To the enduring saga of faith-filled folks who mistake ancient creation myths for science, we can now add this spasm of befuddlement. Pastor Gene Kim of San Jose Bible Baptist Church has thought it necessary to bring his remarkably low brow mockery of evolution to a wider audience. In a six-minute argument from incredulity, Pastor Kim juxtaposes a selection of fairy tales alongside caricatures of the science he — and his narrow Christian worldview — need to be wrong.
 

 
Yikes. Hard though it may be for this pastor to wrap his head around evolutionary biology, it is surely harder to imagine that fellow Christians would find him a serviceable spokesman for the cause. Leaving his reverse eloquence completely to one side, it’s obvious he has no interest in understanding that which he must reject, and engages the opposition only long enough to quote-mine from them. Pairing silly fables with overwrought distortions of established science is then used as a ruse to sow doubt among unsuspecting believers. Poking fun at major evolutionary transitions is meant to create the impression that the underlying science is nonsense on its face — no further inquiry necessary.

Richard Dawkins, in his sweeping book, The Ancestor’s Tale, addresses this tendency to equate evolution with myth and fantasy. In “The Axolotl’s Tale” he writes:
 

“Fairy stories are filled with frogs turning into princes, or pumpkins turning into coaches drawn by white horses metamorphosed from white mice. Such fantasies are profoundly unevolutionary. They couldn’t happen, not for biological reasons but mathematical ones. Such transitions would have an inherent improbability value to rival, say, a perfect deal at bridge, which means that for practical purposes we can rule them out. But for a caterpillar to turn into a butterfly is not a problem: it happens all the time, the rules having been built up over the ages by natural selection. And although no butterfly has ever been known to turn into a caterpillar, it should not surprise us in the same way as, say, a frog turning into a prince. Frogs don’t contain genes for making princes. But they do contain genes for making tadpoles.” (p. 314)

 
Dawkins’s point is that evolution has an internal logic to it. The diversity we observe across nature can be readily explained through the interaction between genes and the environment in which they operate. Caterpillars morph into butterflies because that change has been written into their genes over millions of years. Tadpoles likewise mature into frogs and toads because they possess the necessary DNA for doing so. Indeed, we can identify the specific genes responsible in each case. A report that claimed to have reversed the physiological development of butterflies, turning them into caterpillars, would not be unthinkable on its face, for reasons that bear no relevance to the regime of myth.

Never mind that the transition from land back to the sea by our mammalian ancestors involves a series of some of the most brilliant discoveries in all of science. Or that bodyplans subjected to environmental changes can shift over time and diverge from earlier lineages in accordance with natural selection is as well documented a theory as any other in the literature. That barriers to gene flow encourage population splitting and divergence, and so forth.

One could proceed endlessly with evidence-based rebuttals, but anyone who’s been roped into this rodeo long enough knows that it’s never ultimately the scientific evidence that compels creationists to reject evolution so much as their rigid attachment to doctrinaire Christianity. It’s about faith, not evidence. And evangelical faith, particularly among Americans, is tied to specific and narrow interpretations of the biblical texts. Information, no matter how neutrally presented, is only given a fair hearing if it is not perceived as in conflict with the set of Christian doctrines they consider non-negotiable. The unfortunate corollary is that delving into the science can only prove effective for someone who cares more about what the science says than what (they think) their Bible says.

It cannot be emphasized enough how damaging this can be to one’s intellectual development. When seeking out new and different ideas, vetting your beliefs, and adjusting the strength of your beliefs on the basis of new evidence are systematically discouraged, growth becomes impossible. And the longer one is locked into an echo chamber of like voices and ideological conformity, the more difficult it becomes to break free and adopt new ways of thinking — and the more extreme the response once that freedom comes. As the canny Jane Smiley wrote, “A child who is protected from all controversial ideas is as vulnerable as a child who is protected from every germ. The infection, when it comes — and it will come — may overwhelm the system, be it the immune system or the belief system.”

In one sense this young man is absolutely right: of course it is easier to dodge the difficult questions than to expend effort in answering them — especially when so much is at stake. A worldview reorientation can seem too high a cost to bear. Faced with these anxieties, and the complexities of science and philosophy, why not embrace the soothing balm of the supernatural? Why not opt for the comparatively simpler explanations offered by creationism? Why rock the boat when it’s easier to go on believing what your pastor and parents say is true? The thought of acquiring the resources to approach these questions differently can be intimidating, and many choose to avoid the process altogether.

Misspent Youth

Fear of the unknown can be a powerful demotivator, but it can also come at great cost. How many lifelong fundamentalists could have spent their years not attacking science but doing something truly worthwhile? How many of them could have been placed in professions for which they were better suited and contributed meaningful discoveries to the human condition? How many might have spent their careers fostering a generation of open-minded, tolerant men and women instead of misleading innocent youth?

This is why I tend not to share in the chorus of laughter that often accompanies creationist antics like these. What others find “hilarious” I find profoundly sad. I see lost potential in those formative years of carefully cultivated intellectual deprivation that inevitably culminate in an army of mindless drones who shy away from questioning authority and examining their inherited tradition. Fundamentalists like Kim have been lied to about science and about evolution from an early age, and now take it upon themselves to share those lies with others on the earnest belief they are doing ‘the Lord’s work’. The next time we’re given cause to wince and chuckle, we might take a moment to imagine what a refocused zeal, as opposed to an unkindled curiosity, could look like.

This intergenerational problem of trickle-down ignorance — not unique to America but thoroughly typified here — won’t end until we cultivate a world where the concern for what is true supersedes the felt need to be right, even if it means we abandon those beliefs we dearly wish to be true, no matter how long we’ve held them or how cognitively comfortable we find them.

External link: Pastor offers hilariously bad takedown of evolution: ‘It’s more easier to believe in something supernatural’

This post was featured on HuffPost’s Contributor platform.

 
 
In discussions about science and history and other popular topics, I tend to focus on the ideas rather than the individuals espousing them. Others take a different tack, seeking instead to diminish the credibility of this or that proponent or puff up the credibility of this or that opponent. During a recent conversation about David Barton and his flagrant distortions of history, a commenter decided to loop in his denial of evolution with that of uncontested American history:
 

“You do realize that Charles Darwin had no training in science and had only a Theology degree? So, if I go by your assessment there is no reason to consider Charles Darwin’s scientific drivel either.”

