I’m not happy with the way that headline writers try to attract attention.  My dad once told me that advertisers purposely misspelled words in order to grab attention to their pitch, and I sometimes wonder whether headline writers don’t do something similar.  “New Discovery Overturns Evolution.”  It grabs hopeful creationists, eager to see that William Dembski has been finally vindicated in his predictions that we are in the sunset years of a Darwinist Paradigm that prevents us from truly understanding how evolution works.  So they click and learn that, for example, Ardipithecus ramidus’ new revelation is not a time-stamp with Mr. Deity’s name on it.  What we learned from the teams investigating the remains was instead, while extremely exciting for human anthropologists, the rather mundane and archaic knowledge that “Ardi’s” clasping foot indicates something about our common ancestry with chimps and that chimpanzees acquired this trait long after the Great Branch-Off between Man and Pan.

It is new, and it is cool stuff,  but this isn’t the sort of discovery that will lead to the wholesale dumping of copies of The Descent of Man into the trash bin of history. It is a new piece to a giant jigsaw puzzle of the course of human evolution from the earliest protozoan through the mini-mammals surviving the K-T boundary, up to the Cro-Magnons who are reading and typing on the internet.  It’s quite likely that the pieces we have put together so far are in the wrong places in the picture that the puzzle represents, and that is why paleoanthropologists do what they do.

“All that we know about evolution is wrong” is a close approximation to the truth but not an absolute.  That’s the thing about the process of discovery, and methodologies are continually refined and adjusted, tweaked and teased in order to dig out a bit more data from tenuous strands of DNA and crumbling bones not yet fossilized.  It takes an agonizingly long time for a body to turn to stone, and when you consider how rare an event it is for a dead animal or a plant to turn into a solid piece of rock through mineral replacement under ideal conditions you can see how difficult the task of the extraction of our history becomes.  John Hawks’ quote from Tim White’s paper¹ explains the dangers of haste:

The bony remains of this individual (ARA-VP-6/500) (Fig. 3) (37) are off-white in color and very poorly fossilized. Smaller elements (hand and foot bones and teeth) are mostly undistorted, but all larger limb bones are variably crushed. In the field, the fossils were so soft that they would crumble when touched. They were rescued as follows: Exposure by dental pick, bamboo,and porcupine quill probe was followed by in situ consolidation. We dampened the encasing sediment to prevent desiccation and further disintegration of the fossils during excavation. Each of the subspecimens required multiple coats of consolidant, followed by extraction in plaster and aluminum foil jackets, then additional consolidant before transport to Addis Ababa.

Okay, yeah, I don’t understand all of what is being written about in this quote.  I do know that paleoanthropologists can’t just grab the bones and transport them to California for study.  They have to tease away the setting carefully so as not to further the damage already done by water, wind and crushing weight.  The extraction was completed fifteen years ago and aided by technologies such as CT scanning.

The anthropologists at the time of Darwin’s writings on The Descent of Man didn’t have access to such tools and methodologies, so it should hardly be news nor even a surprise that our murky evolutionary puzzle is being changed from what was written by 19th-century geologists and students of evolution.  What they observed was seen through a glass much darker than the glass current scientists use, but they were very well on their way nonetheless to shaking ancient notions of human evolution.  They were shedding the idea of the Great Chain of Being from bacterium to man and presenting evidence that we really are not so elevated in nature as once was taught.

The nineteenth century was one of the most amazing eras in human discovery yet undertaken, because those methodical explorers hammering away in quarries to find and classify “terrible lizards,” gathering and cataloging rocks and fossils, comparing and contrasting anatomical features from stone to modern skeletons and trying to decipher how humans came about, well, they broke the old picture that illustrated that we are in fact a separate and special creation.  They taught us that we are a part of nature and not separate from it.  Unfortunately, breaking the old picture necessitated the assembly of a new one. We still only have a few soggy and worn pieces and are trying to fit them in place without a complete guide.

