, but it’s clearly untrue. We have to work with the genes we’re given, and some people are simply dealt bad hands.
Even if the game is fundamentally unfair, one thing we can do is give individuals the opportunity to know their genetic hand, without fear of workplace or health care repercussions. Individuals should have the right to learn if they or their children have genetic disorders, so they can make life decisions accordingly, and obtain treatment as quickly as possible. For some genetic disorders, early treatment can be spectacularly successful. This is why states require a battery of genetic tests on newborns - not to burden parents with knowledge of an inevitable illness, but to intervene early, when diseases like PKU can be managed almost completely.
On the other hand, many genetic disorders remain uncontrollable - and unpredictable. Parkinson’s disease and schizophrenia both have late onset; for a young adult, learning that your genes predispose you to one of these disorders must be terrifying. You don’t know if the disease will hit at all, much less how long you’ve got, or how bad it will get. I don’t think I’d want to know, myself - but people should have the right to choose. Obviously, insurers and employers would also like to know if you or your child could develop a costly genetic condition, and they would, if allowed, act on that information to minimize their own risks. The fear that your genetic information could justify discrimination against you is not merely a GATTACA-worthy plot device; it’s a very real deterrent to being tested at all.
To address this reality, both halves of Congress are working on legislation which would establish stronger protections for genetic privacy (The Genetic Information Nondiscrimination Act of 2007, or GINA). Richard Posner and Gary Becker have an interesting discussion at their blog about whether GINA would indeed ensure fair health coverage or promote genetic testing. Posner makes the point that some uncertainty is necessary to maintain a functional private health insurance system:
The broader point is that the more that science reduces uncertainty about individuals’ health, the less risk pooling there will be and the greater, therefore, the demand for social insurance. In the limit, if everyone’s health prospects were known with certainty, there would be no market for health insurance at all and this would exacerbate the effects of differential health on equality of wealth; no longer would the healthy be paying to insure the unhealthy.
In the current, anxiety-inducing age, researchers have identified oodles of risk factors, and perhaps uncertainty about individual health is indeed being gradually reduced. But amidst all this information, we can feel like we have less and less control over our health. We aren’t sure if we should or shouldn’t drink red wine, or eat dark chocolate, or take NSAIDs. The research is rarely unequivocal; we are not all genetically equivalent. Even if I diligently avoid all the known environmental risk factors for breast cancer, I might have a BRCA mutation, which swamps my risk from all other sources. We can’t change our genes, any more than we can change our stars; why even try to be healthy? On the other hand, even if I don’t have a BRCA mutation, I could still get breast cancer anyway; perhaps I should hedge my bets and drink soy milk. . .
No one is perfect, no one is perfectly healthy, and no one is risk-free. We all have defects somewhere in our genome; we are all predisposed to something unfortunate, whether we know it or not. When whole-genome testing becomes routine, will we feel obligated to use our new genetic knowledge to choose our partners, or select our children? How serious will a genetic “defect” have to be to concern us? What about myopia? Baldness? Allergies?
These questions are by no means new. What is new is how close we are to actually having this kind of information. Private companies already offer at-home, a la carte genetic testing. This makes me very nervous: I doubt the average American is qualified to understand that risk is not certainty (10% of BRCA mutation carriers don’t get breast cancer, after all). It’s also unclear what a patient is expected to do with the genetic results if the disorder is untreatable. These companies neglect to tell their customers that too often, genetic knowledge does not equal power - not yet. Until we are able to convert this knowledge into productive action, maintaining some uncertainty about our genetic fates may be a healthy option. At least ignorance is compatible with hope.
Now there’s a proverb for the ages. . . or a random sentence generated with the procrastinatory Random Sentence Generator, which also suggests random words of various types (nouns, verbs, common, obscure, etc.) Be warned: if you choose “obscure” words, you’ll get results like “voetsek” and “whillikers.”
Tim at Sciencesque is using the Generator to supply topics for his random crawl of OMIM, the human gene database. You can read his efforts (thus far) at the new carnival “Gene Genie”; the inaugural issue is up at ScienceRoll.
Unlike Tim, I’m using it for utterly frivolous reasons: as a loquacious Magic 8 Ball! Plus, there are profound cognitive implications: if I hit “new sentence” a zillion times, will I ever get “colorless green ideas sleep furiously?” Let’s ask!
It says:
The conservative rectangle fails.
Hey! This isn’t a political blog.
It replies:
When will the rectangular collective choose?
Darn if this thing couldn’t pass a Turing test!
My custard bays before an under convict.
Ok - cancel that Turing test. But it’s still some fine frivolity.
Just looking at this photostream makes me feel like I’m in an Umberto Eco novel!
This is the Real Gabinete Portugues de Leitura (Royal Portuguese Reading Room) in Rio de Janeiro, Brasil. Founded in 1837 with books sent over from Portugal, it remains a functional public library today. And yet I’d never heard of it. It’s not even listed in the Wikipedia (en) article on landmark libraries. Scandal!