 
The surface claim here is actually patently false, but the underlying logic is, I suspect, of larger importance in the narrative driving reactions of this kind. We’ll deal with them in order, with special emphasis on the latter because many who defend the science tend to waste space on the exterior claim when what really needs to be addressed are the deeper misimpressions of science and other approaches to knowledge.

Those looking into Darwin’s credentials may be surprised to find no “PhD” listed by his illustrious name. Of course, no one else at the time did either, at least in the UK. In fact, PhDs weren’t awarded in Great Britain until 1917, thirty-five years after Darwin’s death. In the 19th century, most universities still followed the medieval tradition of offering degrees in three formalized disciplines: theology, medicine and law. Depending on where you lived in Europe and which university you attended, you could obtain a license in other areas, but the requirements paled in comparison to the modern PhD. It wasn’t until places like Canada, the US and the UK began adopting the educational model pioneered by Germany a century before that the scope of academic qualifications was expanded.

From an early age, Darwin was mesmerized by marine and other animals and showed a keen interest in scientific study. His precocious curiosity and passion for the natural world grew stronger and endured through his father’s entreaties to chart a more pious life. While originally enrolled at the University of Edinburgh to learn medicine, Darwin’s interests were committed to naturalist pursuits, which at that time fell under “natural history,” a catch-all title that would come to represent a number of distinct specialties in the modern day field of biology.

His activities in and out of the classroom brought him into contact with a number of eminent naturalists and geologists. Before embarking on his famed Pacific voyage with scientist-cum-Navy officer Robert FitzRoy in 1831, Darwin studied under such greats as John Stevens Henslow, Adam Sedgwick, Robert Edmond Grant and Robert Jameson. He studied marine invertebrates extensively under Grant, mapped geologic strata under Sedgwick, and gave presentations on his work at naturalist societies around the UK. It was his singular preoccupation with beetles early in his career — a real fascination among naturalists at the time — that caught the admiring eye of Henslow while at Cambridge and which led to Darwin’s work being published in Illustrations of British Entomology. Far from being out of the ordinary, Darwin’s trajectory and intellectual portfolio were right in line with other notable cognoscenti of the day.

David Barton, by contrast, has no equivalent pedigree in the discipline of history — the field on which he purports to speak authoritatively — and can boast of little more than his success in peddling historical revisionism. He is an author whose only background seems to be in religious apologetics and a brief stint as a youth pastor. I have seen no evidence that he has studied under practiced historians, given lectures at academic conferences, published in reputable journals, or submitted peer-reviewed literature of any kind. There is no meaningful comparison to be made between these two men.

The Single Scientist Fallacy

In many ways, however, focusing on Darwin to undermine evolution is a fool’s errand. A scientific discipline or theory may be associated with but isn’t defined by the contributions of a single scientist. Indeed, the convergence of agreement around integral ideas is a fluid phenomenon that requires more than the insights any one person can provide. Progress in the hard sciences, as with other quests for human knowledge, is attained by a plurality of voices communicating across generations, not merely by individuals plucked from a single moment in time. We have learned much since Darwin, whose sharp observations were not guided by DNA, a working understanding of the gene — the physical unit of heredity — or a robust fossil record, the confluence of which, together with Darwin’s mechanism of natural selection, culminated in the modern evolutionary synthesis laid down in the 1930s to 50s.

We have seen the same strategy deployed in the regime of climate science: contrarians have often attacked Michael Mann’s original hockey stick graph from 1998 as if it were the linchpin holding the field of climate science together, despite the fact that the graph has been replicated by other researchers dozens of times since (including by the National Academy of Sciences and the IPCC reports). It has always been more efficient to target individual scientists than try to take down an entire field by engaging its prevailing ideas and conclusions.

In his book, The Hockey Stick and the Climate Wars: Dispatches from the Front Lines, Mann calls this the “Serengeti Strategy.” He draws an analogy with predator-prey interactions to construe the techniques used by moneyed interest groups on both sides of the pond.
 

“I joined a daylong expedition to see one of the world’s greatest displays of nature: Serengeti National Park. Here, zebras, giraffes, elephants, water buffalo, hippos, wildebeests, baboons, warthogs, gazelles, and ostriches wander among some of the world’s most dangerous predators: lions, leopards, and cheetahs. Among the most striking and curious scenes I saw that day were groups of zebras standing back to back, forming a continuous wall of vertical stripes. “Why do they do this?” an IPCC colleague asked the tour guide. “To confuse the lions,” he explained. Predators, in what I call the “Serengeti strategy,” look for the most vulnerable animals at the edge of a herd. But they have difficulty picking out an individual zebra to attack when it is seamlessly incorporated into the larger group, lost in this case in a continuous wall of stripes. Only later would I understand the profound lesson this scene from nature had to offer me and my fellow climate scientists in the years to come.”

 
Denialist groups hope that by diverting attention to a distinguished scientist, he or she will serve as a proxy for the credibility of the field as a whole. A standing consensus, no matter how strong, is cast as the fragile whims of a lone authority. This technique is brutally effective in many cases because the average professor cannot withstand a sustained barrage of investigations and libelous op-eds, as they must now split their time between combating the many witch hunts, misrepresentations and distortions of which they are the focus rather than continuing to advance the state of the science. And as anyone familiar with the effects that press interviews and yellow journalism can have on an ostensibly unbiased jury can attest, once the claims are out there, they become intolerably difficult to crush.

Yet passing judgment on the actions or output of a single scientist, historian or other academician has no relevance to whether the central ideas and conclusions of the field to which that person belongs hold up. It is simple question-begging by people who would rather pretend that the ideas which challenge their world perspective are not broadly shared but terminate with a single individual or group. In short, discrediting Darwin gets you no closer to creationism.

Even the hard-nosed contrarian nonetheless knows that science is an exemplary tool for investigation and discovery that delivers remarkable insights and a more intimate and inspiring look at nature. And yet from time to time, science also gives us inconvenient truths. When it does, it’s best not to shoot the messenger.

