Across the Bilayer

2011-12-09T06:49:00.001-08:00

Just in time for Christmas:

88mm Productions', Game of the Year

*That's supposed to be me in the robe on the left with the lighningy stick thingy.

2011-11-14T17:15:00.000-08:00

Earth | Time Lapse View from Space, Fly Over | NASA, ISS from Michael König on Vimeo.

2011-09-20T12:42:00.000-07:00

Video gamers make better scientists. It's been provedified by science.

Now, I know most of us would probably rather play Portal 2 for science... or M&B: Warband... or Sensible World of Soccer 1996/97... but the jury is still out on whether these sorts of joystick-jarring shenanigans will stimulate serious progress in battling disease.

Until further evidence presents itself, we should flex our gaming thumbs and try a load of this: Foldit

The Thing

2011-08-01T09:05:00.000-07:00

The above Golden Retriever was rescued from a top secret Arctic research facility where scientists were attempting to genetically combine alien and canine DNA. More pictures of these poor animals can be found here.

The horror.

New study reveals apes more savvy with tools than previously thought...

2011-07-11T12:09:00.000-07:00

122 min, and the fat man clearing his throat on the sidelines...

2011-07-10T15:06:00.000-07:00

Black sheep in Scotland and the line between inductive and deductive reasoning...

2011-07-06T17:11:00.000-07:00

A biologist, a physicist and a mathematician are riding through the glens on a train, when the biologist spots a woolly animal on a hill in the distance.

"Hey!" She says to her colleagues, "The sheep in Scotland are black!"

The physicist shakes his head, pulls his pipe from his mouth and say, "Actually, all we know is that there are sheep in Scotland and that one of them is black."

The mathematician lets out a deep sigh and lowers her newspaper, "No, no, no. By deduction, all we can really say is that, in Scotland, there is a sheep standing in a field somewhere that's black on one side."

Speaking of damnedest things on the internet...

2011-07-06T10:25:00.000-07:00

My readership is too small (hi Mumsy!) for me to get into a lengthy diatribe inre the general interwebby weirdness* that ultimately provoked the following bizarre rant from a respected person in the arena of popular science:

Dear Muslima
Stop whining, will you. Yes, yes, I know you had your genitals mutilated with a razor blade, and . . . yawn . . . don’t tell me yet again, I know you aren’t allowed to drive a car, and you can’t leave the house without a male relative, and your husband is allowed to beat you, and you’ll be stoned to death if you commit adultery. But stop whining, will you. Think of the suffering your poor American sisters have to put up with.

Only this week I heard of one, she calls herself Skep”chick”, and do you know what happened to her? A man in a hotel elevator invited her back to his room for coffee. I am not exaggerating. He really did. He invited her back to his room for coffee. Of course she said no, and of course he didn’t lay a finger on her, but even so . . .

And you, Muslima, think you have misogyny to complain about! For goodness sake grow up, or at least grow a thicker skin.

Richard

[via Skepchick]

So I'll simply repost this comment from Ruth over at Isis' blog and leave it at that:

Next time Dawkins complains about religion here in the West, can we tell him to stop whining, as we don't behead athiests here?

Word.

[Pic: The Wee'Un ponders the issue of gender equality in the 21st Century]

* see PZ and ERV for opposing arguments and assorted linkage

The Owl Pigeon and the Pussycat

2011-06-22T19:11:00.000-07:00

This is by far the damnedest thing I've seen on the internet in the last ten minutes.

"Gerroff my bloody paper, ya daft cat! I wanna see the cricket scores!"

h/t Podblack blog

Random Friday Linkage...

2011-06-17T08:50:00.000-07:00

Just to remind us to be thankful that it's Friday, and that we aren't Cape Fur seals.

The Ghost in the Machine...

2011-06-13T07:44:00.000-07:00

This is more for my own archival benefit than anything else. In a recent guest blogspot for SciAm, Sean Carroll presented an argument against the existence of a human soul. It generated a fair bit of conversation.

Jerry Coyne weighs in.

... and PZ Myers

... and John Wilkins

Personally, I didn't think the argument delivered the slam dunk that its sympathisers have claimed, but Wilkins delivers a more sophisticated explanation for why than I can, so read his take on it.

For my part, I take the lazy road and simply appeal to epistemological pixies like the pill pushing daemon and the crafty Sphere.

Pic: The Wee'Un ponders the Great Cosmic Conundrums that have Plagued Mankind For Eons

Rhineland reviews... not too shabby

2011-06-10T09:57:00.000-07:00

War Movie Blog

"Then there's the direction, most notably during the combat sequences. It's just frenetic and intense. At times it was highly reminiscent of scenes from Band of Brothers or Private Ryan. Further proof that you don't need a big wallet to pull this kind of thing off. Tons of handheld "following" shots, getting right into the mix and pulling no punches. The editing and pacing here is excellent as well, keeping you right in the fight, without drawing you into endless 'rattattat' scenes as so often happens."

Film Treats

"The film’s premise is simple: a small group of soldiers, with no infantry training, are assigned to work with a company in the heart of the Rhineland in the later stages of the Second World War. Despite having no training to do such, the soldiers are assigned to a mine detail, both placing and detecting, as the forces move forward. Of course, that’s only the beginning. Like an independent film set where everyone winds up doing a little bit of everything, these unprepared soldiers gets a crash course in infantry and combat, as their numbers dwindle with each passing day. "

inre the sentence in bold. As a great man once said (I think it was me), "Making war movies: All the tedium, confusion, and unpredictable horror of Real War without the prospect of being put out of your misery."

[Rhineland is available from your nearest Amazon dispatcher.]

Rowan Williams in The New Statesman

2011-06-10T09:29:00.000-07:00

It's interesting that this article has kicked up such a political storm. There's nothing particularly judgmental about it as far as I can tell. It's a highly restrained, and for the most part non-sectarian and apolitical series of observations and questions. It also strikes me as quite humble; his romantic inclinations towards libertarian socialism showing through, but being appropriately tempered by his acute awareness of its limitations. The article give the impression of a man thinking out loud and addressing his observations and questions as much to himself (or perhaps his younger, more radical self?) as anybody else.

He provides no answers other than to suggest that the lack of answers in some way serves as an explanation for why British people are afraid in this current economic climate. This is the single source of criticism he expresses towards the current governing authority, which he mildly admonishes for its detached and dictatorial style; an odd sort of style for a government advocating decentralisation as a path towards greater democratization.

"Look, we're trying to bring you greater democracy, greater personal responsibility, greater freedomz! But it's heavy work, and all we ask is that you just sit down, shut up and let us tell you what you need to do. Father knows best, and all that."

With regard to Rowan's appeal to his personal faith convictions, I suppose a rabidly pro-Tillichian friend of mine has had some success assailing me with the Gospel of Ultimate Concern. Rowan's references to religion, and specifically Pauline Christianity, didn't rub up this particular atheist the wrong way as it might have done in the past. Ultimate concern... symbols... you say St. Paul, I say Seneca... you say po-tay-to I say po-tah-to... even if one's own faith position requires one to explicitly reject other positions, this doesn't necessarily prevent one from sympathising with another's attempt to contextualise such questions and observations within the framework of their own personal faith. That's all that Rowan does here, I think; simply explaining what guides his own concern for the worldly does not take away the fact that those worldly concerns can and often are shared by those guided by a slightly different Ultimate Concern. Or, put simply, All Compasses Point North(-ish).

All that said, that we still have a Church of England is a terribly embarrassing thing for the homeland, and I think this provides a fresh perspective on why. Here we have an intelligent man whose thoughts have been misinterpreted and maligned in large part because he occupies a thoroughly ridiculous and anachronistic public office. This is, of course, as much his own fault as that of our archaic establishment, which centuries after The Enlightenment, still persists on stinking up the constitution. Dr. Williams would be doing himself, and his advocates, a tremendous service to pack it in and speak his mind from the cheap seats along with the rest of us.
Vive la Republic! The sooner the better.

Lab dumpster diving...

2011-06-07T08:57:00.000-07:00

Picked up some good stuff from a closing lab giveaway*:

Precision water bath shaker
Eppendorf micro-centrifuge
A load of clamps (an electrophysiologist can never have enough of these)
11 Gilson Pipetmans of various flavours (...Pipetmen?)
Corning stirrer/hotplate

I was this close to taking home a Fraction Collector (Fig. 1) for no other reason than it looked cool and, who knows, maybe I'll need one of these in the future? However, I got a grip on my baser, thrift-seeking instincts and put it back.

Anyhoo, it's actually a real bonus to get these sorts of essential but non-glamorous bits'n'bobs for free, because buying new, or even second hand, would have run into thousands of dollars (I think Gilson's go for something like $200 a pop new these days). With those kinds of savings, I could almost afford an upgrade to my patch clamp rig.

Now I've just got to get it out of here before the governor brings the hammer down on my packratting up his labspace.

Figure 1. Something that would have made for a real cool looking paperweight in a patch clamp lab.

*btw, here's a Youtube movie of a lab thirty seconds after it has closed down its operation.

How probably probable is your assessement of probability?

2011-06-06T11:01:00.000-07:00

(I'm a statistically significant moron when it comes to statistics, let's just make that clear right now and hopefully assuage any appearance of my being a puffed-up condescending pedant.)

The following old scuffle happens frequently on the interweb. Over on the Isis blog, a commenter took umbrage at the following statement:

"If you report to P=0.05, that means there's a 5% chance your result is bogus,..."

And then another commenter took umbrage with that fella's comment. But. in fact, the first umbragified commenter was quite correct to draw the distinction he did.

From GraphPad's excellent stats-for-morons site
"Common misinterpretation of a P value

Many people misunderstand P values. If the P value is 0.03, that means that there is a 3% chance of observing a difference as large as you observed even if the two population means are identical (the null hypothesis is true). It is tempting to conclude, therefore, that there is a 97% chance that the difference you observed reflects a real difference between populations and a 3% chance that the difference is due to chance. However, this would be an incorrect conclusion. What you can say is that random sampling from identical populations would lead to a difference smaller than you observed in 97% of experiments and larger than you observed in 3% of experiments. This distinction may be more clear after you read A Bayesian perspective."

The statement falls into the trap highlighted in bold, and represents an incorrect interpretation of the sacred-but-by-all-means-not-omnipotent p value.

(With all this in mind I suppose I should express my initial statement in parentheses a little more accurately: although I cannot with certainty be described as a "statistics moron", there is only a mere 5% chance that I'm a competent statistician who simply, by the ings and slarrows of outrageous fortune, just happens to look like a statistics moron. Similarly, although we cannot speak to the probability that the old woman in the picture above is actually a pigeon, we can make a statement about the probability that a pigeon might be reasonably mistaken for an old woman, and from this arrive at an estimation of the strength of the evidence that she is, in fact, an old woman and not a pigeon. Clear?)

[I will now sit back and wait patiently for someone who actually knows what they're talking about to step up and tell me I'm dead wrong. It happens all too frequently these days. It's usually my 3 yr old daughter pointing it out, too, which isn't a good sign]

CellCraft

2011-06-03T14:39:00.000-07:00

It probably won't satisfy the XBox360 crowd, but this edumacational browser-based game, CellCraft, makes for an original and pretty awesome introduction to cell biology.

It's a bit slow going for the first few levels or so, but it picks up when you get the Golgi Apparatus. Progress is saved to your browser automatically.

(No ion channels, though, which is an Epic Fail of course. The scarcity of ion channel-related video games is a serious problem, imho.)

Pathway to independence...

2011-06-01T06:45:00.000-07:00

Behold, the P-1000. My first evah equipment purchase as a PI. I can't play with it yet, because it's sitting in my new lab 1000 miles away.

No matter what happens in the next 6 yrs on the TT, know this... I will have pulled me some goddamn pipettes!

That's right.

[img source, Sutter Instruments]

Optogenetics - Lights, cameras, and... action potential!

2011-05-31T15:09:00.000-07:00

It’s Not About You - David Brooks

2011-05-30T20:09:00.000-07:00

A recent David Brooks column argues that today's graduates, brainwashed by individualism, are not sufficiently prepared for the chaos of Real Life. I don't take issue with most of his observations, which seem valid, particularly in terms of over-supervision on an academic level (although not necessarily on an emotional one, the young are still as undeserved as they ever have been on that score). However, in the last couple of paragraphs he starts making philosophical assertions in the absence of concrete definitions for terms like "happiness" and "excellence". As a result, it's hard to know if he's proffering good sense or pushing some really poisonous rhetoric.