DNA and genomics aid in our project to discover who we are and where we come from (and where we are going).  Incompletely fossilized and mineralized bones of ancestors (or non-ancestors as in the case of Ardipithecus) will show us where we have been right and where we have been wrong.

So, all that we now know about human evolution is quite possibly wrong.  But that is what is so exciting about Ardi. Fifteen papers were simultaneously released on what has been learned so far from the discovery.  From those papers will come new questions about humans and our friends the chimps and bonobos.  When did they start climbing trees?  Why did they return to trees while we became ground-walkers?

The focus of the Intelligent Design movement within creationism has been to pick up the discarded pieces which don’t work, those which never really fit but were inserted in deference to religion.  It’s a set of pieces with god-shaped prongs and slots.  When William Paley used them, they made sense in the context of natural theology. Following Mary Anning’s, Charles Darwin’s, William Buckland’s, Alfred Russell Wallace’s, Richard Owen’s and Gideon Mantell’s discoveries, those pieces no longer were needed to explain what the creationists want anthropology to do.  The creationists can’t admit that the pieces are completely extraneous.  The pieces that they want scientists to go back to using don’t answer the questions that anthropologists are asking and answering.  The process is painstaking and yet rewarding.

How much of the differences between human brains and chimp brains can be accounted for by the selective pressure of cooked versus raw meat?  Which genes are responsible for the differences in the way our hands work versus the way their hands work?  Is it a simple matter of regulatory genes controlling development in different ways to develop muscles in chimps which emphasize upper body strength while we develop with a stronger emphasis on lower body strength?

Our past is in our future.  While the fact that we are the products of evolution is not in question, how we came to what we are is still being discerned.  While evolution will not be overturned, all that we now know about how may one day be proved wrong.  While the headline writers at Yahoo News may have been trying to improve click-rate, they were “write” for all the wrong reasons.

1. White TD, Asfaw B, Beyene Y, Haile-Selassie Y, Lovejoy CO, Suwa G, WoldeGabriel G. 2009b. Ardipithecus ramidus and the paleobiology of early hominids. Science 326:75–86.

I remember reading Finding Darwin’s God awhile back.  The first half of the book was an excellent defense of evolution and critique of creationism.  The second half of the book was a poor defense of god belief.  I remember thinking that if Miller had only applied the logic from the first half of his book to the second half, he would be an atheist.

Miller was one of the star witnesses on the side of science in the “intelligent design” case in Dover, Pennsylvania a couple years ago.  He’s now come out with a new book, Only a Theory.

“Darwin’s God” that Miller refers to is evidently a supernatural creator that Darwin implies exists in the final sentence of Origin of Species: “There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”

Miller sees an overall god-intelligence in the universe, but not the day-to-day micromanaging of evolution that Intelligent Design advocates allege.  This god is supposedly the First Cause and set nature’s laws in motion–including genetic mutation, natural selection, and heredity; in other words, evolution–and then stepped back and let the universe run itself.  So, this god works through unguided evolution to create new species.

What Miller didn’t tell us during his talk was that by the end of his life Darwin had become an agnostic.  In other words, Darwin himself had lost Darwin’s God.

One of the reasons Darwin abandoned the all-powerful, all-loving Christian god was because of the cruelty he saw in nature. After Miller’s lecture I spoke with him and asked him how he, a Catholic, could reconcile the cruelty in nature with the idea of a loving god.

I first asked why God couldn’t have made all creatures vegetarians, so that some animals wouldn’t have to painfully and cruelly kill and eat others.  Miller said that that would mean that God would be stepping in and interfering with the natural evolutionary processes that he had set in motion.  (Evidently God avoids miracles these days.)

I then asked Miller about painful human birth defects where the child dies very young.  Why couldn’t God have arranged it so that all genetic mutations were neutral or beneficial mutations?  His answer was the same: that would mean that God would be stepping in and interfering with the natural evolutionary processes that he had set in motion.