Supplement with: Science as a house of cards

 
 
Here’s an example of some of the fascinating research being done today at the interface of mathematics and biology. The two fields have become ever more intertwined as our knowledge of genetics has deepened. The subtle and not so subtle interactions between microbes and their host, the multitudes of genes that give rise to behavior, the modeling of metabolic pathways, large-scale sequencing projects—all are stubbornly complex to puzzle out, and all bend more easily with the aid of innovative statistical techniques and advances in computing power.

Among the more pressing topics in medicine today concerns whether antibiotics have outlived their usefulness or whether we simply need to rethink how we use them. When German pathologist Gerhard Domagk discovered the antimicrobial effects of Prontosil in the 1930s, it was heralded as one of the greatest therapeutic advances in medical history. Yet even then, scientists were wary of the long-term drawbacks of their overuse. Almroth Wright predicted that bacteria would evolve resistance to these agents before we observed the phenomenon directly, while Nobel laureate Alexander Fleming (of penicillin fame) cautioned that they should be administered only in specific circumstances and in the proper dosage so as to minimize the risk of resistant pathogens.

While these words of warning have proved especially prescient in the wake of our current crisis, we are not entirely to blame. Bacteria, fungi and algae have been locked in a campaign of chemical warfare for more than a billion years. Like Darwinian selection itself, antibiotics and resistant genes long predate humanity; we merely gave them names. Microbes, moreover, outnumber us billions to one, with much greater genetic diversity and shorter reproductive cycles. This allows mutations to spread through populations quickly and gain the upper hand before new pharmaceutical trials can even get off the ground. Lastly, bacteria also are fond of passing helpful genes around to their neighbors through a process called horizontal gene transfer, and the immense diversity of the microbial jungle means there will always be resistant DNA close at hand.

As Martin Blaser writes in his latest book, Missing Microbes:
 

“Another implication of the nature of resistance is that there will be no easy solution to the problem. We will never make resistance go away, because Darwin was correct in his theories. There always will be strong selection for resistance when populations encounter stress, in this case, microbes under antibiotic pressure. A corollary is that we will never invent a superantibiotic that cures everything. Microbes are too diverse, and Nature will always come up with new ammunition.” (pp. 80-81)

 
Given the natural processes which govern life on earth, the crossroads at which we now find ourselves was perhaps a biological inevitability. Evolution is an arms race fought with genetics across time. Rewrites that give contestants a replicative edge reconfigure the battle lines; old strategies wane in strength. While most bacteria are beneficial, some, like Streptococcus and Salmonella, are pathogenic, interacting with host physiology in harmful ways. To counter them, we have antibiotics, which work well enough for wiping out particularly devastating ills but effectively wage genocide on our microbiome, killing off both good and bad residents and upsetting gut ecology. Not only can these collateral damage “grenades” lead to unintended complications down the road, evolution does not sit still. Any mutations that limit antibacterial efficacy quickly outcompete those that don’t, in the process generating more resilient microbes for us to outwit.

The doctor-patient relationship, along with common agricultural practices, have certainly not helped matters, however. For decades we have over-prescribed these broad-spectrum solutions for misdiagnosed and nonbacterial infections, relied on them as “just in case” remedies when less invasive ones would do, and pumped them into the animals we farm and the food we consume. This escalating confluence of dependence on antimicrobials and our commitment to an antiseptic lifestyle has served to fast-track evolution in the form of resistance.

Many immunologists have suggested we are moving into the “post-antibiotic” era, but what if we could predict the evolutionary trajectory of certain bacteria when subjected to antibiotics? Might we be able to substitute new drugs before resistance emerges and spreads? That’s the idea behind new research pioneered by Miriam Barlow from University of California and published in PLoS ONE this month. Together with mathematicians from American University in Washington, D.C., they were able to apply a probability analysis to bacterial evolution.

Rewinding the Genetic Clock

The researchers exposed E. coli to 15 different antibiotics, taking note of the differences to TEM-1, a protein involved in 90% of penicillin-derived drugs. A wild type TEM-1—which can be conceptualized as the “standard” form of the protein, or one unexposed to antibiotics—confers resistance to penicillin only, while its variants (other genotypes) tend to expand resistance to other classes of antibiotics such as cephalosporins.

The team’s goal was to see how consistently they could revert a population of TEM-1 genotypes to wild type status, thereby narrowing the range of resistance. Since nearly all known TEM-1 variants differ by no more than four mutations, the team used a four-digit model to map out the changes in amino acids. For example, the wild type TEM-1 was assigned a label of “0000”, and each mutation was represented by a “1” in the location where the substitution occurred.
 

A mutation network for the antibiotic cefpodoxime (Figure 13)

Though these results are encouraging, it is not clear how clinically relevant they are. A lab setting in which tight constraints are maintained throughout is one thing; a crowded hospital overflowing with bacterial and antibacterial diversity is another. Microbes living in communion with other microbes tend to share genetic defenses, a feature not available to those grown in isolation. Moreover, different host environments supply a wider playspace for natural selection to act, possibly serving up a greater variety of genotypes than those captured by the study. And while such algorithmic exploitation could theoretically aid us in our fight against resistance, we would still need a better idea of how long each drug should be in rotation and the recommended dosages necessary to complete the wild type selection process.

That under certain conditions bacteria nestle along statistically predictable alleyways is an interesting result in and of itself, but more research in the form of field tests and clinical trials will be required to comment on its real-world validity.
 

“At the heart of what everybody wants to know is how predictable is evolution—and if it’s predictable, can we reverse it?” he says. “It’s really hard, but you’ve got to try something.”

Further reading:

• New Mathematics Could Neutralize Pathogens That Resist Antibiotics (Scientific American)
• Rational Design of Antibiotic Treatment Plans: A Treatment Strategy for Managing Evolution and Reversing Resistance (PLoS ONE study)

The latest poll is out charting evolution acceptance in the United States. Many of the findings are mirrored closely by earlier polls: acceptance still tends to vary by education (positively correlated), gender (males score higher) and age (negatively correlated). Nothing earth-shattering there that we haven’t seen before. One trend, however, stands out like a sore thumb in Pew’s latest: Republican resistance is increasing.