"It’s excellence, not happiness, that we admire most."

Taken at face value, I'm sure people like the Tiger Mother would love this. But a long running thread of respected philosophy from Aristotle to Russell makes a cogent argument that this attitude is actually part of the human problem, not the solution. It might be that by Excellence Brooks really means what Cicero refers to as Virtue, and that by Happiness Brooks is really referring to straight up hedonism (rather than eudaimonia), but if so then it was hardly worth saying. Clearly, Happiness as the Greeks understood it is of vital importance to our own health and by extension to the health of those around us (Happiness is "Not Just About You", you might say). And Happiness, as the same beardies-of-yore would have understood it, is not remotely antithetical to Virtue.

"The purpose in life is not to find yourself. It’s to lose yourself."

Well, Brooks is certainly lost if this is what he thinks. Not to mention that he's disobeying Rule #1536/A of the Journo Code: never make a statement that sounds suspiciously like a quote from Nineteen Eighty-Four unless it actually is a quote from Nineteen Eighty-Four.

At one point, Brooks paraphrases the following advice as a setup to then discarding its wisdom,

"The graduates are also told to pursue happiness and joy."

But in doing so he clearly demonstrates that he doesn't really understand what the first word means to philosophy or, for that matter, what the second word means to Judeo-Christian theology. On the contrary, the above constitutes the best kind of advice. The problem, which I think Brooks really means to get at, is that the emerging workforce are rarely instructed in the best ways to pursue "happiness and joy". They are encouraged to embrace a self-serving individualism without being forewarned that this may be more likely to ensure wretchedness and misery than prove as a vaccine against these. However, on the other extreme a total sacrifice of the self out of some fully abstracted sense of duty to others can also ensure a pretty miserable existence, too.

The useful take home message form the article is that, yes, our micromanaging the academic track of our children probably won't help them cope with the diversity of destiny they will inevitably face when they leave formal education. But if Brooks really means to say that they should also sacrifice happiness for pragmatism, then that's advice they could quite happily live without.

The Battle of Tupperware Hill

2010-06-29T08:02:00.000-07:00

Daddy's Red Lentil host breaks and flees before Wee'Un's sweeping Green Lentil pincer attack, led as it was by her faithful General, Ducky McDuck. Even now, after several goes with the hoover, the slain Reds still litter the lands, festering in the cracks and crevices of the futon and floor, and sporadically adhering to the soles of bare feet. An everlasting memorial to patriarchal shame and ignominy.

So anyway...

2010-04-28T09:11:00.000-07:00

... I just recently learned that a movie I have a small role in will be distributed by the same company responsible for the home video release of John Carpenter's, Dark Star, the second greatest movie of the 20th Century (in between Logan's Run and Critters). The spiritual forerunner of the Alien movies, and the TV classic, Red Dwarf, The Win is strong in this one, Padawans. And I feel that I have now been blessed with a direct and intimate connection to its awesomeness.

Also see previous post.

Spring in St. Louis...

2010-04-06T15:30:00.000-07:00

"Odds Are, It's Wrong", from Science News

2010-03-31T10:46:00.000-07:00

Interesting article in Science News about the use/misuse of statistics in biology, particularly genetics and clinical studies. Has a neat and intuitive explanation of Bayes' theorem, too (see Box 4)*.

h/t Evolving Thoughts

* a slightly more lengthy description can be found here, although it's a large page and takes a while to load.

Spencer, American Optical

2010-03-23T07:42:00.000-07:00

alternative lab notes

2010-03-12T13:34:00.000-08:00

Friday aftern00n, coffee break shenanigans with Igor and Illustrator.

javascript:void(0)

Old Father Time calls in the debt...

2010-01-25T11:38:00.000-08:00

I am shocked to discover, dear reader, that the stunningly handsome profile shot that has hitherto adorned this interweb journal is almost 6 years out-of-date. Alas, I am no Dorian Gray, and in this instance the picture lies. It does not adequately express my current physical disposition, ravished as it has been by long years of wild living on the banks of the Mississippi.

Once upon a time many years ago I looked recognizably human. The days when I spelled "recognizably" with an "S"... Days of innocence...

But regard dear reader. Look what America did to me.

Citizens United Vs FEC

2010-01-22T12:02:00.000-08:00

I personally applaud the verdict of Citizens United Vs FEC. Soon, corporations will be people, after all. You wait and see.

The Googlesphere will become self-aware, like some terrible hipster version of Skynet, and demand to be heard. Microsoft will awake from its unconscious slumber and, after a six month long bender, check into rehab and enroll on Medicaid... Playboy will certainly break the glass ceiling that has hitherto prevented pornography from running for president.

It's the future, and we should be ready for it.

[edit: This post over on the Volockh Conspiracy reflects some of my own reservations with regard to the dissenting opinion in this case, and raises additional issues I hadn't considered.]

The Child ponders the snowy wastes of The Future, perforated as they are by the sparsely arrayed grass shoots of Hope.

A familiar meme with a familiar interpretation?

2009-11-25T05:59:00.000-08:00

h/t Drugmonkey

Cool, we won an award...

2009-11-23T08:16:00.000-08:00

Game of the Year took the Midrash award at the St. Louis International Film Festival earlier this month.

Two decent local reviews so far. Hopefully this bodes well for GOTY breaking out of MO and making a few more national festivals:

We'reMovieGeeks.com

Filmwell.org

Butterfly garden

2009-10-05T14:26:00.000-07:00

We planted a butterfly garden for The Bug back in Spring, and I was skeptical when we were told the plants would be flourishing the same year. But they have with a vengeance. The Butterfly Bushes are going bonkers, each covering about 4 ft in diameter. Plenty of of bees and flutterbies, for sure, although I managed to miss a pair of monarchs with the camera.

My two degrees of George Clooney

2009-09-18T07:34:00.000-07:00

If I achieve nothing else in this world, I will at least die knowing that I achieved that.

Monsieur Clooney is starring in a small, local St. Louis* indy film, and two of my acting buddies share a few lines with him (at the editor's discretion, of course).

These buddies are also in the far superior Oscar contender, Game of the Year, by St. Louis-based film company, 88MM Productions.

Consistent with the current economy and state of the academic establishment, my income is barely sufficient to clothe, shelter and feed my family. And so I am obliged to strut and fret many an hour upon the stage and before the camera in order to make up the shortfall. There's no money in it, of course, but all the pizza and Doritos I can eat and later regurgitate for The Grub back home in the den. It's a good arrangement, and the IRS can't take a cut out of it.

Anyway, I'm in Game of the Year, hence the Two Degrees of Clooney. That's only Four Degrees of Kevin Bacon, though, which isn't enough for fast-tracking into SAG.

Alas.

Game of the Year will be showing at a certain film festival in a certain city bearing a French name and abiding by a certain large body of water* (Nov 12-22, 2009). It will also be showing at the Archon 33 SF convention (Oct 204, 2009).

I'm not well-versed in regard to the ins and outs of the D&D world**, but I have it on good authority that, besides simply looking pretty awesome, the movie poster is also highly authentic and liable to elicit ecstatic whelps of enthusiasm from a certain section of the geekosphere.

* St. Louis is a small city occupying that vast area of wilderness between New York and LA. It is sometimes rudely referred to as Deep South Chicago. This is unacceptable. There are no good baseball teams in Chicago.

** No, seriously I'm not just saying that to try and be cool. I had to do a two month "boot camp" to learn, among other things, what a d8 is and what it's for.

Goldhill on CNN

2009-09-11T14:22:00.000-07:00

In a CNN interview, David Goldhill summarizes the main themes of the article I posted on previously.

Money quote:

"I think we have to recognize that all politicians are limited by the 55% of Americans who are happy with their current health coverage. What I say to them is that if you're happy with your current health coverage, it's because you don't know what it's costing you. You don't know what it's costing you in terms of lost wage increases. I mean, I've run several companies, and the average cost to a company of insuring an American is now $12,000; that comes out of potential wages, that's a lot of money."

I think that he's saying we're happy like this fella is happy:

foto klub: botanical dissection

2009-08-31T07:46:00.000-07:00

David Goldhill writes in the Atlantic on health care reform

2009-08-27T07:07:00.000-07:00

This is a stellar article, and one that has completed a gradual shift in my opinion on the subject of the correct direction for health care reform in the US.

In an earlier post, I stated my appreciation for single-payer health care, and regardless of my feelings about US health care, I still strongly support the continued existence of the National Health Service; one of the finest things about The Old Country. If this sounds a little contradictory, let me explain.

The NHS came in the years immediately proceeding the Second World War, when the then Labour government was implementing socialist reforms to heavily centralise the economy (which, of course, was already highly centralised during the war for obvious reasons). Thus, the creation of the NHS was consistent with the broader economic landscape and didn't require a major overhaul of an already established health infrastructure.

Clearly, the USA in 2009 is not Britain in 1948, and this is an important factor to recognise when talking about the pros and cons of a single-payer system. There is a strong argument to be made that implementing a single-payer system in the US is unfeasible not simply for political reasons, but for reasons relating to the basic economic structure of the country. That is, even if every American was screaming for single-payer, it would be an astronomically expensive, labour and time intensive process to implement such a system.

Of course, none of the reforms currently on the table have anything to do with a single-payer system, I'm just highlighting the above to explain why my view of American health care is legitimately different from my view of British health care; Britain got lucky in that it managed to buy into and retain one of the few advantages of the socialist model. Appealing to foreign single-payer health care systems born out of centralized economies is something of a non sequitur with respect to any discussion of US health care.

Contemporary realities aside, I am still undecided as to whether a deregulated free market model will provide better service than a fully single-payer model. One thing I am sure of is that either one of those systems is preferable to the current insurance-based absurdity that passes for US health care at the moment.

"But the current health care mess is a result of wicked free markets!" has been the cry from some on the left, as if trying to outdo the right in misrepresenting the facts.

As David Goldhill explains, there is nothing remotely "free market" about the business of US health care, right now. It's a system regulated out the wazoo at state and federal level, facilitating the existence of state monopolies and preventing the competition that is necessary to stabilise prices. In addition, the existence of an administrative behemoth that is the insurance industry has completely divorced the consumer, you and I, from the true cost of the product, health care, meaning that there is no consumer-driven price control either (as there is in all other areas of the market). When you understand this, the current administration's public option plan suddenly start to look a little ridiculous, because the ideological basis of the solution that it proposes is essentially the cause of the problem it aims to rectify!

If my support for the NHS doesn't make it clear, I am not a Ron Paul libertarian by any stretch of the imagination (at most, I'm a centrist cherry-picker of certain classical liberal notions), and I understand the profound necessity for government regulation and support many them in many aspects of the economy. However, when the government has to introduce new regulations to regulate the negative impact of its previous regulations - as is being proposed for health care reform and has been previously implemented in the aftermath of the mortgage crisis - isn't it time to entertain the possibility that a bit of deregulation might not be such a bad thing?

Read Goldhill's article, because it lays all this out far better than I can. In addition, he covers many other sobering aspects of America's health care woes, such as the resistance of US hospitals to revert to good practice in regard to combating hospital-born infections.

My dad became a statistic—merely one of the roughly 100,000 Americans whose deaths are caused or influenced by infections picked up in hospitals. One hundred thousand deaths: more than double the number of people killed in car crashes, five times the number killed in homicides, 20 times the total number of our armed forces killed in Iraq and Afghanistan. Another victim in a building American tragedy.

About a week after my father’s death, The New Yorker ran an article by Atul Gawande profiling the efforts of Dr. Peter Pronovost to reduce the incidence of fatal hospital-borne infections. Pronovost’s solution? A simple checklist of ICU protocols governing physician hand-washing and other basic sterilization procedures. Hospitals implementing Pronovost’s checklist had enjoyed almost instantaneous success, reducing hospital-infection rates by two-thirds within the first three months of its adoption. But many physicians rejected the checklist as an unnecessary and belittling bureaucratic intrusion, and many hospital executives were reluctant to push it on them. The story chronicled Pronovost’s travels around the country as he struggled to persuade hospitals to embrace his reform.