It seems that Miller understands the theological problem with a god who has to constantly intervene in his creation.  He once stated “[I]f God purposely designed 30 horse species that later disappeared, then God’s primary attribute is incompetence.  He can’t make it right the first time.”  (“Educators debate ‘intelligent design’ ” by Richard N. Ostling, Star Tribune, March 23, 2002, p. B9.)

It seemed to me that this god wasn’t of much use.  “So in other words,” I said, “this world operates exactly the way we would expect it to operate if there were no god.”  Miller agreed, citing retired Vatican astronomer George Coyne, who said that the universe doesn’t need God.

Again, I asked him how he was able to reconcile the problem of natural evil with a loving god.  He said that he was able to do so, but he didn’t provide details as to how.  I told him I have never been able to do it.

Other people were waiting to talk with Kenneth Miller, so we parted company, agreeing to disagree.

As I walked back to my car, I thought: Miller has all but admitted that there is no actual evidence for a god, and that certainly a god wasn’t involved in the daily process of evolution.  And yet Miller believes in a god.  This must mean that he believes on a basis other than evidence.  In other words, on faith.  Evidently the belief came first and the rationalizations second.

Miller was raised by Roman Catholic parents and is “coincidently” a Roman Catholic himself.  Of all the varieties of god belief he could have chosen, he “just happened” to pick the one he was raised with.  Indoctrination has trumped evidence.  To me, this seems like a very unintelligent design.

August Berkshire is the vice president of Atheist Alliance International, past president of Minnesota Atheists and member of the board of Camp Quest of Minnesota.

I was reading today about the problems facing the Theological Evolutionists. They accept the science of evolution yet hold on to their faith that an active creator designed the process of evolution to lead to Man. Bart Klink’s essay at Infidels.org spells out their quandary. I was particularly struck by this paragraph:

Had the asteroid which wiped out the dinosaurs 65 million years ago missed the earth, it’s likely that our little branch on the tree of life would never have developed, since the end of dinosaur dominance made it possible for our small mammal ancestors to flourish. How are such chance contingencies in the history of life compatible with the alleged providence of a Creator?

If we step outside of our chauvinistic inclination to look at evolution as a process with humans as the teleological result of its process, the unfolding story of life’s continual divergence makes even more sense. As Klink illustrates, we are but a small twig on a minor branch of the Tree of Life and not necessarily its crown.

In biology, we know that the whole of the aviary are descendants of common ancestors within the mighty dinosaurs. Prior to the great meteor crash on what is now the Yucatan peninsula, the antecedents of modern birds had already begun to fan out from their common ancestry with coelurosaurs (a group which includes velociraptors.)

For the layperson looking at dinosaurs, this relationship is easier to see in the modern raptors such as eagles, owls, falcons and hawks. These magnificent birds have the temperament of what we think of as keen hunters demonstrating the truism that nature is “red in tooth and claw.” The raptors hunt and eat and participate in Dawkins’ “evolutionary arms race.”

But what of the pretty little flutterers that stop by your bird feeder to chirp and nip at the seeds you leave for them? These are perhaps a bit more difficult to visualize as sharing common ancestry, relatively recent common ancestry, with the slashing and flesh-ripping velociraptors depicted in Jurassic Park.

Crows ripping at the flesh of a dead squirrel on the ground? Yes, they are living from meal to meal and cawing their warnings to each other, much as the more vicious dinosaurs of our imagining. The budgie in your cage, playfully bobbing and primping in front of a mirror? It is harder to imagine such a cutie as the descendant of the mighty hunters of 65 million years ago. Nonetheless, it is a survivor of evolution.

Most of the problem that people have in accepting evolution is the popular notion that is often falsely ascribed to Charles Darwin, a phrase he only temporarily accepted. “Survival of the fittest” conjures images of nature constantly at war for food and sex, a battle between predator and prey and suggests that adaptability involves the continual development of “bigger, faster and stronger” predators and the concomitant “bigger, faster and stronger” prey.