The Pew Research Center conducts their polls via telephone interview. In 2013 researchers phoned 1,983 adults aged 18 and up and asked a battery of questions (full questionnaire here) relating to the unifying theory of biology. (The margin of sampling error was +/- 3.0 percentage points set at a confidence interval of 95%.)

The last such poll by Pew was taken in 2009. In four years, the overall numbers have barely budged. When presented with the proposition, “Humans and other living things have evolved over time”, the 2013 poll found a 60/33 split between accept/reject, compared with the 2009 poll’s 61/31 split. In terms of brass tacks, one-third of the American public still does not accept the scientific understanding of human origins.

6 in 10 Americans accept evolution.

Continuing the trend from 2009’s poll, the group most likely to reject evolution is evangelicals, followed closely by black Protestants, according to the study. Nearly two-thirds of those who identify as white evangelical Protestants chose the proposition, “Humans existed in present form since the beginning”. By contrast, just 15% of those identifying as white mainline Protestants responded in this way, down from 23% in 2009.

This particular data point contrasting is telling as it could indicate that the fundamentalism so prevalent in evangelical circles has grown more and more out of vogue, associated as it is with antiscience conservatism and rigid dogmatism, mentalities the rest of Protestant Christianity is working to distance itself from. Given enough time and rebranding efforts, the “mainlines” could become the dominant voice of American Christianity as they wrest control from the evangelicals who so frequently flail their way into the national spotlight.

Note the contrast between evangelical and “mainline” Protestants.

The Catholic community on the other hand, comprising some 78 million Americans, remains unshaken. 68 and 53% of white Catholics and Hispanic Catholics, respectively, affirm evolution over against the fixity of species by special creation.

Evolution, Politicized

Once we drop political valence into the beaker, the numbers take an interesting turn. What this latest poll reveals with clarity and urgency is an escalating partisan gulf standing over this question. While Democrat acceptance of evolution has remained more or less steady since 2009, Republicans are even less likely to accept evolution, dropping from 54% to 43%.

The Republican party lead the way in evolution denial.

By any account, that’s a staggering and troubling swing. Those 11 points represent a sobering blow to the Pollyannas who contend that fewer and fewer will succumb to the siren song of unreason as logic and facts seep into the water supply. Such estimations tend to omit all of the intricate reasons people uncritically hold beliefs and at any rate can only be made in complete neglect of the recent polling data.

Dissecting these new results to unearth an explanation sensitive to the various interlocking parts will require more granular analysis, but one possibility is that party numbers are shifting in rapid fashion. Those who formerly identified as ‘moderate’ Republicans may have moved off into other territory, changing their status to either Democrat or independent. Admittedly, the data do not grant this conclusion exclusively, given that there is no corresponding uptick in the Democrat and independent figures, but it would surprise me if it doesn’t shoulder at least some of the explanation here. Last election’s GOP ticket was bubbling over with members who not only denied evolution, but global warming as well as forays into stem cell research, and who wore their unsophisticated religiosity on their sleeve. Those deserted to the middle may have had their fill of the mania and jumped ship to saner waters.

Another, less sanguine sketch of events sees the Republican party as stumbling upon an ideological accomplishment, to use the term impossibly loosely. The previous season’s GOP nominees delighted in broadcasting a tribal-esque message to the American people—a message of identity, of what it means to be a ‘true’ Republican. Embedded in this transmission was the insistence that creationism entails the true and proper accounting of the diversity of life on earth and that belief in evolution is something to be doubted, distrusted, even challenged. Many, it would appear, have heeded the call. Perhaps the fence-sitters, fueled by their opposition to all-things-Obama, have doubled down, forged stronger affinities with their political party, and jumped headlong into the anti-scientific leanings of their representatives. 

If correct, the fusion of the GOP with an antiscience platform is approaching completion, to an extent that the two have reached a sort of Dark Age synonymy.

America the Outlier

Even so, we should resist the tendency to trap ourselves in a cultural airlock when thinking through these issues. The divide over evolution in America runs deeper than party lines; after all, 27% of Democrats and 28% of independents reject the theory as well, and those numbers haven’t moved appreciably in decades. A most debilitating picture starts to materialize when we place America within a global context. A 2005 study published in Science gauged evolution acceptance across 34 countries. The U.S. ranked 2nd to last, ahead only of Turkey. America is largely an aberration on the global scale and, far from waning in strength, the multifront efforts to keep it that way show no signs of dissipating.

What could possibly account for why the scientific consensus on evolution continues to be doubted by an American populace completely dependent on science and technology for its way of life? Barring some epidemic of collective psychosis (unlikely), the answer it seems to me, albeit proximate and not ultimate, is that the respondents dismissive of evolution aren’t nearly informed enough on comparative genomics, paleontology and biostratigraphy, human and non-human vestigiality, embryology, biogeography and, last but far from least, biblical studies to competently answer the questions they were asked. And against these salvos of scientific and historical inquiry, there is no armor like ignorance.

External Links: Press Release; Full Report; Questionnaire

Feature image: controversy.wearscience.com

 
 
Intriguing riddles such as these often necessitate interdisciplinary brilliance to solve. Theoretical biologist and neuroscientist Mark Changizi has been stockpiling research in these areas for much of the last decade, fixated on some of the fascinating but imperfectly understood precincts of human perception. Not content with asking how our central nervous system functions, Changizi is determined to provide explanations of why its architecture and inter-operative functionality exist as they do. The Vision Revolution, should it withstand the scrutiny of peer review, is a groundbreaking work in vision science that brings forward original research into the evolution of the human visual system.

In the book he pivots between four core ideas, each of which are given mystical titles:

(1) Color telepathy:  “Color vision was selected for so that we might see emotions and other states on the skin.”

(2) X-ray vision:  “Forward-facing eyes were selected for so we could use X-ray vision in cluttered environments.”

(3) Future-seeing:  “Optical illusions are a consequence of the future-seeing power selected for so that we might perceive the present.”

(4) Spirit-reading:  “Letters culturally evolved into shapes that look like things in nature because nature is what we have evolved to be good at seeing.”

