Friday, April 13, 2012

Franklin’s Foibles and Other Closing Thoughts

Having just finished his Completed Autobiography, I have no doubt that Ben Franklin was in many ways an exceptional man.  Following his successful career as a printer, inventor and scientist, he spent his thirty-odd years of retirement as a civil servant.  During the Revolution he secured vital aid from France, which would become the United States’ closest ally in its struggle for independence.  Later, he played a role in setting up the new nation, fighting his chronically painful gout and kidney stones to help draft the U.S. Constitution and Bill of Rights before he succumbed to the ailments of age.  Socially, he was far ahead of his time, advocating for the abolition of the slave trade and then slavery altogether some eighty years before the Emancipation Proclamation.  In his last will and testament, he forgave the debt of his son-in-law Richard Bache on condition that he free his slave, Bob.

Still, it’s a bit reassuring to learn that even a legend like Franklin had his foibles, at least when viewed through the lens of history from our present vantage point.  In his discussion of Native Americans, he was uncommonly sympathetic, particularly in cases where European settlers at the frontiers maliciously murdered innocent Natives without provocation.  He clearly viewed them as equals to the Europeans from a human rights standpoint.   However, he also possessed much of his contemporaries’ cultural and religious chauvinism, which he used to justify the expansion of Europeans deeper into America, as is evidenced in passages like the following:
I often wish’d that I were employ’d by the Crown to settle a colony in Ohio, that we could do it effectually and without putting the nation to much expense.  What a glorious thing it would have been to settle in that fine country a large strong body of religious and industrious people!  What a security to the other colonies, and advantage to Britain by increasing her people, territory, strength and commerce.  Might it not have greatly facilitated the introduction of pure religion among the heathen, if we could, by such a colony, show them a better sample of Christians than they commonly saw in our Indian traders, the most vicious and abandoned wretches of our nation?  In such an enterprise I could have spent the remainder of my life with pleasure.
In other writings, he often referred to Native Americans as “the savages.”  My knowledge of 18th century English is limited, so I’m not sure how derogatory “savage” was at the time.  Furthermore, elsewhere Franklin advocated the honest purchase of their territory rather than forcible seizure by war.  However, it’s clear that he had no compunction about encroaching on Native lands for the sake of promulgating his own people’s culture and religion, which he clearly implied to be superior.  It's hard to fault him too gravely for this, considering the cultural milieu in which he was raised; even the sight of giants has its horizons.

On the topic of religion, he was more tolerant than many of his time.  For instance, he referred to his rationalist friend Joseph Priestly as an “honest heretic,” opining that “…’tis his honesty that has brought upon him the character of heretic” and “…I think all heretics I have known have been virtuous men.”  He continually advocated the importance of virtue and maintenance of good, honest character.  On the other hand, he was not above using religious language in pursuit of his carnal fulfillment.  Here is one excerpt from one of his many letters to an object of his affection and lust, Madame Brillon, a married woman who was young enough to be his daughter:
And now as I am consulting you upon a case of conscience, I will mention the opinion of a certain father of the church, which I find myself willing to adopt, tho’ I am not sure it is orthodox.  It is this, that the most effectual way to get rid of a certain temptation is, as often as it returns, to comply with and satisfy it.  Pray instruct me how far I may venture to practice upon this principle?
This series of exchanges happened after his own wife’s death, and there’s no clear evidence from this autobiography that he had any sexual affairs during his marriage.  However, considering the fact that Franklin spent most of the last 20 years of his marriage overseas, as well as his rumored reputation as a philanderer, it’s conceivable.  Some have accused Franklin of neglecting his wife by traveling so much, though Skousen suggests in the epilogue that Benjamin and Deborah had both drifted apart from one another in their later years (she repeatedly refused his many offers to take her to England with him in the years prior to the revolution).  In any case, it would be interesting to hear what Mrs. Franklin had to say about their relationship.

I imagine Franklin’s political enemies and other acquaintances had other negative things to say about him, but his writings convince me that he possessed an advanced moral compass for his time and on the whole earnestly strived to do the right thing, while cognizant of his own limitations to determine the best course of action.  Sounds like a decent guy to me.