“Survival of the fittest” did not originate with Darwin. It was coined instead by philosopher Herbert Spencer and applied by “Social Darwinists” to describe a condition of raw power in economics, unfettered by regulation or oversight. Evolution, properly understood, does not entail survival of the fittest. It is not a matter of the fastest, the strongest and smartest proceeding to the next generation. It is a matter of populations surviving well enough to continue until they eventually face extinction.

Small birds find various niches to fill. The budgie and the robin survive because there is enough of the food energy that they can use to last through successive generations, and all they need to pass on their genes is to reproduce in great enough numbers that their predators can’t overwhelm and destroy their species. Malthus’ essays on population and economics are said to be prime inspirations for Darwin’s ideas on natural and sexual selection. A species which can outnumber and outlast its competition will continue, if it can adapt to changes in the environment.

When the great rocks collided with the Earth at Chicxulub, (and possibly others at the same time in Ukraine and in the Indian Ocean,) a mass extinction ended the reign of the dinosaurs, the large beasts who ruled as the number one predators on land for 160 million years. It ended the reign of the plesiosaurs in the oceans. It left open, after Earth’s recovery, niches for new forms to arise from the common stock shared by dinosaurs and birds, and here we are in the modern age feeding sparrows and chirping birds outside of our windows.

The smaller birds survived because the massive disasters left for them room to build their populations. Out of the ashes of the K-T extinction arose new plant life, new forms of food for the taking by hungry birds. (To return to Jurassic Park for a moment, Ian Malcolm explains “Life finds a way.”) The massive disaster also likely made it possible for mammals to diversify and embiggen, and transform to the point where arose humans smart enough to make and fill bird feeders.

The quick answer to Bart Link’s question I quoted above is that the meteors colliding with earth at the K-T Boundary was a deus ex machina, that the dinosaurs had finished their role in paving the way towards the eventual development of man. The big bad rocks were the Hammers of the God(s) and a necessary step for Theistic Evolution.

That answer is unsatisfying to me for the simple reason that it really adds nothing but a violation of Occam’s Razor. It’s an unnecessary addition to the point of inquiry. Evolution takes advantage of catastrophes, and often the fit to survive are not the biggest, strongest nor the fastest; just the ones who make it through.  I am happy that the meteors struck, because if not for their destruction there would have been no key lime pie and no humans to eat it.  There would have been no birds calling outside my window on a Sunday morning to wake me.  I just don’t think they were intentional.

Consider the lowly bird. It’s outside my window. Consider the mighty T. rex. Its bones are in a museum.

Unique Shapes of Caterpillars

In general, caterpillars are elongated and tubular in shape but there are a few that have peculiar and bizarre shapes.

Here are some of the most uniquely shaped caterpillars. Pick your own choice which one on the list you think is the weirdest-looking of them all.

Impact Lab

Teens capture images of space with £56 camera and balloon

Proving that you don’t need Google’s billions or the BBC weather centre’s resources, the four Spanish students managed to send a camera-operated weather balloon into the stratosphere.

Telegraph

Color Vision: How Our Eyes Reflect Primate Evolution

To our eyes, the world is arrayed in a seemingly infinite splendor of hues, from the sunny orange of a marigold flower to the gunmetal gray of an automobile chassis, from the buoyant blue of a midwinter sky to the sparkling green of an emerald. It is remarkable, then, that for most human beings any color can be reproduced by mixing together just three fixed wavelengths of light at certain intensities. This property of human vision, called trichromacy, arises because the retina the layer of nerve cells in the eye that captures light and transmits visual information to the brain uses only three types of light-absorbing pigments for color vision. One consequence of trichromacy is that computer and television displays can mix red, green and blue pixels to generate what we perceive as a full spectrum of color.

Scientific American

Illuminating Reuse: 15 Recycled Lights and Lamps

Egg cartons, Legos, ballpoint pens, blenders and plastic spoons: these are just a few of the items that have been transformed into awesome light fixtures by creative DIYers. Why buy new when you could have a stunning chandelier or lamp that puts junk to good use? These 15 examples of brilliant eco-illumination show just how stylish and fun recycled materials can be.