Each entrée of this technical collation is truly mind-altering, and it is a joy to tag along as Mark architects the empirical struts of his developmental theses. Let’s dive right in.

Color Vision

His first course of business is to provide an alternate explanation of the origin of color vision in primates. While we take it for granted today, color sensing is a relatively recent adaptation in the mammalian order. Until now, the default view among vision scientists is that color was selected for to distinguish between various types of fruit and leaves. The regnant explanation has survival value on its side, but Changizi believes it is not the complete answer. After all, not all mammalian diets are alike, but our color sensors and attendant properties are strikingly continuous with other color-sensitive primates.

Changizi instead makes the case that color acuity evolved to detect changes in skin oxygenation. When blood and oxygen levels fluctuate, we see an instant feedback effect on our skin. These shifts in skin tone and color signal us to changes in mood and emotion states and, more importantly, alert us to physiological dysfunction. A mother who can sense the full range of hue, saturation and brightness deviations in her baby’s face and body is in a better position to detect when something is amiss and take proper action.

This hypothesis puzzles out well enough for bare-skinned animals like humans, but what about hairy primates – the ancestors which supposedly evolved these traits long before our debut? It turns out there is a neatly correlated distribution between color vision and bare-faced primates. Changizi surveys the animal kingdom and finds that primates lacking color vision have furry faces, while those with hairless spots on their faces and body tend to have color vision just like us. He notes that this more “fleshed-out” explanation does not swear mutual exclusivity with the dominant explanation; indeed, they could be co-occurring drivers of selection.

X-ray Vision

Have you ever wondered why we have forward-facing eyes, as opposed to sideways-facing eyes like most reptiles, birds and fish? As Changizi demonstrates, this element of our physiology was selected for to better suit the habitat in which our ancestors evolved. This might at first seem like a non-intuitive proposition, as surely our survival would be better served by the ability to see both in front of and behind us (as animals with sideways-facing eyes most certainly can). But there’s a more marvelous, some might say superhuman reason our current orientation was favored.

Close one of your eyes. Notice how your nose is suddenly visible. The result is the same when you close your other eye. With both eyes open, however, the portion of your visual field occupied by your nose is no longer blocked. You are, effectively, able to see through your nose. Remarkably, this trick can be reproduced with any object whose width is narrower than the width of your eyes. Hold up your hand, position it vertically in front of your face, and you can see through it to read the screen behind it.

According to Changizi, this ability was helpful in leafy habitats, enabling our predecessors to see through grass and other foliage to spot predators and food. As life transitioned from water to land, those acclimatizing to heavily verdant environments gradually evolved the optical design shared by humans today. The binocular region for animals with sideways-facing eyes, on the other hand, is far too narrow to be effective, explaining why this arrangement is less commonly found in lush surrounds. While we may be manifestly less dependent on this feature today, it is nonetheless fascinating that evolution has gifted us with a passive form of X-ray vision.

Optical Illusions (and why they trick us)

As we move into the book’s third unit, we listen in as Changizi disassembles the aura of visual illusions. It’s estimated that eyes first evolved around 500 million years ago. Why then, after all this time, aren’t our eyes and brains complex enough to avoid being fooled by simple visual tomfoolery? Shouldn’t we process these images correctly by now?

The answer lies in the communication protocols linking our optical and brain arrays. The deep relationships governing the brain and the eye help us function appropriately in a three-dimensional world. The architecture of our central nervous system is such that a gap of 1/10th of a second exists between the moment light first hits our photoreceptors and when that signal is processed by the brain. Our brain then compensates for this delay by projecting images 1/10th of a second into the future.

Courtesy of Comics & Memes

These premonitions aid us in catching a thrown ball, for example, but can trick our senses when viewing static imagery on a two-dimensional plane. In effect, our in-built neural lag causes us to intuit motion-like characteristics to inert images, per the example above. Alas, our future-seeing ability is too favorable to our survival to ever part with, so the minor bug of awkwardly processing 2D geometry will remain an acceptable trade-off.

Nature’s Alphabet

“Spirit-reading” is Changizi’s nimble way of referring to all of the knowledge, thoughts and ideas nesting in the world’s books, literature and other written material. Thanks to language and writing, we have the ability to peer into the minds of our ancestors. And what an uncanny ability it is! Written language is not a technology we could have guaranteed would mesh well with our biology. So how did it come about? And why was it such a glowing success?

Changizi seeks to explain the contagion of written communication by linking its design to the shapes and contours found in our natural environment. If the basic strokes, junctions, marks and symbols of writing were adapted from familiar objects in nature, then our streamlined visual system would be well-prepared to process this information effectively. In fact, if we rewind the clock to our most ancient writing systems, we find they are unmistakably logographic (object-like), including Sumerian cuneiform (the very first writing system ever developed organically ~3200 BCE), Egyptian hieroglyphs, Chinese characters, and the independently derived writing of the Mexican Indians appearing sometime before 600 BCE.

Through some involved visual linguistic analysis, Changizi submits that the fundamental structures of letters are akin to object parts observed in nature. The more common configurations we find in nature tend to find prevalence in human writing schemes. This relationship was no accident; our ancestors mimicked natural scenery to optimize information retrieval through the instrument of writing. In this sense, the clues to writing’s triumph are lurking in the letters themselves.

Closing Thoughts

There should be more books like The Vision Revolution. Changizi presents a highly compelling, evolutionarily grounded case for four intriguing ideas, distills the related focus areas into readable prose, and tailors it to the nonspecialist. The abundance of visual aids is a thrilling, effective way to convey his ideas and goes a long way toward making this more engaging than the average non-fiction work. The Vision Revolution is concise, well-argued, easy to wade through, and comes enthusiastically recommended. These ideas will change the way we think about vision and our perception of the world, and I hope it spawns even more exciting research going forward.

Note: This review is mirrored over at Goodreads and at Amazon.

 
 
Last week science writer Carl Zimmer moderated a cross-disciplinary discussion on the newly sequenced genome of the elusive coelacanth (pronounced ‘seel-i-kanth’).