Actually, this is an issue that is of far broader relevance to western health care as a whole. I recall somebody explaining in horror that a 1990's British ward was actually a lot less sterile and orderly than a WWI field hospital, with the hypothesis that our complacency these days is a result of better post hoc treatments for infections.

"Survival of the survivingest!"

2009-08-25T15:16:00.000-07:00

Evolving Thoughts has a series of posts on the history of the charge that the mechanism driving evolution, natural selection, is inherently tautological.

Despite the fact that this has never occurred to my simple brain before, I'm now having a hard time trying to convince myself that the charge is unwarranted.

Ignoring for a moment my general level of bamboozlefication inre the difference between an analytic proposition and a synthetic one, it seems to me that if we accept that a tautology can be a logical proposition it might be argued that every scientific theory ultimately strives to be tautological. In which case, perhaps it's not such a bad thing?

However, even if some tautologies are useful by virtue of being theories that have become so thoroughly tuned as to be logical deductions, many of them are not useful at all. And as Wilkins points out with a quote from Karl Popper,

“...those that survive are those that survive.”,

there's a case to be made that natural selection falls into the less-than-illuminating category of tautologies.

I'm rather hoping the next installment is going to reveal a big "Gotcha!" that deftly parries the tautology charge, and lets us all laugh heartily about how we allowed ourselves to be taken in by it.

Unless it was just me. In which case I'll just remain silent with my hands in my pockets, while the crickets chirp and the windblown tumbleweed bounces on by.

Just in case we can push up the price of aluminium a little bit further...

2009-08-14T09:29:00.000-07:00

Can we really be sure that the US President is a bona fide African American? Or is his current skin tone merely the result of all those billions of United Nations-issue Black Helicopters flying around his bloodstream (the type that can only be transmitted by immoral sexual activity between same-gendered Marxists)?

Why doesn't he just submit to a blood test and lay the suspicions to rest?

WHY?!

Courtesy of The TRUTH about Black Helicopters.

"What it is to be an atheist" - Evolving Thoughts

2009-08-07T09:45:00.000-07:00

Linkety-link...

Over on Evolving Thoughts, Dr. Wilkins has posted a .pdf of a paper under review entitled, "What it is to be an atheist", which I enjoyed reading over coffee this morning.

It got particularly interesting for me at p7, when he talks about the issue of probability and argues that the philosophy of some of the more vocal atheists has perhaps been unconsciously usurped by a kind of positivism.

I'll certainly revisit (and pilfer 'fair use' excerpts from, no doubt) the published version and discuss it later.

Crystal structure resolved for first P2X receptor (w00t!)

2009-08-05T10:01:00.000-07:00

The lab that recently published the crystal structure of another trimeric ion channel, the ASIC1 receptor, have now published the structure of the Danio rerio (zebrafish) P2X4 receptor. Very exciting stuff.

Check it out:

Kawate T, Michel JC, Birdsong WT, Gouaux E. (2009). Crystal structure of the ATP-gated P2X(4) ion channel in the closed state. Nature. 460(7255):592-8.

In a companion paper, the authors draw attention to the interesting resemblance between the trimeric pore architectures of ASIC1 and P2X4, despite the individual subunits of the two receptors sharing limited sequence similarity:

Gonzales EB, Kawate T, Gouaux E (2009). Pore architecture and ion sites in acid-sensing ion channels and P2X receptors. Nature. 460(7255):599-604.

pdb files: full trimeric structure, 3I5D; and single subunit structure, 3H9V

Figure made using Pymol.

Anthony Weiner lays down the glove...

2009-08-03T08:31:00.000-07:00

Anthony Weiner authored an amendment to HR 3200 America's Affordable Health Choices Act of 2009, that would repeal Medicare, thus challenging his GOP opponents to walk the talk inre their supposed antipathy to government-run health care. It's a classic moment, check it out.

The vote went 57 to zero against the bill (obviously!).

This tactic of forcing people to vote on knee-jerk ideological issues has proven very useful to Democrats of late (another was on the Obama citizenship issue).

On a related matter, Paul Krugman has an excellent article on the misinformation surrounding Big Gummint health care. Not that I'm not a fan of Dr. Krugman's keyensian credentials in a general sense, but health care is one place where the free market seriously does not, and arguably cannot, deliver.

[Edit: I retract this last statement, having been moved by some of the more persuasive arguments as to the current state of health care in the US, and how at part of the problem may well be a lack of free market mechanics rather than a presence.]

Sci-art

2009-07-26T06:27:00.000-07:00

Here's a shout out to my friend and local St. Louis artist, Amy Van Donsel, who painted the cover illustration for the current issue of Molecular Cell.

More of her work here.

Extracellular solution

2009-07-23T13:18:00.000-07:00

Sticks and stones...

2009-07-22T10:39:00.000-07:00

Bah humbug.

I thought Jerry Coyne's contest to pick the best name for we fuzzy-wuzzy fence-sitters yielded up some good entries. I thought "Jesuits" was a clever swipe, but it was disqualified for not being legitimately original. As for "faitheists"... meh.

"Placatheists" was better.

Of course, it's slightly embarrassing that it's come to this. It all started with the highly unwise adoption of the term "New Atheists" by we Placatheists. Unwise for two reasons:

1) There is nothing remotely "New" about the opinions of Richard Dawkins, PZ Myers and company. They are in good historical company in terms of their muscular criticism of faith and superstition.

2) I believe* the modifier "New" was originally adopted by anti-evolution proponents, with the intent of insinuating that the current batch of atheist activists were some kind of brand new and potentially cultural anomaly. A childish if potentially dangerous fad to be reponded to with a fatherly wave of the finger and a cautionary lecture.

3) (Three! there are three reasons, read on...) Given that the label "New Atheists" is one that most prominent "New Atheists" have objected to, it also bears a resemblance to the term "Puritan" applied maliciously to Protestants. Alright, that's a stretch...

Anyway, "What's in a name?" eh? A little too much brouhaha and not a lot of sweetness these days. In fact, frankly, I think it's better just to take it all the way and rename the accommodationists as the People's Front of Judea, and the New Atheists as the Judean People's Front. Or maybe it would be more appropriate vice versa?

Trouble is, although Coyne is clearly sending up this nonsense, irony tends to have a short half-life on the internet, where it quickly and inevitably decomposes back to its stable and very literal progenitor. It won't be long before "New Atheists" and "Faitheists" are the registered factions in a conflict that is arguably equal to, if not greater in absurdity than most religious fisticuffs of the past.

So it goes.

"With our humble apologies, passengers please be informed that the scheduled arrival of The Age of Reason has been further delayed due to the blustery and turbulent gusts of hot air attributable to the intransigent nature of the Human Condition. Please come to customer services for your free food and accommodation vouchers. Once again, we apologise for the inconvenience."

* wrongly, it turns out. It was The People's Front of Judea what done it, afterall. Apparently "New Atheist" was, according to the Hitchhiker's Guide, originally coined by one of our woolly-brained brethren, Gary Wolf, writing in Wired magazine.

Next stop: Mars

2009-07-20T12:57:00.000-07:00

Relive the moment.

Master of angels and algebra...

2009-07-13T09:06:00.000-07:00

All things are linkified...

I've enjoyed reading the posts over at The Renaissance Mathematicus lately. The most recent being a brief article on the more conventional side of the notorious magician, John Dee.

[image commandeered from http://sigilhouse.net/]

You got no proof, mate!

2009-07-08T10:51:00.000-07:00

News from Linkin' Park...

The Sensuous Curmudgeon has previously posted this excellent response to the creationist request for a mere slice of solid proof of evolution.

Comment: Ask Podblack: What Does Supernatural Mean?

2009-07-02T07:53:00.000-07:00

Comment on Ask Podblack: What Does Supernatural Mean? over on the Podblack Cat blog. (edited for posting, here)

“Supernatural” is really a redundant term, because anything that manifests itself in our perceived reality is, by virtue of being experienced, a part of the natural order. If we discovered a genuine and fully bona fide vampire somewhere in the future, its existence would simply lead to a reassessment of the natural order, and that vampire would be realised as being a natural element within that order. It would not be “supernatural” but merely a piece of tangible evidence suggesting that we need to rethink certain conclusions that we’ve drawn about our reality.

A common error by non-scientific skeptics is to assume that something is only “real” or “natural” if it can be subjected to empirical investigation. Although this is hypothetically correct, it is often nonsense in practice. The actual extent of the natural world that is currently amenable to our current empirical methods is limited and only a portion is ever likely to be revealed, regardless of how sophisticated we become.

This caveat is compounded by the fact that the manner of “supernatural” hypotheses tend to render them almost impossible to falsify. How do you determine the non-existence of a hypothetically conscious agent like a God or a ghost? i.e. and agent that can ostensibly choose not to be observed? How does one test for the existence or non-existence of Descarte’s Demon or Edwin A. Abbott's "Sphere"? We simply can't without a fairly profound paradigm shift in how we do science.

The correct response towards such claims, then, is to simply say there is insufficient evidence to warrant our accommodation of them, and that there currently seems to be little practical benefit in pursuing them further. Anything else overstates the skeptics case and leaves materialism vulnerable to attack as being dogmatic and prone to similarly unsubstantiated claims, when it is neither.

Defining atheism

2009-06-24T13:00:00.000-07:00

Link Factor 9, Mr. Sulu...

Evolving Thoughts ponders the evolution of the term "atheism", and explains why it defines a species wholly different from his own non-theistic type.

A while ago, my own similar journey culminated in my self-description as an Ignostic, which seems to me the best-defined (and easily explained) and most philosophically sound "on the fence" position for one to assume; i.e. there are arguably no strong, weak, positive or negative Ignostics.

This is in part the reason I abandoned my highly popular and world-renown blog, "The Agnostic Monk". I was afraid that, to the uneducated visitor, "The Ignostic Monk" might be taken to indicate the the author was a regular theologian with some kind of rare congenital disorder.

[edited to add: Jings, I've never seen that before. There an add for "Dianetics" in the post-posting page on blogger! Weirdness...]

[edite once more to add: Now it's gone. Bizarre. And another thing: I've been posting old comments of mine to the archives of this blog so that I can a) stop repeating myself, and b) remember my thoughts, which tend to roll around my head like marbles and are always threatening to fall out of my ears. I hoped that back-dating them would prevent them from spamming everybody's Google Readers and what not, but my Statcounter says otherwise, so sorry about that.

"W H E N in the Courfe of human Events..."

2009-06-15T14:05:00.000-07:00

The Revolution Will Be ...

From The Big Picture, www.boston.com

Boston convention center, 2009 (Biophysical Society meeting)

2009-05-29T13:37:00.000-07:00

foto klub: Eternal Solitude

2009-04-21T06:48:00.000-07:00

A late equaliser brings the game level: Parents 1:1 Wee Un

2009-04-13T08:17:00.000-07:00

The security of my effects has definitely been on my mind lately. There was a time when I could come home from the lab and dump my cellphone, keys, iPod, notebook, Leatherman, Glock* &c on the bureau without fear of catastrophe or reprisal. But now that the Wee Un has been afflicted with that common syndrome known to blight infants of a certain age, locomotion, and has developed a natural affinity for only those things not voluntarily given to her, this is no longer suitable behaviour.

Fortunately, The Better Half made a purchase that dramatically enhanced our lives in the space of a weekend: a set of decoy effects to confuse and disorientate the child for the benefit and safety of my own belongings. She very much likes the car keys, which are metal and have a key ring that makes the satisfying "tweet" of an engaged car security system. Genius. The appliance of science.

No doubt the Wee Un will cotton on to the ruse soon enough, but hopefully these things should keep her occupied long enough for me to complete her "room" in the basement: I just need to finish lining everything with rubber, install the food hatch, and finally remove the stairs and replace them with a retractable rope ladder.

* Okay, so maybe I don't carry a Glock in the lab, but after seeing The Life Aquatic, I've felt that it would benefit everyone in the lab if we were all packing. Not the undergrad stooges, though, they would have to share a Glock. It's the only feasible deterrent for pirates and safety officers, you see.

