Friday, January 9, 2015

Ideologues Gonna Ideologize - and Use Misleading Graphics





Looks like a real trend, right?  


Mighty suspicious.

Saturday, November 3, 2012

The Riddle of Irreducible Complexity

Is life too complex to have evolved without guidance or design?  Proponents of Intelligent Design (ID) like Michael Behe and Kirk Cameron think so.  They claim that even the simplest bacterium has so many interdependent parts -- like the gears and springs of a watch -- that it could not have sprung into being without the direct input of an intelligent creator.

At first glance, they seem to have a point.  Deleting even a single gene in a developing fly embryo can be lethal to the fly.  Changing just one or two letters out of 3 billion in the human genome can give rise to a variety of deadly diseases.  If living things are so intricately balanced, how could they have evolved gradually, as evolutionary biologists claim?  Wouldn't all of the parts have to spring into existence at the same time?

To answer this, consider the following analogy.  Suppose a hunter-gatherer from the deep Amazon encounters an iPad.  Opening its case to peer at the microelectronics inside, she is puzzled: who could design and build such intricate parts?  Even when she finds out what each piece of silicon and metal is for, she is baffled.  Nobody has small enough hands, or a large enough intellect, to build a microchip from scratch.  They must have had the help of a computer -- but then, who built that one?  She might conclude that the first computer must have been a gift from an ultra-intelligent, and perhaps divine, being.

Of course, our friend is overlooking history.  As she investigates further, she learns that the predecessors of computers did not have microchips, but ran on manpower or steam.  Engineers later capitalized on inventions from electronics and the materials industry, as well as centuries of advances in physics and mathematics.  As computers became more complex, they helped people to design smaller, faster, and more complex computers, as well as the sophisticated microfabrication systems needed to build them.  The first computers helped to improve the hardware, which in turn helped to build faster computers, and so on.

It's an imperfect analogy, of course.  Unlike biology, even primitive computer technology is the product of intelligent designers driven by a set of goals.  But that's giving modern computer engineers too much credit.  The rise of the information age depended on the work of thousands of innovators spread over many centuries.  Their ranks include mathematicians, physicists, and chemists who had no idea that their work would give rise to microprocessors, Google, or Twitter.  In most cases, their goals had nothing to do with building a powerful computer, but were adapted for this purpose later.

Similarly, Biology has a goal: survival.  To get an edge on their competitors, living things capitalize on whatever past innovations they carry in their genes.  They re-purpose molecular bilge pumps for use as tiny propellers.  They transform their ancestors' solar power plants into cameras.  They even copy and build upon entire developmental blueprints from other living things, which is why it's so hard to tell the difference between the early embryos of humans and crocodiles.

Since evolution is blind, it can't predict whether an innovation will be successful.  And it's usually not.  Recall the supposed quote from Thomas Edison, "I have not failed; I've just found 10,000 ways that won't work."  As long as a creature can sacrifice a little time and energy on mistakes -- and every genetic disorder could qualify as a mistake -- it will occasionally hit upon a great idea.  Then comes the payoff.

In terms of our understanding of biology, we are like our fictitious hunter-gatherer: bright and curious, but almost completely ignorant of the past.  To worsen matters, no one was around to document evolution during 99.99% of its history.  If we want to understand how life arose and evolved, we have to take every little miraculous piece of biological machinery, and examine it.  What are its genetics?  What evolutionary path could it have taken?  Are there any paths we can rule out?  It takes a long time.

Understanding the natural world is tedious.  But it's infinitely more satisfying than exclaiming "Impossible!" and walking away.

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






Tuesday, April 3, 2012


So, 230 years on, how are we doing?