WebEcoist

Who Owns Organic Brands?

The Cornucopia Institute provides a link to Dr. Phil Howard’s webpage, which has all kinds of awesome graphics to illustrate concentration in the organic food sector. This one shows acquisitions by several major food corporations (sorry the images are small–there’s a link after each one that takes you to a bigger version, or you can easily see all of them at Dr. Howard’s website). For all but the third image, the color scheme is yellow = multinational processor, green = organic brand, blue = investment firms, and red = organic versions of mainstream brands.

Sociological Images

Amazon Defense Coalition: Chevron Lawyers Explode In Anger After More Oil Found at “Remediated” Sites In Ecuador Trial

After a frustrating week of setbacks in an environmental trial in Ecuador’s rainforest, two Chevron lawyers exploded in anger at representatives of the victims after a technical expert demonstrated for the third time in a week that oil was visible at a well site that the company claimed to have “remediated” a decade ago, said lawyers for the plaintiffs in a lawsuit against Chevron.

Yahoo! Finance

Islands Disappear in India

As islands in eastern India disappear under rising seas, residents are losing land, homes, and farms. (video)

National Geographic

New Honda Takes on the Prius

The road is about to get a little more crowded for the Toyota Prius. Starting Tuesday, the Honda Motor Company will offer American consumers what it bills as “the world’s first affordable hybrid.”

Costing just shy of $20,000, the Honda Insight promises to let drivers respond to both of the leading crises of our day: the environment and the recession.

New York Times

Calling ‘em Out: The World’s 10 Worst Greenwashers

As the green movement sweeps the globe, companies, trade groups and government organizations are eager to get a piece of the pie. ‘Green’ can definitely translate into big profits if you do it right – but all too often, these money-hungry entities choose to fudge the facts in an attempt to make themselves seem more environmentally friendly and responsible than they really are. That’s called greenwashing, folks, and here are 10 of the world’s worst offenders.

WebEcoist

Photographing the Big Melt

For more than 30 years, photographer James Balog has been seeking new ways to visualize the natural world. His artistry has been featured in dozens of magazines, from National Geographic to The New Yorker. But his most recent project, the Extreme Ice Survey (EIS), has a scientific goal. It seeks to document an unprecedented melting of the world’s glaciers, a phenomenon that many scientists agree is proof of human-caused global warming. As director of the EIS, Balog considers himself a modern hunter-gatherer, collecting vital information to feed a public hungry for real evidence of climate change. In this audio slide show, let Balog whet your appetite in his own words.

PBS

Unique Killer-Whale Pod Doomed by Exxon Valdez

Most of Prince William Sound’s animal populations will someday recover from the lingering effects of the Exxon Valdez oil spill. One, however, will not: a community of killer whales unlike any other in the world.

“It’s a separate population. Their genetics, their acoustics, are different from any other killer whales that we see in the North Pacific,” said Craig Matkin, director of the North Gulf Oceanic Society, who has studied the region’s whales for three decades.

Wired

Cape Cod sees rare large gathering of right whales

The number is about six times greater than last year and represents about 24 percent of the estimated 325 right whales left in the world, said officials at the Provincetown Center for Coastal Studies, which is conducting aerial surveys of the whales, and the National Marine Fisheries Science Center.

Reuters

Congress approves landmark conservation bill

The Democratic-led U.S. Congress gave final approval on Wednesday to sweeping land and water conservation legislation that environmental groups praised as one of the most significant in U.S. history.

Reuters

Shampoo in the water supply triggers growth of deadly drug-resistant bugs

The warning has been made by Birmingham and Warwick university scientists, who say disinfectants and other products washed into sewers and rivers are triggering the growth of drug-resistant microbes. Soil samples from many areas have been found to contain high levels of bacteria with antibiotic-resistant genes, the scientists have discovered – raising fears that these may have already been picked up by humans.