Monday, April 9, 2012

Magnetic Healing and the Importance of Reproducibility, Then and Now

As a scientist, reproducibility is the little demon always lurking in your shadow.  At the helm of a series of often delicate experiments and complex analyses, you always wonder what will be discovered by those in your wake.  Did you carry out your study properly?  Were there any variables you didn't account for?  Above all, can an equally competent scientist independently reproduce your results?

In the past couple of years I’ve noticed increasing concern for reproducibility.  It’s an essential part of science, since it helps to cancel out the effects of human fallibility and conflicts of interest.  The more often a research finding is reproduced, the stronger a foundation it forms for future knowledge-building.

The problem is that most scientific journals do not publish straightforward reproducibility studies, with occasional high-profile exceptions -- for example, the apparently erroneous measurements of faster-than-light neutrinos mentioned in last week’s Nature podcast. Clearly, we need a place for reports like these to be routinely filed so that the value of any and every study can be more accurately judged.  Last week's Science podcast mentioned one such initiative in the field of psychology, called PsychFileDrawer.  I think every scientific field needs a repository like this, and the reproducibility studies should be linked to the original articles to minimize the time wasted following dead-end roads.  

As scientists, we need to be our own worst critics, for two main reasons:
  1. People outside our own specialties are not trained to critique our work properly; and
  2. When external audits discover problems, the whole of science suffers a blow to its reputation.
Of course, problems in scientific reproducibility are not a new phenomenon.  In his Compleated Autobiography, Ben Franklin mentions the case of a quack named Franz Mesmer who popularized a form of magnetic therapy based on his “theory” of animal magnetism:
We were much amiss’d in France for the past two years with the pretended new art of healing by what was called Magnetisme Animale.  The professor of this art, Mr. Mesmer, had in a short time made nearly twenty thousand Louis d’ors by teaching and practicing it.  He proposed the presence of a universal animal magnetic fluid that could heal the sick and prevent illness through a simple laying of hands, gestures, and signs… The remedy met with enough success to encourage the hopes of the ill; and even educated people, including doctors and surgeons, admitted to the school of magnetism.
One of Mesmer's devices, a magnetic tub called a baquet.  (Source
Franklin and others were curious and a little skeptical, so on orders of the King of France, he and a group of independent experimenters of the Academy of Science carried out their own study of Mesmer’s art of healing:
In our investigation, we tried to detect the presence of the magnetic fluid; but this fluid was imperceptible to all the senses.  The experiments we conducted on ourselves, including blindfolded subjects, caused us to reject it absolutely as a cure of illness.  We concluded that the system of magnetism did not cure anything; that both magnetism and his brilliant theory exist only in the imagination; and that a spectacle such as this seemed to transport us to the age and the reign of the fairies.
Unfortunately, Mesmer and his successors proceeded to swindle many credulous patients after this report was published.  Perhaps Mesmer earnestly believed in the technique.  Maybe his patients derived some comfort from the practice.  In any case, at least the study of the Academy of Science helped prevent magnetic healing from becoming an accepted mainstream medical treatment.

Non-reproducible science is bad science, and bad science is anti-science.  It's better to publish nothing at all than to publish an incorrect result.  As Franklin put it:
…one must not be indifferent to the ill-founded reign of false opinion: the sciences, which grow larger with the truth, have even more to gain by the suppression of an error.  An error is always a spoiled yeast which ferments and eventually corrupts the substance in which it is introduced.  But when this error leaves the empire of the sciences to spread among the multitude, and to divide and agitate minds when it presents a misleading way to heal the sick whom it discourages from looking elsewhere for help, a good government has an interest in destroying it.
Given the explosion of scientific inquiry in our era, we need a more concerted, systematic approach to finding the “spoiled yeast” and removing it before it spreads.  I think these reproducibility repositories are a step in the right direction.

Thursday, April 5, 2012

Giant Tyrannosaur relative discovered... and it's fuzzy!

Chinese paleontologist Xing Xu and his colleagues announced today in Nature that they've uncovered beautifully preserved fossils of three large Tyrannosauroids (relatives of the infamous T. rex).  The showstopper: they apparently had feathers.