This deepwater, lobe-finned fish was one of the most surprising discoveries of the 20th century and a powerful object lesson for understanding evolution. The coelacanth is often colloquially referred to as a “living fossil,” a situation in which fossils of an animal are found before the living specimen—in this case over one hundred years before. Presumed extinct for 70 million years, it was found flopping around in trawler nets off the coast of Africa in 1938. Today there are only two extant species of coelacanth, both among the most critically endangered species on the planet.

If you’re looking for a useful launching pad for explaining the principles of evolution, look no further than this enigmatic fish. First, it shows how critical a role environment plays in the formula of natural selection. According to the fossil record, coelacanths could once be found in abundance densely hugging the littoral regions of Africa and south Asia several millions of years ago. It was then thought to have gone extinct at the time of the impact event marked by the Cretaceous-Paleogene (K-Pg) boundary. Its later re-discovery tells us that certain species of the fish were able to survive in narrow pockets of their environment where selection pressures operated at reduced magnitude.

The volatile climate brought about by the K-Pg impact thus signaled the death knell for the coelacanth (along with 75% of extant species at the time) in many of its most densely inhabited areas. However, the climate aftermath was not uniform across all coelacanth habitats, which is why we still find them in remote regions today.

Those that survived were nudged, genetically and morphologically, in some rather interesting directions, which brings us to our second point. The modern coelacanth is quite distinct from its ancestral counterpart. From morphological comparisons capturing the last ~400 million year history of this species we can see an elegant transition from its ancient to its modern form. In the image below, a profile view of the Latimeria and its closest fossil relative, you can see a number of skeletal differences among the fins, main body and vertebrae.

Courtesy of scienceblogs.com/pharyngula

All things considered, the coelacanth is one of the most beautiful examples of a “transitional” form on record. It’s believed to be one of the main species linking up gill-bearing, finned fish to air-breathing, limbed amphibians. Its unique fin structure, auditory system and vestigial lung are all precursory to the Devonian divergence of tetrapods like reptiles and amphibians, and in fact the modern coelacanth shares more in common with these orders of organisms than with other modern fish.

Today this distant relative, which has an average lifespan of 60 years and can grow as large as 6.5 ft (2 m) in length, can only be found along the coasts of the Indian Ocean and Indonesia. Learn more from the discussion below.

http://www.youtube.com/watch?v=-BSOFor1IsA&feature=youtu.be

Image courtesy of Todd Huffman

Feature image courtesy of Todd Huffman

 
 
Here on earth, life has evolved multicellularity dozens of times since the first proto-biological forms took shape — at least 25 times according to Grosberg and Strahmann. There is no need to teleport to the past, however, as we can now observe directly this metamorphosis by experiment alone.

In the past month two separate trials with single-celled yeast have shown how yeast respond in the face of different selection pressures. Instead of separating from the mother cell into two distinct daughter cells (mitosis), or untethering itself from the parent cell after maturity (budding), new yeast cells globbed together in both of the experiments, creating an amorphous blob geared to outcompete its neighbors. That is, the transition from unicellularity to multicellularity has now been observed and monitored in the lab.
 

This increase in mass provides various functional benefits, such as conforming to a sucrose-based diet in the case of the trial at Harvard.
 

This latest experiment at Harvard (and various others like it) illustrates elegantly the degree to which biology is shaped by its environment. Changing up food sources or food scarcity can dramatically reshape populations as natural selection determines which individuals are better suited to the latest pressures operating in their habitat. This bottom-up process of “design by adaptation” is a one of great ingenuity and flexibility.
 

 
 
External link: Another Path For Evolving Bodies

Feature image credit: Wikimedia Commons

 
 
Life on earth is symbiotic. We are deeply interconnected with and inseparable from the rest of the biosphere. This deep alliance manifests in our genetic distance from other animals and plants, and by the vast array of microbes for which we serve as worthy hosts.

As many as 1¹² microbes are at this very moment foraging and scuttling about inside each and every one of us, some providing beneficial aid, some promoting harm, and some just along for the ride. Our ties run deeper, however. Advanced sequencing methods show that a whopping 8% of our genome is inherited viral DNA. Moreover, 37% of human genes have homologs in bacteria and 28% are traceable to unicellular eukaryotes.

This tangled web of co-dependency suggests that studying humans and other animals in isolation no longer makes sense. Instead of viewing ourselves as freestanding individuals, we are perhaps best thought of as integrated biological ecosystems. Bacterial colonies with legs.

A recent piece on i09 probes this connectedness by asking a question indissociable from Darwin’s great theory: is every living thing on earth related? After all, to talk about Darwinian evolution is to talk about universal common ancestry (UCA), the idea that all of life on earth is genetically linked to a single progenitive forerunner. Dogs, corvids, cetaceans, worms – if you follow the chain far enough back in time, you’d eventually converge upon a primordial bundle of life which gave rise to the biodiversity witnessed today.

We still can only speculate on the specific characteristics of this last universal ancestor (LUA), but recent statistical analysis provides further support for this key pillar of Darwin’s theory. Douglas Theobald, a research professor at Brandeis University in Massachusetts, now lends compelling mathematical evidence toward UCA and against multiple ancestry.

Theobald and his team started with twenty-three proteins common to twelve different organisms alive today. The twelve chosen are distributed evenly (four a piece) among the three basic domains of life: Archaea, Bacteria and Eukarya. Using model selection theory, the team then ran the genetic sequences to determine whether single or multiple ancestry was more likely.
 

Various patterns of descent can be grouped according to how much commonality organisms share in terms of their DNA. This can easily be done for specific phyla, but the statistical work done at Brandeis integrates all three of life’s branches, concluding that the overlap in gene relationships points to a genetic center, existing most likely 3.5 to 3.8 billion years ago. A number of variables were fed into their model, choosing to rely on more than just sequence similarity. The results strongly favor single ancestry over a multiply threaded origin scenario.

Various attempts have been made to distill and visualize earth’s great chain of being. The collaborative, peer-reviewed Tree of Life Web Project, which began back in 1995, is a superb rendering of relatedness and perhaps the best source freely available. Go ahead. Meet the family below.

Courtesy of the Tree of Life Web Project

The image (click here for a larger view) collates all major phyla and locates them according to the best available molecular and cladistic data. It’s a tidy picture of the history of life on earth.