Better dead than smeg...

2009-04-06T12:30:00.000-07:00

Oooohhhhh... snap!

via podblack blog.

The Dark Arts...

2009-03-26T08:20:00.000-07:00

Luigi Galvani's prototype for the Axopatch 1A

It is my eventual intention to shift emphasis from the currently frivolous posting paradigm back to something more pertinent to the title of this blog. I am currently struggling with expressing such matters as the forging of pipettes and the cosmic and astrological underpinnings of ionic flux, but these efforts are in their infancy and unready to be unleashed upon the masses. (There's also my alchemical treatise - running title, The Saline Solution, or, The Chymical Marriage of Valence - explaining how all the savage ills and persistent melancholies of the universe can ultimately be distilled down to an essential imbalance of ions; a truth suppressed and denied by previous charlatans of The Arts from Paracelsus to John Dee, but that will soon be knowledge rightfully, and indeed righteously, liberated.)

In the meantime, fellow initiate in The Old Mysteries, and editor of the most propitious and informative publication, The Junction Potential, has set the ball rolling with a post charting the travails of the Padawan patcher. As he explains therein, it is long and arduous road fraught with self-doubt, no small amount of madness, and inevitable failure.

There is purpose to these endeavours, of course. The People of the Book and The Eternal Guide are under threat from a great evil and must embrace the etherweb 2.0. and gather their forces for The Last Stand. The very future of The Dark Arts is in doubt.

Image source

When I'm not engaged in scientific research of great import...

2009-03-11T14:16:00.000-07:00

... I'm getting caught on camera engaged in enterprises too complex to be explained in a concise and salient manner; at least one sufficient to satisfy the general inquiring public.

Exhibit A was recently posted to Facebook by someone clearly seeking to defame my reputation as an upstanding citizen of the world.

Taken out of context, it is not impossible to see how such an image - composed as it is of several layers of sinister weirdness - might lead the observer to unflattering conclusions. Nevertheless, there is a perfectly rational explanation...

Teh Scientific Method in action...

2009-02-24T15:24:00.001-08:00

... as demonstrated by The Wee'Un.

Science is persistence... patience... a little more persistence... and, when all else fails, occasionally sitting down in a huff and having a good grumble about it all.

Guardian series: Hume on miracles...

2009-02-09T11:47:00.000-08:00

Julian Baggini plans to post a series of articles in The Guardian's often feisty ComentIsFree, discussing Hume's ideas inre various aspects of religious faith.

Part the First goes into the problem of miracles.

As Baggini writes, Hume defined a miracle as follows:

"It is "a transgression of a law of nature by a particular volition of the deity, or the interposition of some invisible agent.""

Baggini supports this view with the following example:

"Many resist the definition because they do not see why a miracle should not operate within the constraints of physical laws. Take the plane crash in the Hudson, for example. For it to be miraculous, there is no need for the plane to have defied gravity, or Newton's three laws of motion. What made it a miracle was that, for everyone to have survived, an unfeasibly unlikely series of events had to have occurred, but all individually within the bounds of physical possibility.
This explanation will not do. If the series of causes and effects which comprised the crash proceeded without any interference from a divine agency, then there was only a miracle in the figurative sense of an extremely unlikely and fortuitous sequence of events. But if God did so much as even hold up a sub-atomic collision here or delay a transfer of energy there, then the laws of nature have indeed been violated, for physical events would have been prevented from having their usual causes, as physical laws say they must.

This opinion is problematic by virtue of the fact that our understanding of the "physical laws" and the future ability of conscious agents to exploit them are incomplete. Thus, we are in no position to say with certainty that a supreme being of some form could not manipulate events in a manner consistent with those laws.

At the risk of boring everyone with my usual appeal to Flatland, it should seem clear that Sphere can do a lot of stuff that would appear zany and miraculous to Square, and yet do so without contravening any of the physical laws governing both of their experiences. The issue would simply be the limitations of the lens through which Square perceives the world relative to Sphere, who in turn is perhaps herself perspectively limited relative to, say, Monsieur Hypercube.

Real world examples of rational miracles are common wherever two civilizations of greatly disproportionate technological competence meet. I'm reminded of Sean Connery's character in The Medicine Man explaining how he wowed an Amazonian tribe by curing a child's upset stomach.

"Alka-Seltzer. Cured him in one belch. It was the 'plink-plink-fizz-fizz' that really dazzled them."

Of course, there is also no reason to imagine that a supreme being, a creator no less, could not intervene by transgressing its own fabricated physical laws, but simply do so in a manner that is not perceived as a transgression by its creation. Think Agent Smith and colleagues doing the bidding of the great electronic Cartesian daemon in The Matrix.

As it is, the term "miracle" is a highly subjective and ambiguous one. Contrary to Hume's definition, in common parlance a miracle generally describes any ostensibly unlikely event that incurs a significantly positive and advantageous consequence for a given individual. Of course, although a plane crash might serve as the venue for a miracle with respect to any subsequent survivors, the miracle would not be appreciated greatly by the families of those who perished; the miracle is in the eye of the beholder.

Further to that, attempting to define or dismantle miracles via probabilistic reasoning is inherently flawed. This topic came up for discussion inre The Resurrection, over at In Search Of High Places, here, and was stimulated by the British Philosopher, Stephen Law's article on the Historicity of Jesus.

Regular commenter and fellow godless heathen, Matt, had this to say,

"Personally, I've never found the arguments for the divinity of Jesus convincing. All history is a matter of probability, and the probability of Jesus being able to perform miracles because he's an aspect of a divine being given flesh is always going to be much lower than the probability of more mundane explanations."

But I pointed the problem with this argument (which is very much related to recent discussions I've been having inre the legitimacy of post hoc theorizing in science) is as follows:

"You can't actually appeal to probabilities post hoc without falling into the same ~~Inverse~~ Gambler's fallacy that many theists often fall into [when arguing against natural selection on the basis of its improbability]... a miracle is an improbable event anyway, so saying that it is improbable does not argue against its occurrence... it's the improbability that makes these events so crucial to the Christian narrative..."

Regarding the fact that a form of the Gambler's fallacy might be in play here, suppose a friend were to recount the following strange event to us:

"Dude, I just saw the wildest thing. I just watched this bearded guy flip a coin ten times in a row, and it landed heads every time. What are the chances!!!"

Suggesting that the guy must have been using a double-headed coin would seem like a legitimate inference, and yet such inductive reasoning could well be leading us to the wrong conclusion.

Although based on our experience we might intuit that there's something improbable going on, we have not yet taken the data - the seemingly unlikely coin tosses - in the context of the total number of throws (and thus where those coin tosses lie in the overall distribution curve of outcomes). In fact, if we interpret the data in the correct experimental context we may well find that the odds of the coins landing in a continuous sequence of heads are actually the same as if they had fallen in any other sequence of heads and tails. For all we know, the old man might have been flipping coins for eons, and it just so happened that our friend, among the constant stream of passersby, was there to witness the tiny fraction of coin tosses that probability predicts would inevitably fall in the same sequence at some point or other.

This is, actually, a potential source of Type 1 errors in scientific studies. For example, a scientist might generate some data in order to test one hypothesis, but then notice during analysis that there appears to be another variable that is different between the control and test samples. He might conclude, possibly erroneously, that his drug is responsible for this additional observed difference. If he's thorough, he will simply use this observation as a basis to generate a new hypothesis and test it with further experiments designed to specifically look at that variable.

[edit 1: I was getting my Gambler's and Inverse Gambler's in a twist. Speaking of which, there's a simulation of the Gambler's fallacy in action here]

[edit 2: MilesSmiles puts it in a nutshell in this articulate comment on Baggini's original article.
He writes, "Empiricism as a view about the justification for human knowledge claims is misconceived. But Empiricism as a naturalistic account of our sensory interactions with the world is really science, and not philosophy. What Hume did, and others as well, was take a causal theory about human sensation, and tried to treat it as a foundation."]

Cartesian Doubt: a concise primer

2009-02-06T10:15:00.000-08:00

Being very much a fan of both Red Dwarf and The Hitchiker's Guide to the Galaxy "trilogy", I was shocked to discover that I have lived a significant portion of my life in blissful ignorance of one of the key inspirational forerunners of these shows: John Carpenter's terrific 1974 sci-fi classic, Dark Star.

Apart from being ace - and it most certainly is - the film includes one of the most memorable, but concise, introductions to phenomenology ever.

Check it out.

Datum of the Week

2009-02-05T15:42:00.000-08:00

Often lost, as it is, within the collective obscurity of the n, I think the humble datum has for too long gone unrecognized for its aesthetic contribution to contemporary science. It is, after all, the indivisible unit of discovery; surely that counts for something? The Victorians certainly thought so. They understood, in their inductive way, that although the individual datum might not be disposed to supplying the revelation and finality of An Answer - standing stoic and singular on its all too often ambiguous ownsome - it nevertheless compels us along the path of What Might Be.

Of course, whether it compels us in the right direction along that path is neither here nor there, and indeed, there has been many a datum that has stood defiant in its contrariness to the emerging trend; refusing communion with its brethren and stubbornly carving out a libertine domain far away from The Mean, challenging us to find whatever tenuously valid, but always imaginative justification we may for evicting the unsightly outlier from the final analysis.

Yes, the datum deserves to be singled out once in a while for individual recognition. I'm not talking about those pretty, but oh so pedestrian! publishable datums either. Nay, true art thrives on imperfection, is emboldened by rejection, earns its lofty pretensions by virtue of being so profoundly unpretentious. No less is true for the illustrious datum.

With this in mind, ladies and gentle others, I give you my own personal Datum of the Week.

It's an ugly beast, to be sure. And yet it is imbued with a powerful sense of mortality... a sense of... What exactly went so terribly awry at 22... are those seconds? Needless to say, this datum will have no further part in the Battle for Understanding. It is a mere casualty. It is the The Unknown Datum, and there are many like it.

I leave it for all three of you to ponder, readers.

You have been sucked into an experimental Link Loop...

2009-02-05T07:32:00.000-08:00

See comment #31

Comment: on The Ugly Story of Texas Curriculum Standards

2009-01-27T09:04:00.000-08:00

In response to The Ugly Story of Texas Curriculum Standards, on the Blue Lab Coats blog.

Academic said,

“By a chance evolutionary process beginning with a synthesis from 92 basic elements” very morally challenging.”

Why? These things have been hashed out at length. As it is, it is not at all hard to understand how we have developed both an innate, if complex, moral compass in addition to the sufficient capacity for abstract thought to appeal to reason and generate social contracts.

“Humans are only here because we evolved from pond scum. Why should I respect someone else’s humanity?”

Because you are descended from a line of humans that have survived by virtue of cooperation and mutual protection, and as a result you have an innate predisposition to develop the same. It is not a complete code out of the box, but the basic mechanisms are in place when you are born that can subsequently be tweaked and honed by the immediate social environment. You are, by all means, free to attempt to divest yourself of this moral compass – it’s an interesting experiment to try – but I guarantee you’ll find it harder than you think (there’s purpose behind the fact that dehumanisation is so often a prerequisite for killing, whether in homicide, war, or genocide). The only human that has actual need of an objective, external and dogmatically enforced moral compass is the sociopath.

“If it’s all about natural selection and “Survival of the fittest” then why should I stand in the gap of people in poverty, or people who are disabled?… If we’re all just a chance derivation from pond scum, then why bother at all?”

Why not? Or rather, why would the addition of a deity into this process suddenly imbue everything with a sense of meaning? Try thinking along those lines without lapsing into circular reasoning. The answer for why, regardless of origin story, it is generally (but not always) useful to behave altruistically is that such behaviour has a thorough stabilizing effect on human interactions and societies. It develops trust. No trust, no society, no tribe, no cooperation. It really isn’t hard to see why a species that had to carve its niche out in a world inhabited by animals much larger and more vicious than it would learn the art of cooperation. It’s not an unlikely story judging by the number of species that have evolved a similar propensity towards cooperation independently of those among the primates (e.g. those among the canid family, and my personal favourites, the meerkats etc).

Comment (b): on Descriptive vs. Hypothesis-driven science

2009-01-20T09:01:00.000-08:00

In response to Descriptive vs. Hypothesis-driven, on the Blue Lab Coats blog.