Guardian

How Air Pollution Causes Heart Disease

We are used to thinking of heart disease as a product of genetic factors or lifestyle choices, such as what we eat and how much we exercise. There is another road to heart disease: breathing.

Accumulating evidence indicates that an increase in particulate air pollution is associated with an increase in heart attacks and deaths. Research has begun in the relatively new field of environmental cardiology – a field that examines the relationship between air pollution and heart disease.

TerraDaily

I have a friend from my early days as a Christian youth growing up in Hallock, Minnesota. I had looked to him as an extra-churchory adviser on matters related to prayer and integrating fun into the practice of everyday religion. I had lost touch with him after he graduated from high school.  Alden and I both shared a love of sixties rock music, and he assured me that a Christian needn’t trap his ears in the Christian music aural ghetto.  Mutually, our favorite secular band was The Guess Who, and I still remember late evenings singing the song “F-I-D-D-L-I-N-G” outside of a nearly-abandoned Baptist Church in Hallock.

It is a song that celebrates drinking and gambling.

Alden found me as the result of a blog post I wrote four years ago regarding the northern lights and their frequent appearances in northern Minnesota.  I mentioned his name because he had bragged to a pair of missionaries from the Baptist church to Hallock, and he said that “The northern lights practically live here.”  The funny part of the story was that in the two months that the missionaries spent in Hallock, the northern lights didn’t light.

Alden happened to be googling his name four years ago and found my post.

Over the years since then, Alden and I have traded friendly yet pointed barbs on each other’s blogs.  When I needed help desperately last fall, Alden was among those who generously answered the call.

Here’s the main point of our disagreement.  Alden is a strong Christian who thinks that modernism has had a disastrous effect on our culture and our individual abilities to determine the answers to important questions.  As an atheist, I am unable to see where religious belief and faith yield any sort of objective understanding of the nature of life and origins.  In his mind, I have succumbed to the prejudice of natural methodology, and in my mind, he is all too willing to accept the writings of anybody who displays a philosophical skepticism over the historical explanatory power of cosmology and evolution.

It may be that as the days stretched on without being able to blog at Tangled Up in Blue Guy, I was suffering withdrawal and was more likely to lash out at ludicrous and ill-informed attacks on the settled science of evolution.  It may be that he didn’t correct one of his peanut gallery commenter’s inane statements that “evolution is scientists’ subconscious way to deny the Living God that they hate” and that evolution wasn’t necessary for understanding biology in the seventies and that Skell is right that it is still unimportant.

I lost my cool and lashed out.

Steve, you just blew my irony meter.

How well do you then understand biology? Enough to get by?

What you both ignore is that the battle over evolution and religion was hashed out in the 19th century and evolution was unearthed and investigated by people who were creationists trying to prove the accuracy of the bible and the creation story. You should take the time to acquaint yourself with the full development of the theory before you start insulting the motives of people who have been unearthing nature’s secrets as some sort of justification for affirming their “hatred of the living god.”

It is just your sort of thinking and talking that drove me away from religion in the first place. If I have to suspend my disbelief in science so much so in order to practice religion, and if the things that religion teaches contradict what I can see with my own eyes, then religion loses out.

If Augustine wrote one thing that makes sense, then it is his statement that misstating the facts of the natural world in order to promote religion is a fool’s game.

Your continued denialism in the face of the evidence of evolution leads me to the conclusion that you will never be interested in anything that contradicts your “faith.” Instead you will continue to follow the lead of those who don’t understand that the process of science is a matter of investigation and not faith.

And Alden, I am still trying to figure out how a method of science that includes the supernatural is supposed to work in yielding objective information.

Finally, as to the accusation that scientists are only interested in protecting their money, power and authority; I would suggest that religion is lashing out on this issue because of its fear of losing hegemony.