While we have much to learn about the details, the results are in: we are intertwined with an imponderably vast chain of life reaching back to precellular material and to the interstellar maelstroms from whence it derived. We share kinship, however distant, with every form of life on earth – with those that once paced and stalked the steppes of Europe, with those that paddle and float in the chemosynthetic depths of the Pacific, with those that soar, swoop and sail the skies above us, and with those that have yet to come.
 

External link: Is every living thing on Earth related?

Feature image: “Redwood Extreme” by colindub.com

 
 
We share little in common with our forebears’ understanding of the universe. In ancient times the earth was ensconced by a dome or firmament which held back rain and other effusions from above. Drought and wetness were tangible indicators of the pantheon’s impression of earthly behavior, with a blue sky betokening the rain that lay just beyond the earth’s protective shell. For many of our ancestors, the stars influenced the health of those on earth; for others, calamity and human hardship could be ascribed to nothing more than the shifting dispositions of the local deities. Maladies of the skin and throat and other physiological dysfunction were regarded as plagues, or instances of pestilential terror cast down as punishment. It was not until our discovery of the virus that these superordinary affiliations were shorn in favor of the vanishingly tiny world thriving right under our noses.

Viruses have been invading other life forms for billions of years with nary an invitation, yet our knowledge of this relatively young science is still fairly limited. Helming this microcosmic thrill ride in A Planet of Viruses is Carl Zimmer, first-place recipient of the 2012 AAAS Kavli Science Journalism competition and one of the most illustrious science reporters of our time. Author of Microcosm and Parasite Rex, pathogen science has long been his forte. In his latest and most abbreviated work, Zimmer marshals his treasure of insights and provides us a sweeping introduction to this fascinating, if ineluctably unnerving world.

The book is organized as a compilation of well-connected short essays, a format that suits the material well. Each of the chapters spotlights a specific strain or type of virus which has wreaked considerable chaos on human welfare–from  rhinovirus, smallpox, and influenza to HIV and West Nile–and Zimmer’s characteristic story-centric style makes each vignette as rousing as the last. As you progress, Zimmer slowly raises the curtain on virus ingenuity, weaving accessible tales and the latest research and statistics throughout.

The Infiltrator

Since viruses first breached the scientific periphery in the 19th century, over 5,000 separate strains have been identified, with possibly tens of thousands more harboring in the oceans and lining the guts of every species on earth. While they can vary broadly in physical size, shape, number of genes, and mobility within and between hosts, they all borrow from the same playbook. At the first, a virus requires a host to survive, unlike bacteria, so its blinkered priority is to gain access to the cellular machinery of other life forms. Whether it’s animals and plants or bacteria and archaea, a virus does not discriminate.

I like to think of them as the world’s smallest stealth agent, as resourceful as they are deadly. In what makes Ethan Hunt look like an amateur, a virus has the ability to infiltrate a host’s cells in a variety of ways, a skill which amplifies as evolution takes its course. Once the virus descends upon the host’s genetic structure, it can really begin its work. With full access to the genetic database the virus begins installing its own DNA onto the cells of its host, overriding the host’s DNA. At this point, the virus is replicated by the host’s hijacked DNA at a prodigious rate until many thousands of identical copies line the inside of the host’s cells. Depending on the genetic mixture, this assimilation can disrupt a host gene’s ability to make proteins, unleashing havoc on the unwitting custodian, or the virus presence can trigger the release of antibodies which scramble to shut down the intruders, subjecting the host to nasty symptoms in the process.

There is ongoing debate over whether viruses qualify as a form of life. They cannot survive outside of a host cell and are absent any kind of cellular architecture, rendering them little more than small, self-assembling clusters of nucleic acids. Even so, Zimmer is quick to point out their indispensable role in shaping and sustaining life over the aeons. “We humans are an inextricable blend of mammal and virus. Remove our virus-derived genes, and we would be unable to reproduce.” (p. 93)

Viruses have also been implicated in the origin of life, as their capacity for self-replication may hold the keys to how precellular material jumpstarted the chain of life on earth.1 The uninvited stowaways have been shuffling genes among different host species ever since, comprising as much as 8% of the human genome.2 Thus not only have viruses been a tremendous force in the evolution of life on this planet, they are essential to our survival.

Zimmer also discloses plainly just how near are viruses and other infectious agents. Each of our trillions of cells can contain hundreds of viruses and bacteria.3 Human papillomavirus (HPV), most known for inflicting cervical cancer and killing over 270,000 women every year, is actually quite common and can be found nestled in your skin cells.4 We constantly shed our outermost layer of skin after cell death, depositing the virus-laden DNA all around us. That means that right now you likely have more than a few HPV viruses on the desk and laptop in front of you. Not the cheeriest thought perhaps, but you will find solace in the fact that the majority of HPV strains are benign and pose no immediate risk.

Cat, Meet Mouse

It is true that the lion’s share of known viruses introduce no changes to infected cells or simply lie dormant within our DNA. But it is also true that pathogens evolve more quickly than any known form of life. For this reason microbe trajectories always lie one step ahead of us and are difficult, if not impossible, to predict. Zimmer relates this chilling reality by describing why scientists are urging against the over-use of antibiotics. Not only do antibacterials have a null effect on viruses, they upset the delicate ecosystem inside our bodies and ‘incentivize’ bacteria to evolve countermeasures, potentially resulting in more noxious versions of both benign and harmful strains.

In response to this dilemma, many medical biologists now have their eyes on an alternative approach to fighting bacteria: phage therapy, an area in which precious little research has been conducted. Somewhat confusingly, a bacteriophage is a virus used to combat resilient bacteria. Essentially, pitting pathogen against pathogen. Zimmer tells of a lab-engineered phage (pictured below) developed by a team from Boston University and MIT that can wipe out 99.997% of E. coli strains. More impressively, “scientists at the Eliava Institute have developed a dressing for wounds that is impregnated with half a dozen different phages, capable of killing the six most common kinds of bacteria that infect skin wounds.” (p. 38) Among many microbiologists, this approach to resistant bacteria is a heavily favored alternative to antibiotics. But until a wider body of research is explored, such precision warfare is confined to the lab.