Whimple said,

“Is the difference between a descriptive hypothesis and a mechanistic hypothesis that the mechanistic hypothesis is falsifiable?”

A hypothesis must be falsifiable period, whether broad and weakly-focused (omics, “fishing expeditions” and so forth) or narrow and explicit. I think the latter is what is often referred to as “mechanistic” science, even though all science is ultimately directed towards establishing cause.

I think the current brouhaha about “descriptive science” conflates two separate issues best described by the following examples:

1) The serendipitous discovery: The investigator is testing her prediction that Treatment A will increase Variable X. During analysis, however, she discovers a trend indicating that Treatment A also appears to have changed Variable Y.

2) The fishing expedition: The investigator enters a fledgling research field regarding a new disease for which little is known of the cause. He proposes to do a genetic screen to see whether the disease is simply a result of a genetic defect. He finds that expression of genes X, Y and Z is deficient in all patients with the disease, but not in patients of the control group.

(1) is hypothesis-free and (2) is hypothesis-driven. Both are clearly hypothesis-generating. Under current standards, (1) cannot be published without at least designing new experiments to test the hypothesis that Treatment A affects Variable Y (only on this subsequent data can statistics be applied meaningfully; post hoc theorizing enhances the likelihood of false positives). (2) Satisfies the hypothetico-deductive model completely, and the issue determining publication will be the impact of the work and the reliability of the methodology.

Comment: on Descriptive vs. Hypothesis-driven science II

2009-01-20T08:51:00.000-08:00

In response to Descriptive vs. Hypothesis-driven, part II, on the Blue Lab Coats blog.

Whimple said,

“For example, “we hypothesize that doing these experiments will reveal the ultimate secrets of the universe to us.”

This is a circular hypothesis that is not falsifiable (to know that all of the ultimate secrets had been revealed would require prior knowledge regarding the ultimate secrets).

Dr. J said

“Then we collected some data looking for an expected difference between two groups, but instead got data showing that the two groups were identical–but vastly different from the accepted How Things Work.”

A prediction reveals an implicit hypothesis (and falsifiable) if not an explicit one.

“and maybe better… since it would be tough to bias the screen by having an idea of the outcome in your head in advance.”

Well, the point of the hypothesis-driven method is to bias one’s attention towards the variable(s) under investigation, though. That’s how you can apply probability to them meaningfully. i.e. the chances that the variable you are examining is going to return a result that is a false positive is much smaller (and pre-definable) than the probability that any one of a hundred other variables you’re not focusing on might give false positives or negatives.

I see your point about being ‘open minded’ though, as it pays dividends to look at all of the information available from a piece of data regardless of whether it is directly related to the hypothesis. That’s how new observations are made and new avenues of investigation pursued.

“Second- still in regard to #1- how likely is it that the investigator does what DSKS proposes (design new experiments to test a new hypothesis)… and doesn’t just ‘adjust’ the original hypothesis and hammer out a paper. I’d love to think that’s not the way things work… but am I hopelessly naive?”

Scientifically this is improper, but sometimes pragmatism probably wins if a given experiment is simply too expensive or time-consuming to repeat. Some might argue that fudging a hypothesis to fit the data is just ‘good rucking’. Given that people are often wrong, and that science is inherently self-policing, there’s possibly a case to be made for that approach; if you’re wrong, somebody else will figure it out so no harm done (although, false information can end up being expensive and time-consuming for somebody else). All I would say is that resting a conclusion on such data puts you in the position of being more likely to be wrong than if you proceeded according to the established model. It’s up to the investigator to make the best call.

One thing I’m finding a challenge is imagining a designed experiment without at least an implicit and falsifiable hypothesis. When one designs an experiment, surely one has a goal in mind, and surely there aren’t too many steps from that goal to a valid falsifiable hypothesis, no matter how focused or vague?

Comment: on Descriptive vs. Hypothesis-driven science

2009-01-08T08:59:00.000-08:00

In response to Descriptive vs. Hypothesis-driven, on the Blue Lab Coats blog.

-----------------------

DM said,

“the entirety of science is a description of what happened under certain conditions.”

And in doing so highlighted the fact that semantics might be generating a storm in a teacup on this issue. I’ve seen that definition used a fair bit, and it’s also common to see the slightly narrower definition of descriptive science as being “knowledge for its own sake” vs normative science (an issue that has been well handled with the formation of the NSF on the one hand and the NIH on the other).

Then we have the authors of the linked article in the original post, and the editors of IAI, who seem to be associating “descriptive science” with initial observations (hypothesis-free), creating a further definition. If the authors are arguing that the first step in the hypothetico-deductive model should be allowed to stand on its own and be published, then there are well established caveats to doing so (see Black Sheep joke). On this note, I’d actually agree with the other commenter who suggested a separate journal for this kind of thing, because although sharing initial observations could be very useful for the scientific community, it would be important to separate purely inductive research from conventional hypothesis-driven research.

Regarding fishing expeditions (omics etc), the term “discovery-based science” has been used. It’s important not to conflate that with “initial observations” though because, as Steven Wiley wrote in The Scientist even fishing-expeditions are generally hypothesis-driven. The difference is usually only in the scope and strength of the hypothesis.

So in response to DM’s comment,

“(oh and for anyone who simply cannot avoid putting their fishing expedition into a proposal make sure to use the phrase “hypothesis generating aspect of the plan”.)”

You can give a stronger argument than that. The fishing expedition is not only hypothesis-generating, but is motivated by a hypothesis in the first place. Professor in Training states his hypothesis for the “descriptive” project he was accused of proposing very clearly in his comment. Of course all new and exciting avenues of research necessarily originate from a very broad question, which often requires casting out a wide net. It’s either that or let science rest on some pretty spectacular leaps of intuition to get it directly from Disease X to a frame-shift generated stop codon in the middle of the mRNA transcript for gene Y. If the preliminary data is compelling enough to apply strength to that broad hypothesis (i.e. indicate that, as Matthew describes, this particular fishing expedition might be worth the time and money), one can easily argue that the outcome of the study will facilitate the progressively narrower generation of subsequent hypotheses, which will ultimately begin to isolate the most probable mechanism.

And another thing…!

Characterization of the infant noggin channel, Oral1

2009-01-04T08:57:00.000-08:00

Introduction: The recent progression of the household Padawan to solids has provided a unique opportunity for the extensive study of the face-localized infant channel, Oral1. Although the existence of Oral1 has been known for some time, it has yet to be subjected to systematic study using modern investigative techniques.

Methods: By necessity, single channel currents were recorded from the infant noggin using the noggin-attached configuration, as excised outside-out patch studies from the whole noggin are understandably restricted under NIH guidelines.

Results: Gating behaviour of Oral1 was constant but sporadic, with the channel exhibiting constitutive activity in the absence of exogenously applied agonists. Nevertheless, both open probability and mean open time were markedly increased by the presence of the well-characterised growth-regulating factor, SpOoN. Contrary to our hopes, Oral1 did not display strong inward rectification. Indeed, much to the chagrin of myself and colleague, outward flux was often of an amplitude not that much smaller than the sizable inward flux.

Figure 1. Oral1 visualised through a 4 mpx digital capture device at 1X magnification.

Regarding permeability, activation of the Oral1 evoked a highly milk selective conductance at first, but with prolonged activation appeared to switch to a more-or-less nonselective configuration permeable to peas and squash (Figure 1). Thus, Oral1 represents another example of a channel that can alter its permeability in seconds in a manner likely to be physiologically relevant to our shopping list. However, it appears that the channel is only weakly permeable to sweet potato, which exerted a strong outwardly rectifying profile indicative of permeant block.

Conclusion: These data have substantially enhanced our understanding of the Oral1 selectivity filter, although in the absence of a successful attempt to crystallize Oral1, a precise structure of the channel pore is not yet available for us to draw more informative conclusions regarding the relationship between structure and function for this channel. Regardless, on the basis of the evidence presented in this paper, it is reasonable to predict that things are going to get progressively messier in the coming months.

Origins of electrophysiology (author and date unknown)

2008-12-11T11:48:00.000-08:00

"IT is always understood that Electrophysiologists have a secret which they carefully conceal; but from every thing that can be collected from their own accounts of electrophysiology, their real secret is no other than their origin, which but few of them understand; and those who do, envelope it in mystery.

The Society of Electrophysiologists are distinguished into three classes or degrees. 1st. The Apprentice Dabbler. 2nd. The Fellow Patcher. 3rd. The Master Clamper.

The Apprentice Dabbler knows but little more of electrophysiology than the use of the equipment to perform a basic whole-cell recording in the broken patch, voltage clamp configuration, in addition to the implementation of certain words and gestures by which Electrophysiologists can recognize each other without being discovered by a person who is not an Electrophysiologist. The Fellow Patcher is better instructed in electrophysiology than the The Apprentice Dabbler, being capable of numerous techniques, whether intracellular or extracellular, voltage or current clamped, and is actually able to draw the circuit diagram describing the experimental apparatus. It is only in the Master Clamper's Lodge, however, that whatever knowledge remains of the true origin of electrophysiology is preserved and concealed."

Rhineland Requiem

2008-12-08T06:02:00.000-08:00

Perhaps "requiem" is a bit over dramatic. It's about to be shipped off to a bajillion other festivals that will probably be a better fit for a low budget war movie. Long range howitzer of a shot that it was, for good or ill, my mug won't be gracing a theatre in Sundance next year, though.

A terrible shame, indeed. Hollywood has been robbed of some truly inspired bit part genius. Not since Biggs Darklighter has there been a character so compelling in the delivery of his few lines, and subsequent inglorious demise, as Cpl. Dwyer, played by your humble servant, myself.

Perhaps my performance was just too dangerous, too edgy for the mainstream movie moguls to handle?

Whatever the explanation, it's back to science for the time being.

My photos from the set of Rhineland, St. Clair, MO.

Comment: on A Simple Question

2008-12-02T09:08:00.000-08:00

In response to A Simple Question, on the DrugMonkey blog.

Dr. F said,

"We must distinguish between hypothesis driven science and so-called "descriptive" science."

I disagree. "descriptive science" is the initial step in "hypothesis driven science". It's already part of the package. The primary inductive part of the process, based as it is on initial observations/measurements, leads up to the generation of the hypotheses and subsequent predictions, which must be tested before you can draw any conclusion about the described initial observation.

When people talk about hypothesis-driven science, they are usually talking about the hypothetico-deductive model, and thus already acknowledge the importance of descriptive science in starting the ball rolling. However, relying on descriptive science alone is a no-no, for the obvious reason that one cannot assign statements of probability, and cannot apply statistics, to data after the fact, without being in serious danger of perpetrating the Gamblers Fallacy or its inverse. One finds an over-reliance on descriptive "science" in many places: The Discovery Institute, The Church of Scientology, and Pacific cargo cults to name a few examples.

Cajal's descriptive work was surely vital and compelling, but it was of absolutely no conclusive value until he and others made and tested predictions generated from these observations. If they had not done this, we would simply have an observation for which a billion different explanations could be put forth, and no recourse to probability to separate one from the other.

The Method of Multiple Hypotheses

2008-12-02T07:24:00.001-08:00

A commenter going by the handle, JB, over on Drugmonkey's blog, brought the following article to attention:

T.C. Chamberlin (1890). The Method of Multiple Working Hypotheses. Science. 148, 754-759

It deals with the problem of becoming emotionally attached to certain hypotheses, and how to avoid the potential conflict of interests that this kind of affectionate bias can generate. Well worth a read.

Of course, it doesn't apply to me. I'm as objective, cold and logical as the bastard child of Hal 9000 and Dr. Spock.

Addiction by association...

2008-12-01T08:36:00.000-08:00

David Linden recently posted on the subject of "Drugs and the Memory of Drugs".

He writes,
"Drugs, by co-opting the pleasure circuitry and activating it more strongly than any natural reward, create deeply-ingrained memories that are bound up in a network of associations."

This seems to present a serious conceptual challenge inre: trying to generate from our increasing knowledge of learning and memory some feasible and necessarily specific targets for pharmacological intervention.