I'll never see Jurassic Park in the same way again.

"Ian, Freeze!  Stop laughing!"
"Ha ha!  I can't help it.  This Tyrannosaur looks, uh, silly."
(Bottom image cropped from drawing by Brian Choo).

Xu named the new species Yutyrannus huali, a hybrid of Mandarin and Latin meaning "beautiful (huali) feathered (yu) tyrant (tyrannus)." Although smaller than T. rex, the largest of these three dinos is estimated to have weighed about 1.5 tons, making it the largest feathered dinosaur yet discovered -- in fact, about 40 times as large as the previous record-holder, Beipiaosaurus.  The authors opine that other large dinosaurs might have had feathers, but that "the discovery of Y. huali provides solid evidence for the existence of gigantic feathered dinosaurs and, more significantly, of a gigantic species with an extensive feathery covering."

It's not known what the plumage may have been used for, but the authors suggest it may have served as insulation.   There is no fossil evidence that T. rex bore a similar fuzzy coat, but it seems this is still up for debate.  Since T. rex appeared later in the Cretaceous, it's possible that it either had feathers, or lost them as the climate warmed up and insulation became less important.  There are many examples of mammals losing most or all of their fur coat (elephants, humans), even as their relatives did not (wolly mammoths, chimpanzees); why couldn't this have happened with dinosaurs?

Several smaller, early Tyrannosaur relatives had feathers.  Did T. rex have them, too?
(Source: Nature 484, 92–95.)
Whether a minority or a majority of dinosaurs had plumage is up for debate, but there is evidence that other dinos were feathery, including velociraptor.  It seems more and more accurate to say that dinosaurs were just early birds, and that birds are late dinosaurs.

In any case, there's something freakishly alluring about a predator that combines the fearsomeness of a T. rex with the beauty of a bird-of-paradise or the silliness of a chicken.  I'd like to see that remake of Jurassic Park.

Wednesday, April 4, 2012

Some baby steps towards better self-driving cars

Imagine you just spent a great night out with some friends.  You have some delicious food, good conversation, and perhaps a few drinks.  You don't worry about driving home, because you know your car will deliver you there safe and sound while you snooze in the back seat.  Such is one of many possible uses for the autonomous car.

I confess that I feel ambivalent about the idea.  Can we ever fully trust a computer to perform the complex cognitive task of driving as well as a human?  Still, it would be awesome to have your Chevy conduct you from errand to errand while you catch up on the news, or to send your Subaru out to pick up your clothes from the cleaners while you're at work.  As a commuter, I'd particularly benefit from the extra time a cybernetic chauffeur would give me each day.

I do think it'll happen eventually, and maybe within a couple of decades.  Google is already test-driving automated cars in California and Nevada.  If the proper sensing and judgment algorithms are perfected, robots may actually outperform human drivers in some respects.   Unfettered by the sluggish speeds of human nerve conduction velocity (mere tens of meters per second), they might have ultrafast reaction times.  If engineered properly, they will have no blind spots, will never misjudge distances, and will be free of distractions.  They will never get drunk.  They might even be able to accurately sense ice or other obstacles on the road and quickly communicate its location to other cars in the area so that they can take appropriate precautions.

University of  Michigan grad student Nick Carlevaris-Bianco has been working on the sensing part, using various lasers and cameras mounted on a Segway robot to help it build an accurate high-resolution map of its surroundings.

This technology must be introduced very carefully and slowly to avoid serious accidents.  The public and insurance companies need time to catch up.  But with some more development in this field, our grandchildren could be driving -- or rather, riding -- on roads that are virtually accident-free.  

Tuesday, April 3, 2012

Ben Franklin: "Sometimes I Regret I Was Born Too Soon"

I came across a great, partially prophetic quote in Ben's Compleated Autobiography today:
The rapid progress true science now makes occasions my regretting sometimes that I was born so soon.  It is impossible to imagine the heights to which the power of man may be carried over matter in a thousand years.  We may perhaps learn to deprive large masses of their gravity and give them absolute levity for the sake of easy transport.  Agriculture may diminish its labour and double its produce.  All diseases may by sure means be prevented or cured, not excepting even that of old age, and our lives lengthened at pleasure even beyond the antediluvian standard. 
So, 230 years on, how are we doing?