I invite readers to to the full exchange over at Alden’s blog, because my intention is not to provide a rehash here at Quiche Moraine. In reference to Augustine, I had in mind this passage:

Usually, even a non-Christian knows something about the earth, the heavens, and the other elements of this world, about the motion and orbit of the stars and even their size and relative positions, about the predictable eclipses of the sun and moon, the cycles of the years and the seasons, about the kinds of animals, shrubs, stones, and so forth, and this knowledge he hold to as being certain from reason and experience. Now, it is a disgraceful and dangerous thing for an infidel to hear a Christian, presumably giving the meaning of Holy Scripture, talking nonsense on these topics; and we should take all means to prevent such an embarrassing situation, in which people show up vast ignorance in a Christian and laugh it to scorn. The shame is not so much that an ignorant individual is derided, but that people outside the household of faith think our sacred writers held such opinions, and, to the great loss of those for whose salvation we toil, the writers of our Scripture are criticized and rejected as unlearned men. If they find a Christian mistaken in a field which they themselves know well and hear him maintaining his foolish opinions about our books, how are they going to believe those books in matters concerning the resurrection of the dead, the hope of eternal life, and the kingdom of heaven, when they think their pages are full of falsehoods and on facts which they themselves have learnt from experience and the light of reason? Reckless and incompetent expounders of Holy Scripture bring untold trouble and sorrow on their wiser brethren when they are caught in one of their mischievous false opinions and are taken to task by those who are not bound by the authority of our sacred books. For then, to defend their utterly foolish and obviously untrue statements, they will try to call upon Holy Scripture for proof and even recite from memory many passages which they think support their position, although they understand neither what they say nor the things about which they make assertion. (1 Timothy 1.7)

[Saint Augustine (A.D. 354–430) in his work The Literal Meaning of Genesis (De Genesi ad litteram libri duodecim) provided excellent advice for all Christians who are faced with the task of interpreting Scripture in the light of scientific knowledge. This translation is by J. H. Taylor in Ancient Christian Writers, Newman Press, 1982, volume 41.]

Evolution is not what turned me against religion. I was able to reconcile evolution with my faith. Honestly, I didn’t give it a lot of thought, this contradiction between faith and evolution. I knew for dang sure that the literal belief in the 6,000-year-old creation was not to be taken seriously, but a form of “guided evolution” was something I could accept until I started thinking more deeply about the role death, disease and starvation play in the development of a diverse tangled bank.

No, this ancient Christian philosopher got at least one thing right if nothing else. It was an insistence that religion should have prima nocta over any understanding of nature that finally drove me away. If it came down to a dispute over whether or not tiktaalik was a transitional fossil (which I can plainly see to be the case) or a denial that evolution is a valid historical science that yields current insights into the modern study of biology based on the religious authorities’ insistence that I should deny evidence, I would have to discard religion.

The progenitors of intelligent design creationism have clearly not thought through the theological implications of teaching their stance. By inserting an insistence that there is more to evolution than can be learned through the scientific method, and then by deliberately misstating science in ways that can be easily fact-checked, they are setting up a situation through which students will learn to distrust religious authority. By drawing a direct relationship from the natural methodology used to study evolution to atheism they are paving a road towards atheism for kids who might not otherwise have even considered it.

For me, the value of inserting religion into science is that we can see we are inserting an extraneous variable into our statistics and our mathematical equations. The formula most beloved by people who are interested in science is the famous “e = mc².”  It is useful in understanding the relationship between energy, mass and the conversion thereof.  It has been tested and verified through the observation of matter and light in the labs and in astronomy’s galactic lenses.

My friend insists that through denying the role of faith in understanding, modern scientific practice has limited itself.  By eliminating the role of the supernatural in science, modernism is unnecessarily stultifying my thinking and the thinking of those of us who are no longer open to a supernatural creator/designer.