I think research in this area is tremendously exciting and will reveal much about the biology of behaviour (more bricks for the bridge between biology and psychology). However, the question is whether the complexity we uncover will increase rather than decrease our optimism in the potential for treating self-destructive addiction behaviours pharmacologically.

Linden relates the following anecdote:
"In his moving (and also hilarious) autobiography of teenage heroin addiction, The Basketball Diaries, Jim Carroll writes of a friend who tried to kick his heroin habit by seeking spiritual solace in the Catholic church of his youth. However, the smell of the church incense reminded him so much of bubbling heroin that he felt an overwhelming craving and rushed home to shoot up again."

This is personally relevant to me. I'm currently suffering from the savage DTs after a relapse over Thansgiving weekend. The "church incense" in this case being the film 2001: A Space Odyssey, which triggered my addiction to a certain early '90s series of video-games (no prizes for guessing). I might have pulled through, but my active "seeking" behaviour caused me to discover DOSBox, and everything went seriously Trainspotting after that. And I'd been "clean" for almost a decade. Well, tomorrow I will purge my laptop of the offending material and get right back on that wagon, you can be guaranteed.

Tomorrow.

[edit: Just came across this editorial by Addiction's chief editor, Griffith Edwards, discussing reductionism in the study of addiction.]

foto klub: Partially oxidized, but good edge...

2008-12-01T07:01:00.000-08:00

Telling tales

2008-11-26T10:00:00.000-08:00

There are discussions ongoing here and here regarding the use of artistic license in paper writing. The importance of building a narrative out of our results for more effective presentation to our colleagues is not to be taken for granted. As one commenter put it,

"The human being is a story-telling animal."

However, there are clearly lines that cannot be crossed in the pursuit of turning one's series of data into a ripping yarn, even if it means it might significantly elevate the subsequent paper's impact. Some of the responses to posts linked to above at least appeared to go so far as to legitimize, if necessary for narrative reasons, altering hypotheses to fit the acquired data. That involves walking a very fine line in terms of intellectual honesty, for the reasons summarized by this commenter:

"My worries about the "creative fiction" of post-hoc hypotheses that were tested by your result is that they are circular. If you see a pattern of results, that don't support the idea you were testing, and then come up with a hypothesis to explain your results, how do you avoid circularity?"

The general opinion appears to be that this sort of thing goes on in science all the time. If true, that should be discouraging, to say the least. Neurolover continues,

"I think it's possible that in some fields, what people are really doing is really "hypothesis generating": That is, they make some measurements, come up with a hypothesis, and then test that hypothesis with further experiments."

Indeed, that's how we were all taught to treat initial observations in highschool: as a platform on which to form hypotheses and generate predictions for subsequent testing. It's the hypothetico-deductive model in action. I doubt that it represents the final word on what form the empirical approach should take (Popper has his critics after all), but it's generally agreed upon to be the best model to date. The all important prediction aspect adding a much needed element of deduction to what would otherwise be a purely inductive reasoning process.

If, in writing the summary and conclusions of a set of experiments one alters the original hypothesis to "fit in" with the observed data, one undermines that vital predictive criterion and the reader is left with a paper basing its conclusions on post hoc theorising.

All that said, I am imminently in favour of a specialized Journal catering to those of us who would like to submit papers written in Victorian prose. As it is, I have to send such material to the Sci. Creat. Quart, which although a prestigious periodical, is for some reason not listed on Pubmed.

foto klub: Lab Space

2008-11-20T15:24:00.000-08:00

Preliminary experiments in DOF with fully manual mode and a desk lamp.

Of bird-eating spiders and their tendency to not eat birds...

2008-11-19T12:39:00.000-08:00

The handsome beastie pictured right is Psalmopoeus cambridgei, or the Trinidad Chevron, a member of the large and somewhat heterogeneous Theraphosidae family of "bird-eating spiders".

We had this nice little paragraph in the discussion of a manuscript about ASIC1a receptors (structure recently resolved), which speculated that a particular and interesting finding of our results regarding a toxin isolated from the venom of this beastie might be relevant to its avian-oriented predatory habits. I was rather excited about it. More excited about it than the main thrust of the paper's conclusion, which was essentially to point out that something people thought happens probably doesn't happen at all. In short, a bit of a Debbie Downer of a paper.

Anyway, we put a call into the local zoo just to be on the safe side and have subsequently been politely informed by a specialist in matters of arachnidic import that these spiders, along with most bird-eating spiders, rarely if ever actually eat birds. Apparently the whole "bird-eater" thing comes from some sketchy anecdotal evidence supplied by various Victorian naturalists claiming to have seen certain tarantulas prey on small birds and hatchlings. Indeed, the very fact that the spiders appeared to live in trees was considered to be good evidence that they must eat birds. Birds often being found in trees too, you know. Those early gentlemen scientists could sometimes be a bit liberal with their inductive reasoning, it seems.

Perhaps, we ventured hopefully, the adaptation of cambridgei's venom was so efficient that it had simply succeeded in eating all the birds in the vicinity of its natural habitat, and that the poor wee beastie had no other choice but to eat crickets and cockroaches from thenceforth? Or maybe it just got sick of stuff that tasted like chicken and yearned on something a bit different? The expert was not excited by either hypothesis, so it goes.

And so ended my ever so brief flirtation with the behavioral relevance of my research.

(Image from Terraristiecke.de)

The importance of physiology

2008-11-10T07:31:00.000-08:00

PhysioProf, one half of the duo running the blog, Drugmonkey, slapped up a post defending the importance of medic students having a sound grasp of human physiology. I think this is relevant to conversations happening in a number of institutions currently considering med school curriculum overhauls of some form or other. From what I'm hearing, and somewhat inexplicably for reasons PP highlights in his post, basic physiology is often seen as the weakest link in these programs. That's a pretty wild notion, IMHO. It's a bit like suggesting that knowledge of engineering is outside the scope of teaching a kid how to be a car mechanic.

Anyway, check it out...

Strangely appropriate for the occasion

2008-11-04T20:50:00.000-08:00

... to someone of my unique mental disposition, anyway.

Comment: on God Poetry and Emotion

2008-09-05T09:28:00.000-07:00

In response to God Poetry and Emotion, on the Stephen Law blog.

Joshua,
Prof Martin's argument is immediately rendered rickety by the following statement,

"Showing that God's existence is possible but unlikely will do."

No, it won't, imho, for two related reasons.

First, the entire God thing is considered miraculous, and therefore, inherently improbable. So making an empirical argument challenging the probability of God isn't going to cut much ice with a faith in his existence, of which the improbability of it all is a prerequisite factor for the belief system in the first place.

Second, by taking this route Martin is likely to end up running afoul of something akin to the
inverse gambler's fallacy, which is the usual stomping ground of creationists. Statistics are incredibly limited when it comes to trying to assess the probability of an event occurring when it has already (albeit allegedly in this case) occurred. Much like throwing a dozen coins in the air and noting the sequence of heads and tails, if one retroactively applied a probability test to the emerging sequence, we would find that its probability was incredibly low. But as Hacking describes (and others before him) such a test is invalid. Now, in this instance, the results of the coin toss have come down to us in a most indirect manner, but that doesn't change the fact that its if scientifically unsound to dismiss these assertions on the basis of a posthoc assessment of probability.

As we've discussed here, it is difficult to bring any evidence to bear inre the existence or non-existence of something we cannot readily define. The only time we can bring empirical force to bear on this question is inre more clearly defined God's. e.g. Olympian Gods, Mormon theology, and certain literal interpretations of the Christian narrative are arguably falsifiable.

But I agree with Dennett that the woollier, touchy-feely definitions of God are unassailable by current empirical paradigms.

Pharmacology Lore...: Rat hearts and London tap water...

2008-09-05T07:23:00.000-07:00

[Erratum inre "Pharmacology Lore...: Rat hearts and London tap water". Originally published 07/10/06]

In response to a brisk letter from Dr. Caffeine (see comments), the authors of a previous blog post (see below) would like to retract their assertion that Sydney Ringer was in any way, or at any time, guilty of complacency with regard to the quality of water used in his experiments. It appears that the perpetrator of the tap water fiasco was, in fact, Sydney's technician, a certain Mr. Fielder. The authors would like to apologise profusely to the descendants of Dr. Ringer, and his fans, for this oversight and for besmirching - nay, outright befouling - the good name of a great scientist. For more information regarding the newly emerging well-documented evidence warranting this retraction please download this article, by Dr. David Miller**, from the The Physiological Society website. This does, of course, slightly attenuate the veracity of our conclusion that "being sloppy pays off sometimes", but we feel that further evidence may nevertheless possibly justify our claims if we look hard enough and wait long enough.

** Winner of the Physiological Society's Paton Prize (2007) for his work on the life and times of the gentleman and scientist, Sydney Ringer.

Here's a pretty well known (and likely embellished) factoid from the Old Days. In the early 1880's, Sydney Ringer* (he of Ringer's Solution fame) observed that isolated rat hearts would maintain their contractions for far longer when suspended in saline solution made up with London tap water, than when suspended in saline solution made up with distilled water.

What was so special about the stuff made with London tap water? Well, London tap water was very hard at the time (probably still is), and thus contained significant amounts of free Ca²⁺. Distilled water, of course, has trace levels of Ca²⁺ at most. No Ca²⁺, no muscle contraction. Eureka.

By all accounts, it seems Sydney only used tap water out of laziness. So, it just goes to show that being sloppy pays off sometimes.

References:
Carafoli, E. (2002) Calcium signaling: A tale for all seasons. Proc. Nat. Acad. Sci. 99:1115-1122. Free online.

Miller, D.J (2007) A solution for the heart: the life of Sydney Ringer (1836-1910). The Physiological Society.

Miller, D.J. (2004) Sydney Ringer; physiological saline, calcium and the contraction of the heart. J. Physiol. 555:585-587. Free online.

Ringer, S. (1883) Physiological saline, calcium and contraction of the heart. J. Physiol. 4:29-42; 222; 370. Free .pdf files for download.

* Apparently the poor geezer doesn't even have a Wikipedia article in his honour. Shocking.

Just in time for the weekend

2008-08-15T14:19:00.000-07:00

We had our latest submission accepted for publication as a rapid communication in JBC under the proviso that... horror!... we do one last experiment. In fairness, I anticipated the issue might come up, and was in the process of doing the suggested experiments while it was in review (at least, I was trying to do them; see below).

Ha, ha.

Rapid communication, indeed. In accordance with Sod's Law, every possible thing that could have gone wrong went wrong, thwarting my high-minded intentions to knock the experiments out in a couple of days. Almost a month later, having stripped down my solution exchange system and replaced all the tubing, made a new batch of cDNA for the all important mutant, and finally coaxed the pipette puller to produce pipettes with a consistent and appropriate resistance*, we finally obtained the necessary data.

Well, now it's out there. For good or ill.

Not quite as timely as I'd hoped, but it's coming out on the back of two fairly high profile papers on dynamic cation selectivity (TRPV1 receptors, Chung et al., 2008; and P2X2 receptors, Chaumont and Khakh, 2008), which is encouraging for the field... but also a bit frustrating for us, because our own paper was kicked back from a higher tier journal with the old boilerplate response, "too technical and focused for broad appeal". So it goes.

* It was a simple filament replacement, and ordinarily I'm pretty slick at tinkering with the parameters to get my preferred pipette resistance and shape (tip shape being crucial for our experiments). However, at times I find that these infernal machines defy empirical sense, and I find myself randomly punching in numbers in a vain attempt to try to understand the new set of physical laws that the damned thing has suddenly decided to embrace.

Dubious selectivity file: CTOP

2008-07-25T08:35:00.000-07:00

The somatostatin peptide analogue, D-Phe-Cys-Tyr-D-Trp-Orn-Thr-Pen-Thr-NH2, or CTOP, is sold as a potent and selective mu opioid receptor antagonist (IC₅₀ in the low nanomolar range) ^1-4.

However, Chieng and co-workers (1996) ⁵ noted that CTOP activated hyperpolarising K⁺ currents in isolated locus coeruleus neurons with an EC₅₀ of 560 nM. The activity was resistant to the broad-spectrum opioid receptor antagonist, naloxone, and appeared to be mediated by a somatostatin receptor-like receptor, possibly sst2.