Power over gravity: check.  Well, sort of.  We can at least defy it for a while with the help of the Bernoulli effect, strong propulsion, or electromagnets.

Improved agricultural efficiency: check.  In the developed world, a small minority of the population provides a surplus of food at dramatically improved yields per acre.  This was made possible almost entirely by science and technology.  Now, if we can only make it more sustainable and environmentally friendly...

Curing all disease: not so much.  We've lengthened the life expectancy by a few decades in the developed world, and a large proportion of the developing world is catching up (in fact, maybe developed/developing world is becoming an outdated concept).  Infectious disease is well controlled by better hygiene, vaccinations, and antibiotics (for now...).  Chronic diseases like cancer and diabetes will take longer to conquer.

There have also been many surprises.  Franklin never saw Darwin, Einstein, Planck, Schrodinger, or Turing coming.  Sometimes I furtively imagine taking somebody from the 18th Century on a tour of all the technology and gadgets we now have thanks to paradigm changers like these, and it makes me appreciate my car or smartphone a little more.

What lies in the future?  Sustainable solutions to feeding the world's billions?  Hopefully.  True antigravity?  Genuine biological immortality?  Not likely in my lifetime, but we have 770 more years before Franklin's thousand are up.  Let's get on it.
O that moral science were as fair a way of improvement, and that men would cease to be wolves to one another and that human beings would at length learn what they now improperly call humanity!
Amen to that.  Still a long way to go on that front.

Sunday, April 1, 2012

Systems biology: How bacteria use their sense of "smell" to navigate

What is it that distinguishes a living thing from lifeless matter?  It's not the molecules it's made of -- chemists can synthesize proteins, DNA, RNA, and lipids, but to breathe life into these lifeless ingredients, a higher level of order is needed.  It's the networks of interactions between these molecules -- biological circuits -- that allow cells to respond to their environment, harness energy and funnel it into their growth and development, and pass their genes on to the next generation.  In fact, if we ever find life on another planet, I doubt its molecular building blocks will closely resemble those of life on Earth, but I am sure that its biological information networks will.

I've been learning a lot about these networks from Professor Uri Alon of the Weizmann Institute, who has posted several of his enlightening lectures to YouTube.  In one lecture he discusses chemotaxis, the ability of many bacteria and other cells to swim towards nutrients and away from toxins.

In order to perform chemotaxis, organisms like E. coli have to detect tiny gradients of nutrients or toxins, sometimes as small as 1 molecule in 1,000 over the length of their one-micrometer-long bodies.  Ultimately, they accomplish this by randomly swimming in different directions, and when they sense an increase in a nutrient (or decrease in a toxin), they are less likely to turn.  It's kind of a unicellular version of Hide the Object ("You're getting warmer!").

Before it can detect changes in the levels of a nutrient or toxin, the cell has to "subtract out" whatever level it currently sees in the environment.  This is adaptation, and is related to how your eyes adapt when you step outside into the sunlight, or how your sense of smell adapts after first smelling those chocolate chip cookies baking in your oven.  If you smelled cookies baking in a strange house, your nose could lead you to the kitchen, largely because your sense of smell adapts to the amount of cookie aroma in each room you visit.  You can tell if you're getting closer, because the cookie scent will become stronger.

Based on the model Alon describes, I built a little simulation showing how this works.  In the video below, each white dot represents a bacterium, and the green color represents a delicious nutrient such as aspartate.  On the left, the bacteria cannot sense the nutrient, while on the right, they can. You'll notice that the bacteria on the right wiggle and jiggle quite a bit, but they generally stick to the green part of the screen, where all the goodies are.  They sometimes move away from the green area, but usually realize their mistake and turn back.  The bacteria in this simulation have the properties of gradient sensing and adaptation, even though they are using just three virtual enzymes!


The real system in E. coli is based on only six proteins in total, so it's not much more complicated.  Their solution to the problem is different than anything we humans would design, but it's a simple and elegant system that, according to Prof. Alon, resembles many other networks throughout the tree of life.  Maybe it can even tell us something about the higher-order functions of our own brains?