Let’s be honest: biologists sometimes get a little intoxicated by the beauty of the natural world. My friends know I will break off mid-conversation to crawl into the brush, mesmerized by a snake or a liverwort. My good china is full of dead insects, and my freezer is packed with unlucky birds. I collect things. To be surrounded by those wonders on a daily basis, to unpack and unravel and discover them, is to be constantly at play. Becoming a biologist is the perfect excuse to never grow up.
My favorite “biology poem,” by Atlantic Monthly poetry editor David Barber, perfectly captures that playful wonder. It’s from his latest, phenomenally diverse book, fittingly titled Wonder Cabinet. I’ve been carrying it with me all winter, and can’t recommend it highly enough. This book is a real Wonder Cabinet.
Pam at Phantasmaphile recently noted the unfortunate proliferation of self-declared “Wonder Cabinets” that are basically random juxtapositions of objects. The original wonder cabinets (or wunderkammeren, or cabinets of curiosities), were somewhat haphazard - they predated modern scientific taxonomies, freely mixing natural specimens with artificial objects of interest; their contents reflected the eccentric tastes of individual collectors. But above all, a wonder cabinet was the world in microcosm: what Francis Bacon described as “a small compass, a model of the universe made private.” They weren’t just accumulated stuff; they were windows into unprecedented geographic and scientific vistas. Today, it’s difficult to imagine the awe an authentic wonder cabinet must have evoked. Many scientists disapproved of wunderkammer fever: according to Descartes, “What we commonly call being astonished is an excess of wonder that can never be otherwise than bad.”
Descartes, for all his contributions to neuroscience, was clearly not my kind of biologist. Biology is all about excess - often quite messy excess. Wonder cabinets were just loosely edited selections from the excessive complexity of Nature. Furthermore, a cabinet provoked novel connections between collected artifacts and the remembered artifacts of the viewer’s experience. Within a wonder cabinet, there’s no single, prescribed path of analysis, but an excess of intuitive possibilities. It’s a cabinet of curiosity, a cabinet of questions, not answers. And that’s also very close to my personal definition of a successful poem.
To make sense of the unfamiliar, the astonishing, the messy, we resort to history and language; definitions and names; systems of organizing and explaining the evidence before us. In Wonder Cabinet, David Barber considers all of these things: excess of wonder (”Thumbnail Sketch of the Tulipmania”), the personal wonder that moves the scientist (”Ode to William Wells”), wonderful names (”Chimerical”, “Aphrodite’s Mousetrap”). It’s a pleasure to see my own inarticulate instincts about the delight and wonder of biology expressed so well. It would be a guilty pleasure, if it weren’t such good poetry.
The fin is the finest thing of its kind.
The wing’s a wonder the world over.
The tongue is a form of eternal flame.
The stone’s a story that never grows old.
O fin, it’s certain you want for nothing.
Yo wing, you’re everything we’ve ever dreamed.
You said it, tongue: of arms and men you sing.
Here’s looking at you, stone: a star is born.
Who doesn’t burn for a soul on the wing?
Where is the man that can fine-tune the fin?
When shall we learn to read the mind of the stone?
What in the world holds its own like the tongue?
Stone says fin’s the one that schooled the wing.
Story goes one singer could charm the stones.
Rock, paper, scissors; worlds without end.
One slip of the tongue makes the whole world kin.
All together now: the many in the one.
Brush fire of fins stirring the fathoms,
Cairns of lost tongues, the chorus in the wings
Riffing on the omens of the heavens.
Soul knows it can’t live on breath alone.
When the tongue wags the dog, the fur’s gonna fly.
The stone is a kind of recording angel.
The wing’s got the beat. The fin makes waves.
Wing it, mother tongue: the world’s your whetstone.
We’re wired for sound. We’re unfinished business.
Let’s hear it for the phoenix, all fired up.
Sirens, rock us to sleep with the fishes.
Let’s hear it for descent with variations.
Let him without fin go back to the grindstone.
The bat is the manta ray’s soul brother.
The dolphin’s glossolalia speaks volumes.
Hosannas for sea changes, the wish made flesh.
As the silkworm turns, as the chrysalis
Is my witness, leviathan’s no fluke.
Blood from a stone is a thing to behold.
Blow me down with a feather, fishers of men;
Rock of ages, take me under your wing.
Muse, make it new: leave no tongue untuned.
Rock my world, winged gods: begin again.
Atlantic Monthly interview with David Barber (if you are a subscriber, this poem is available as an audio file on their site)
Is it scary that I would qualify for so many merit badges? Actually, I could invent a few more, such as “I have administered illegal drugs of abuse to insects,” but then I’d be giving away all my Science Secrets. (See the link for the meaning of these badges).
Note that there is also one for, well, cephalopodmania (although I am not yet worthy):
by Guillaume de Laubier, Jacques Bosser, and James Billington.
by Candida Hofer and (gasp!) Umberto Eco.
, do that too).