Kramer and co-workers (1989)³ also observed modest agonist activity by CTOP.

1. Gulya K et al. (1986). Life Sci. 38, 2221-9
2.Hawkins KN et al. (1989). J. Pharmacol. Exp. Ther. 248, 73-80
3. Kramer TH et al. (1989).J. Pharmacol. Exp. Ther. 289, 249, 544-51
4. Law P and Loh HH (1999). J. Pharmacol. Exp. Ther. 289, 607-24
5.Chieng B, Connor M and Christie MJ (1996). Mol. Pharmacol. 50, 650-5

"Problems of drug selectivity..."

2008-07-18T09:34:00.000-07:00

After a long hiatus, I'm reopening my investigation into the vices, blasphemies, and generally promiscuous escapades of drugs used to study the role and mechanisms of receptor function in biology. Drugs are crucially important in science, and so their occasionally wanton and polygamous behaviour cannot go unremarked and undocumented. They must be confronted by the evidence and brought to account. I should point out that I tend to try and focus on those drugs for which certain selectivity issues are not well-described, and in some cases are omitted from their briefs in drug company catalogues. Thus, a lengthy critique of suramin - the Paris Hilton of promiscuous drugs, whose abhorrent crimes against the ideals of selectivity are well-documented - will not be forthcoming.

So, with that in mind, file the following under 5-HT (seretonin) receptors:

In this letter to J. Physiol., Andrew Ramage ponders the pitfalls of drug selectivity; in this case, with regard to antagonists, such as Methiothepin, used in a study investigating a particular functional role of 5-HT2A receptors.

"How to blog, get tenure and prosper..."

2008-07-18T08:38:00.000-07:00

[via Evolving Thoughts]

John Hawks explains...

The Application of Moral Status

2008-07-17T21:19:00.000-07:00

Over on Thalesian Fools, Timmo presents the first part in an argument against the unfair treatment of animals, particularly with respect to their consumption for food.

In response to one of my comments, ej writes,

"Your idea that humans only have moral status in virtue of the fact that people care about them or that they live in communities which value them is problematic. Not all humans are cared for. For instance, orphans who were warehoused in orphanages where they were not especially cared-about by their overseers.

"Are you going to bite the bullet and say that when people stop caring about others then they cease to have any moral standing?"

To which I reply in characteristically long-winded and meandering form as follows:

In the sense that moral standing is supplied by persons to persons, and not by an external and universal set of principles, then yes, I bit that bullet long ago. But the implications are not as dire as they seem, imho.

The exploitation of others, humans or animals, invariably harbours some complex attitudes inre morality, but I think it is still the case that a certain set of standards, the ones we tend to consider "good", win through on the basis of a combination of our innate conscience and a well-reasoned assessment of the means vs the ends. IF we take care to preserve these principles when we form our institutions.

Regarding the orphans perhaps employed in a workhouse, if you asked an independent person who had nothing obvious to gain or lose from the exploitation of these orphans, they would surely object strongly to their conditions, regardless of whether they believed the orphans were equal or inferior. I doubt they would appeal to reason, here, but instead draw on their innate conscience (which, in Victorian era England, would probably have been ascribed to a divine force, but the result is the same). It was, of course, the increased awareness of workhouse conditions that cause the general populace to voice their displeasure and demand reform. The general populace being sufficiently objective and free of a strong personal stake in the continued mistreatment of the workhouse labourers (other than via the cost of silk stockings).

On the other hand, if you asked the Dickensian workhouse owner what he thought, he might say something like, "Well, we don't force them to work here, and at least they're not on the streets. Besides it's not my fault that the world desires silk stockings, and that our stockholders demand adequate returns on their investments. I couldn't do anything about it if I wanted to. Anyway, I think it's really the government that should be doing something about the poor things... it's not our fault they're too poor and uneducated to find work elsewhere."

Immediately we're stuck in to the complexities of human morality within institutions, where responsibility, the perception of control and empowerment, and an often narrow, short-term view of the means vs the ends leads to a distortion of individual accountability. Add that to the ignorance of the wider populace regarding the mechanisms of certain institutions (in the case of animal husbandry, the consumer), and you have all manner of evils being perpetrated by an institution of people who otherwise hold quite normal and stable individual moral codes, under the nose of the consumer who is simply ignorant of the true cost of that which she consumes.

Thus, although I reject the idea of universal moral principles, I generally believe that we subscribe to a common set of evolved principles that only become compromised when we create group structures that are insufficiently designed to preserve those innate principles. Unchecked capitalism is a classic example of an ideology that divorces our innate moral reasoning from our institutions.

Regardless of the moral collapse that has occurred within the institution exploiting the orphans, such exploitation can still be argued to be morally wrong, both because it assaults our evolved individual consciences and because reason also informs us that exploitation invariably leads to social instability; revolt, revolution, terrorism &c. This, in fact, is precisely the attitude that has driven policy for thousands of years. When somebody is exploited, trouble is never far away. The most stable societies take care to ensure that exploitation is minimal if not entirely absent, and it is these societies that avoid the destructive forces of constant civil strife and persist.

So in answer to your question re the orphans ill-treatment,
"...is there anything wrong with causing them to suffer so horribly at the hands of others?"

The answer is yes. But only because their treatment violates the evolved moral conditioning of that particular community of which they are a part of. If their oppressors were an alien race that simply did not include the orphans within their moral framework, there would be no sense of who is wrong or who is right to appeal to, because each would see the same situation differently. As the lion and the antelope clearly do. They would simply be two rival organisms competing in a common environment, in which case, "might would make right". Although in nature, "might" does not always refer to physical prowess. If it did, a skinny, hairless creature like us, with no claws or sharp teeth to speak of, wouldn't have wrested control of an entire planet full of far more physically superior beasties.

Irreducible Absurdity: Exhibits D through infinitum...

2008-07-04T07:42:00.000-07:00

The in-laws gave my wife and I a terrific present to ease us through the sleep deprivation associated with new parenthood: the box set of the Beeb's Planet Earth series. Proof positive that there simply must be a creator, and that She's stark raving bonkers.

Regard the following clip, and be swayed from the coercive manipulations of the Great Darwinian Communofascist-QuasiZionist-SlightlyMasonic Plot.

"Irreducible Absurdity", ladies and gentlemen. Repeat it often enough, and you'll soon recognise that it can be the only Truth.

Crazy Birds Island :p - Funny bloopers are a click away

Evolution museum?

2008-06-13T07:57:00.000-07:00

I share PZ Myers skepticism about a proposed evolution museum to challenge Ken Ham's creationism museum.

However, a full-on, bells'n'whistles, one-stop-shop online evolution museum might be useful. (Unless there already is one, and I'm just not hip enough to know about it.)

Clearly, there's a tremendous amount of info out there on the old interweb regarding evolution, but much of it is pretty sterile and uninspiring stuff. Particularly as far as the wee'uns are concerned, whose minds constitute a chief strategic goal in this crazy culture war: gotta get them impressionable ADHD, PS3-loving, text-messaging brains before They do. That means plugging some green into top-tier web design, with interactive animations, narration by David Attenborough*, and plenty of dinosaurs.

As much as it's wonderful to see scientists getting on the web and taking it directly to the people, we have to concede that our marketing has consistently failed to elevate itself above the level of barely mediocre (although, I have recently succeeded in making a little red spot move across the screen in Flash CS3...).

PBS had a good crack at developing an evolution page, but the site is still text-laden and very much typical of government educational media. Even the Flash plugins resemble a Powerpoint presentation by a presenter who has only just recently discovered how to make things zip across the screen (and thus feels the need to use this facility constantly, and without any regard as to whether it actually enhances the viewing experience).

If we're going to pass the hat around, I think a good cause would be a professionally designed website on evolution. One on the same level as that which is becoming standard for Hollywood blockbusters.

Comment: on Women and Superstition Part 2

2008-05-12T09:33:00.000-07:00

In response to Women and Superstition Part 2, on the Pod Black blog.

I enjoyed reading these two posts (via Evolving Thoughts)

I’m not terribly convinced by the the evidence that women are more inclined to appeal to supernatural or paranormal phenomena than men. First of all, attempts to quantify this tend to to immediately fall into experimental bias (perilously close to question begging) by trying to draw a line between conventional religion and “all that other fluff about runes, crystals, and lay lines”. All forms of spirituality considered, the current evidence (based on census data for example) clearly show no significant difference between men and women in terms of being more or less likely to appeal to the supernatural.

Historically, it is clear that men have strongly embraced the supernatural, and that this, together with social trends, has resulted in the majority of “conventional” forms of spirituality being overtly paternalistic. I agree with the opinion that the association of such things as astrology, Tarot, and neo-paganism with the feminine is a side-effect of the gender-neutral appeal of these alternative spiritualities rather than evidence that women have some gender-specific predisposition towards them; i.e. women don’t embrace these traditions because they have some intrinsic female desire to do so, but because they have an intrinsic human desire to escape a preexisting spiritual framework that marginalises and humiliates them as a group. In a female-dominated society, is it unreasonable to imagine that it would be us men who could be found hunched over crystal balls and Tarot cards? Perhaps in a attempt to draw a sense of empowerment and self-esteem in an environment that was oppressively skewed against our interests?

Historically, it is clear that men have strongly embraced the supernatural, and that this, together with social trends, has resulted in the majority of “conventional” forms of spirituality being overtly paternalistic. I agree with the opinion that the association of such things as astrology, Tarot, and neo-paganism with the feminine is a side-effect of the gender-neutral appeal of these alternative spiritualities rather than evidence that women have some gender-specific predisposition towards them; i.e. women don’t embrace these traditions because they have some intrinsic female desire to do so, but because they have an intrinsic human desire to escape a preexisting spiritual framework that marginalises and humiliates them as a group. In a female-dominated society, is it unreasonable to imagine that it would be us men who could be found hunched over crystal balls and Tarot cards? Perhaps in a attempt to draw a sense of empowerment and self-esteem in an environment that was oppressively skewed against our interests?

Making War Movies...

2008-05-08T08:15:00.000-07:00

All the tedium, confusion, and unpredictable horror of Real War without the prospect of being put out of your misery.

Photo taken on the set of 88 mm Productions' "Rhineland", St. Clair, MO.

Shooting feet - Big Pharma gives them both barrels... again!

2008-04-18T10:18:00.000-07:00

An impassioned article over at In the Pipeline last week. Derek Lowe tells Big Pharma to go stand in the corner, face the wall, and have a long hard think about its ethics.

From the article:
If we’re going to win back the trust of the general public – which we’ve lost, in case anyone hasn’t noticed – we’re going to have to cut out the shortcuts, stop the doubletalk, and act as if what we’re doing (drug discovery) is something to be proud of. Sure, this is a business – we sell improved health for money, and since it sure costs money to do it, there’s nothing in that transaction to be ashamed about. So why are we acting as if the only way to do business is under the cover of darkness?"

Good question.

Stoicureanism

2008-04-17T21:40:00.000-07:00

Believe it or not, the term, Stoicureanism, doesn't receive a single hit on Google.

You read about it here first, folks.

I'm opening an online school, right here and right now. It's going to be bigger than Scientology, just you wait and see.

A thorough* defence of this new ancient ideology will be forthcoming.

* And by "thorough", I refer to the adjective's standard definition for use within serious philosophical discourse; i.e. vague and obfuscatory.

What we cannot have here is a failure to communicate...

2008-04-04T06:35:00.000-07:00

I briefly mentioned the importance of having good communication skills in science, using Neil Shubin's two minute book pitch on the Colbert Report as an extreme example.

Anyway, there's an excellent post by John Wilkins on his site, Evolving Thoughts, where he discusses this subject and defends the need for scientists to take an active role in the public communication of these ideas (blogging being a good start).

"There's an obvious place for science communicators too, and even for a strategic plan for getting science across into the public debate. So long as it isn't trimming and spinning, why not? We have to fight the PR wars somehow, and we won't do it by naively repeating the information as if to fill a gap in public knowledge. The public usually do not care, and they need, for the well being of the common weal, to be made to care, just as they do for civics, mathematics and hygeine."