A coliphage, courtesy of GrahamColm

Exit: Stage Left

By all accounts, the most uplifting installment is that of smallpox, which Zimmer recounts in a coda entitled “The Long Goodbye.” When this dark scourge first started replicating inside of human hosts remains an open question. Telltale signs can be seen in the 3,000 year old mummified corpse of Pharaoh Ramses V, while other scientists date its emergence as early as 10,000 BC. Based on extant medical records and fatality rates, it’s been estimated that smallpox caused 400,000 European deaths each year during the 18th century and another 300-500 million deaths in the 20th century alone, bringing down three empires in the process. Its final death toll across human history and its legacy in shaping civilization may never be fully realized, but it met a worthy competitor in one Edward Jenner.

Among the venerated elite in science history, Jenner used cowpox, a member of the same viral family as smallpox, to inoculate potential smallpox victims. It worked, and while Jenner did not discover the antigenic properties activated by vaccination, it was his “trial by fire” testing and scrupulous documentation of his findings that led to its widespread adoption against smallpox. In 1979, the World Health Organization declared smallpox an eradicated disease. The unflinching bravura of those who risked their lives in the global eradication effort functions as a testament to human possibility. WHO’s vaccination campaigns, which achieved success largely by isolating the infected from the non-infected and administering vaccines to quarantined communities, is perhaps the greatest success story in all of medicine and lends hope for the outcome of future travails.

Closing Thoughts

Thanks to one of the finest science communicators today, the remaining essays assembled in A Planet of Viruses are every bit as informative and accessible. As stepladder to the scientific community, Zimmer has a knack for engaging readers of all stripes, from the layperson to the armchair scientist to anyone who simply likes reading good stories. His way is precise, not overly simplified, choosing just the right level of linguistic precision to divulge this teeming underworld to his readers. While certainly not as detailed as some of his earlier expositions, this brilliant anthology serves as a perfect preamble to the bustling field of microlife. Clocking in at just under 100 pages, I highly recommend you target this one for your next free weekend, preferably before, and not after, having eaten.

Note: This review is mirrored over at Goodreads and at Amazon.

Feature image credit: rost9 — 3D illustration pathogenic viruses causing infection in host organism.

1. “Virus self-assembly within host cells has implications for the study of the origin of life, as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules.” (Koonin et al 2006)

2. “To put that figure in perspective, consider that the 20,000 protein-coding genes in the human genome make up only 1.2 percent of our DNA”. (p. 52) Zimmer offers that our identity is tied up more in ancient virus than in anything we can call “us”.

3. Viruses are the most abundant form of microorganism on the planet. There are an estimated 10^31 viruses (read: not distinct strains or species) currently flourishing within the cells of unwitting hosts. Written out, that number looks like:

   10,000,000,000,000,000,000,000,000,000,000

   Parenthetically, there are also 10^30 bacteria on earth, so naturally they’re the most abundant hosts for viruses. It could in fact be said that biology is 99% micro.

4. Cervical cancer is the third leading cause of death in women, just behind breast cancer and lung cancer.

 
 
An official resolution to commemorate the birth date of Charles Darwin has been proffered by Democratic Congressman Rush Holt (D-NJ) in collaboration with the American Humanists Association. Citing the British naturalist’s momentous contributions to human knowledge and the untold advances rushed in by his ideas, Rep. Holt has asked Congress to dedicate February 12, 2013 to the timeless icon.

Holt, only the second research physicist to hold Congressional office, commented in yesterday’s press release, “Only very rarely in human history has someone uncovered a fundamentally new way of thinking about the world – an insight so revolutionary that it has made possible further creative and explanatory thinking. Without Charles Darwin, our modern understandings of biology, ecology, genetics, and medicine would be utterly impossible, and our comprehension of the world around us would be vastly poorer. By recognizing Darwin Day, we can honor the importance of scientific thinking in our lives, and we can celebrate one of our greatest thinkers.”

Similar resolutions have appeared before Congress over the past decade, yet none has escaped the cutting room floor of the House. Pete Stark, another Democratic representative, lobbied for the same concession back in 2011, where it then lay dormant before a GOP-controlled House committee.

From a political vantage point, Holt’s overture might have more opportunistically been seized by the party beset with the graver image problem. The GOP have long regarded evolution science as their bête noire, and virtually all of this past election’s candidates held dissenting views on established science. A similar gesture originating from a member on the right could possibly have kickstarted a partisan-wide reformation, one focused on ensuring voters that it is more in touch with reality in contrast with the past election cycle.

For the moment, however, a GOP rebranding appears far from imminent, and Holt’s resolution, once again, seems dead on arrival. It now lies in the hands of the House Committee on Science, Space, and Technology, occupied by Paul Broun (R-Ga.), who last October decried evolution and the big bang as “lies straight from the pit of Hell.” Moreover, the committee’s senior chair, Ralph Hall, rejects the scientific consensus on climate change, stating: “I’m really more fearful of freezing. And I don’t have any science to prove that. But we have a lot of science that tells us they’re not basing it on real scientific facts.” The views of the other GOP members on the committee are not well-advertised, which is itself a troubling sign.

One can scarcely hold back a chuckle, or perhaps a frightful shriek, upon making contact with the roller coaster of contradiction described here. To the outsider, such statements might seem to connote some warped version of reality or a rather low attempt at humor. Indeed, science denialists lining our science and intelligence committees sounds more like linguistic staccato than a faithful description of America’s leadership environment. Were Jefferson and his contemporaries alive at this moment, they might describe such a paradigm as symptomatic of collective psychosis.

And while all this political posturing and heel-digging prevails on Capitol Hill, America’s reputation continues to fall behind in the scientific arena. A greater percentage of its population rejects evolution compared with most other developed nations.

Image via National Geographic

Darwin Day may seem like a trivial measure, but it could be a good step in lifting the mephitic stain of antiscience and scientific illiteracy long-effused by America. If you’d like to get involved, contact your representatives and urge them to cast their support for this resolution.

External link: HR-41: Expressing support for designation of February 12, 2013, as Darwin Day and recognizing the importance of science in the betterment of humanity

Feature image courtesy of kT LindSAy, a hood mockingbird indigenous to the famed Galapagos Islands.