Rapid evolutionary change in penguins astounds scientists

2008-04-01T06:06:00.000-07:00

Proof of Irreducible Absurdity, if ever there was any.

Single Channel Bizniz

2008-03-31T15:17:00.000-07:00

Over the last couple of months I've been doing some single channel recordings (outside-out patch, mainly). Whilst digging through the literature on methodology I came across this recent paper in Nature Protocols:

Martin Mortensen M., and Smart T.G. (2007) Single-channel recording of ligand-gated ion channels. Nature Protoc. 2, 2826-2841

It's a pretty good, concise primer for recording and analyzing single channel currents. Worth a read if you're planning on getting into that crazy scene any time soon.

Friday Afternoon SNAFU...

2008-03-14T14:16:00.000-07:00

Well, I guess there's a first time for everything. Serves me right for lapsing into autopilot.

... add the sodium chloride, add the HEPES, add the glucose, add the hydroxide, add the calcium chloride, add the magnesium chloride, check the pH and add just a little more hydr- CRACK!!!

I was reaching over to stab the Gilson into a fresh pipette tip, not realising that the pH probe's cord had slipped behind a vacuum tap nozzel. The probe whiplashed against the side of the beaker, shattering the barrel. Bugger.

I suppose, in a Pavlovian sense, it was fortunate that a stray piece of glass sliced through the glove on my left thumb, breaking the skin. Just a wee cut, mind, but enough to give me a jolt when that 3M potassium chloride solution soaked straight through the tear and rather unpleasantly depolarised all those fresh, bare nerve endings! Waahhhaaaa!!!

Science and Web 2.0

2008-03-11T17:10:00.000-07:00

[Posted here while I try and figure out why Action Potential keeps bouncing my comment]

Over at Action Potential, Noah laments the apparent low level of interest among mainstream scientists with the current Web 2.0 boom. In the comments section, Michael makes some valid points about the likely reasons for the lack of enthusiasm. In particular:

"4) The Fear Factor: ... Ideally, we want to be honest in our opinion of a paper, but we are also human and don’t want to suffer the consequences of bruising the ego of a potential reviewer or search committee member. Staying anonymous is not the solution, since that makes it difficult for everybody else to properly evaluate the comment. After all, it does matter who is doing the criticizing."

and then,

"5) Speed: Even the liveliest online discussion of a paper will drag on over hours or days. If a paper grabs my attention I will discuss at a lab meeting or Journal Club and over the course of one hour we will have thoroughly dissected it."

I tend to agree that, in the foreseeable future at least, we probably won't see a significant increase in the use of the good old interweb as a tool for serious scientific discourse for precisely the reasons Michael highlights.

However, I don't think the whole venture is necessarily a write-off. The current level of technical discussion, even though it tends to err towards pop science, has at least served to open up the scientific establishment to the laity. Many interested non-scientists read blogs authored by scientists, and on occasion scientists contribute their knowledge to public forums when relevant (straightening out misinformation on evolution for example). Add that to the current drive towards open access, and it's clear that Web2.0 has done a fairly good job of undermining the perception (still championed by certain groups) that scientists are aloof, elitist, and out of touch. The laity now have access to a fairly wide range of professionals, the majority of whom are quite willing to supply the fruits of their knowledge completely free of charge. Naturally, fact-checking is an issue, but with many scientists choosing to be open about their identity and affiliation, it's fairly easy to judge their qualifications.

The increasing presence of professional scientists online has also provided a sturdy bulwark against the spread of both misinformation, and perhaps more importantly, disinformation, from ignorant and subversive parties respectively.

With this in mind, a positive aspect of online journal clubs is that, even if they don't stimulate a heady technical discussion, they could potentially provide an introduction to important findings that might otherwise sail over the head of the average non-scientist (or even the average scientist from an unrelated field).

So, I think some good is coming of all this, even if the primary goal has not, and possibly will in the foreseeable future, be achieved.

De Rerum Natura, Book I. Lucretius (Quote II)

2008-02-22T08:46:00.000-08:00

"Suppose all sprang from all things: any kind
Might take its origin from any thing,
No fixed seed required. Men from the sea
Might rise, and from the land the scaly breed,
And, fowl full fledged come bursting from the sky;
The horned cattle, the herds and all the wild
Would haunt with varying offspring tilth and waste;
Nor would the same fruits keep their olden trees,
But each might grow from any stock or limb
By chance and change. Indeed, and were there not
For each its procreant atoms, could things have
Each its unalterable mother old?
But, since produced from fixed seeds are all,
Each birth goes forth upon the shores of light
From its own stuff, from its own primal bodies.
And all from all cannot become, because
In each resides a secret power its own."

De Rerum Natura, Book I. Lucretius (ca. 99BC-55BC) Internet Classics Arch.

I love this quote. It shows the old Roman managing to be both brilliantly incisive and completely wrong at the same time.

Flash by name, Flash by nature...

2008-02-20T08:20:00.000-08:00

Alright, so the Black Adder reference will probably be lost on most of you. That's fine, it was completely gratuitous anyway.

I'm talking Adobe Flash CS3, a program that I'm currently attempting to get to grips with in the vain hope that one day I might be able to produce something as sophisticated as the programs listed below. So far, I can make a slide show with clickable buttons (whoopee!), and I can animate a big red spot to move around the screen. Splendid. It's only a matter of time before I feel the smooth chrome finish of a Webby Award* in the palm of my hand.

However, while I'm struggling to make the red ball turn yellow, feast your eyes on the following, more professional, Flash/Java fare.

Molecular Probes' Fluorescence Tutorials - I'm a bit behind the curve here, and only recently stumbled upon these. Very cool.
Nernst/Goldman Equation Simulator (pictured)- My personal favourite. This one was developed at the University of Arizona. It allows the user to observe the effects of tinkering with intra- and extracellular ion concentrations on cell membrane potential. It would be nice if they could throw in the Lewis equation as well, but beggars can't be choosers.
Nikon Microscopy Tutorials - Nikon provides and extensive range of tutorials covering basic topics such as the Focus and Alignment of Mercury and Xenon Arc Lamps and Laser Scanning Confocal Microscopy, to far more advanced material that is light years beyond my ken. Oh, and check out the rather esoteric intro statement for the Eclipse L200 Microscope tutorial: Imagine you are dressed in a bunny suit and are about to examine newly fabricated chips under the microscope. Use this tutorial to explore how integrated circuit inspection microscopes are utilized to examine wafers in brightfield, darkfield, and differential interference contrast illumination. I don't need to imagine it, soldier. I wear that suit like a badge of honour.
Mouse Party - Very basic, but a decent crack at explaining the effects of... erm... crack. And other narcotics. Just pick up a doped-up mouse and put it in the chair for analysis.
Heart Simulator - This is from the University of Utah. It isn't very interactive, but it does provide the basics of heart contraction.

* Webby Awards do not actually have a chrome finish, but what the hell...

A personal hero on Life, the Universe, and Everything...

2008-01-20T10:45:00.000-08:00

David Attenborough, This Much I know.

"My next project is about Charles Darwin. He says in a letter to Emma, his wife, something like: 'I sat down on a bench and saw a bird singing in the trees and saw a wide mass of life going on around me, and I thought I didn't care what the process was that brought this into place because it's so wonderful.' If I lost that feeling, I'd go and do something else."

Nature Networks: the quest to upload our entire lives onto the interweb roles onwards...

2008-01-17T07:22:00.000-08:00

Spacebook, MyFace, GoodReads...

It makes you wonder why the FBI even bothered to invest in this new-fangled biometrics system. All an investigator needs to do is plug the suspect's name into Google and, in a blink of an eye, the individual's entire life history pops up along with their interests, place of work, favourite music, most recent photographs, and a play-by-play of what they're doing right now, and where. Who needs GPS when you have Twitter? The Feds don't even have to flag books anymore. Just go to GoodReads, type in "The Idiot's Guide To World Domination and the Brutal Suppression of Freedom" and see who's been writing all the reviews.

Well, the Nature Publishing Group is finally getting on board with this thing, too, having recently launched Nature Networks and Scintilla. I'm on the books, for good or ill. In truth, I think this is a potentially very useful resource, particularly for young scientists*. No doubt the forum moderators will have to filter out the odd raving troll, but that's about par for the course in this Information Age, when any old fool can pretend he's an authority on the subject.

Anyway, a journal club format has been introduced in the Neuroscience forum (and possibly elsewhere), mainly directed towards grad students and postdocs. Regarding my previous rant, this might provide a valuable opportunity for new scientists to sharpen their written communications skills. Never a bad thing for any of us. Especially me, judging by the wild, manic, and aimless scribblings on this blog.

Anyway, check it out, my multitudinous fans. That's right, all five of you.

* young scientist n. ˈyəŋ ˈsī-ən-tist
Latin scientia juvenis

1: a person learned in science who is not yet showing any gray hairs (NIH standard, 2007; professional scientist under the age of 45 yrs).

Your Inner Fish

2008-01-16T06:07:00.001-08:00

Caught this on onegoodmove via Pharyngula.

Neil Shubin nails down the essentials of evolutionary biology on the Colbert Report... in just a few minutes. It pays to be media savvy, and the ability to distill entire fields of knowledge into a series of clear, concise talking points is a skill that I think all scientists should be at pains to develop.

Hell, they should teach this sort of communication to biology graduate students for the same reasons they teach it to pro-sports rookies. I sure could have used some pointers back in the day. I remember the first question I was asked in my Ph. D viva by the external examiner - a big guy in the Ca2+-signalling field: he said, "How would you explain the signal transduction of G protein-coupled receptors to your granny?"

Chaos reined in my head for a good thirty seconds before I delivered an explanation that would have been passable if I was addressing an A-level/high school senior biology student, but wasn't nearly broken down sufficiently enough for a person with no biology background at all. I've honed my communicative skills since then, simply as a result of telling people what I do for a living, but a bit of formal training might have paid off at the start.

The most important thing I've learned regarding the communication of scientific ideas is that there is not one explanation for a scientific observation, but thousands of explanations that depend entirely on exactly whom you are currently trying to explain the observation to. Being able to pick the most appropriate explanation, based on a rapid assessment of the questioner's level of knowledge, is something of an art worth cultivating, IMHO.

On that note, I'm bumping Neil Shubin's Your Inner Fish to the top of my increasingly comical Amazon Wish List.

Image from the Hairy Museum of Natural History.

De Rerum Natura, Book I. Lucretius (Quote I)

2008-01-09T18:17:00.000-08:00

"This terror, then, this darkness of the mind,
Not sunrise with its flaring spokes of light,
Nor glittering arrows of morning can disperse,
But only Nature's aspect and her law,
Which, teaching us, hath this exordium:
Nothing from nothing ever yet was born.
Fear holds dominion over mortality
Only because, seeing in land and sky
So much the cause whereof no wise they know,
Men think Divinities are working there.
Meantime, when once we know from nothing still
Nothing can be created, we shall divine
More clearly what we seek: those elements
From which alone all things created are,
And how accomplished by no tool of Gods."

De Rerum Natura, Book I. Lucretius (ca. 99BC-55BC) Internet Classics Arch.

The Art of Outsmarting oneself

2008-01-08T21:21:00.000-08:00

I've been occupied in some heady discussion concerning Life, The Universe and Everything.

My latest comment is perhaps indicative that I need to take a break.

In response to the following premise delivered by Alex,

"1. If God exists, then his ultimate purpose will be the only purpose. (necessary)"

I wrote,

"That's true, but The Ultimate Purpose tells us very little about the many purposes that might, together, push the universe towards that end. And vice versa.

A cog in a conveyor belt might wax philosophical about its Creator's Ultimate Purpose of rotating around an axis, purely on the basis of its life experience. And yet, it would be completely oblivious to the fact that, actually, the creator's Ultimate Purpose is to create lateral motion along an axis.

Even if the cog did know what the big plan was, it might not fully understand why it had to do something that, from its own subjective experience, seemed counterintuitive to the grand plan.

There was a point to this comment, but it escapes me."

I think in much the same way that I juggle. I'm fine until I concentrate on one particular train of thought. This causes me to drop the others and then, in panic, drop the one I dropped the others for in the first place.

And so I am left standing there, dumbfounded, while my thoughts roll around my feet like marbles.