When I look at the equation “e + God = mc²,” I see the same result as the equation “e = mc²,” and I don’t see the value of the extraneous variable “God” in explaining the relationship between energy and matter.  With the insistence of inserting that variable, creationists of whatever stripe are making things worse for their cause when the thinkers of tomorrow consider the implications of their folly.  They should leave science for science and stop meddling.  As an atheist, I should be happy that they are weakening their argument better than I possibly could on my own.

For my friend’s sake, I am actually a bit saddened.

He Was Also Right

Newton was wrong, too.  If astrophysics had relied on Newton and Einstein not corrected Newton, space exploration would be a dicey game indeed.  We would never be able to find our way around.

On Tangled Up in Blue Guy, I often post a “Friday 419″ piece. Today I will talk about a different kind of scam.  Magazines and newspapers are selling you copies of their publications with the shocking revelation that Darwin’s work was not completely accurate, based on new knowledge gained since his time.

We are not shocked by inaccuracies in Darwin’s works of description.  We would be, instead, shocked if he had gotten everything completely correct.  He described the processes of natural and sexual selection based on the knowledge to which he had access.  Did you know that he had not even known about “genes?”

There are other things he got wrong as well, but some science bloggers took great trouble to explain why a recent spate of pop science articles were just plain inane.

John S. Wilkins had a go with “Darwin was wrong…ish“:

The targets journalists I wish to attack here are those of New Scientist, Newsweek, The Telegraph, and the media release writers for Texas A&M University. And some of the scientists and philosophers whose comments are reported therein are equally guilty. But not wanting to spoil my own nest I shall leave the readers to work out who I mean…

Jason Rosenhouse at Evolution Blog:

Part of Abbie’s point was that when science journalists hype some small advance as a fundamental change in our view of the world, it is usually scientists themselves who pay the price for the irresponsible reporting. She could have asked for no better illustration of her point than the cover of the current issue of New Scientist magazine.

The cover sports a big green tree with the words “Darwin Was Wrong.” I hope they sell a lot of magazines with that load of tripe, since they certainly were not thinking about the generations of school kids and church-goers who will now be treated to that cover in every creationist power point presentation between now and the Rapture. How many people do you think will actually read the article to discover what it was, precisely, that Darwin got wrong?

Larry Moran at Sandwalk:

I happen to believe that the science of evolutionary biology has moved on since 1859, and I happen to be a proponent of evolutionary processes that Darwin new nothing about. Nevertheless, proclaiming that “Darwin was wrong” is a different story. That’s an egregious example of journalistic hype and it’s unacceptable in a magazine like New Scientist.

The main article is Why Darwin was wrong about the tree of life. The author is science journalist Graham Lawton.

The essence of the story is that the early history of evolution is probably characterized by a net of life and not a traditional tree. The “net” metaphor is due to many example of lateral gene transfer.

Evolutionary Novelties:

1. It is an oversimplification to say that Darwin was “wrong” on this point. It is not a clear cut case of right or wrong. Instead, the facts as we understand them today are more complex than what Darwin envisioned, or could have envisioned (given he didn’t know about DNA).

2. The primary, most general implication for the history of life is not changed. Darwin’s tree of life posits common ancestry of all life. This is the central scientific fact that anti-evolutionists rebel most against (because they don’t want to admit we are all related to slime-molds, etc). In fact, the new observations about biology continue to reinforce Darwin’s history-changing insight that all life shares a common ancestry. Yes, we share a common ancestor with a chimp and a fungus, get over it.

PZ Myers on Sharon Begley’s piece:

This is just wrong on evolution:

Water fleas pop out helmets immediately if mom lived in a world of predators; by Darwin’s lights, a population of helmeted fleas would take many generations to emerge through random variation and natural selection.

It misses the whole point. The population of water fleas have a genetic attribute that allows the formation of spines under one set of conditions, and suppresses them under others. This gene regulatory network did not pop into existence in a single generation! If it did, then Begley would have a big story, evolution would have experienced a serious blow, and we’d all be looking a little more carefully into this ‘intelligent design’ stuff. The pattern of gene regulation was the product of many generations of variation and selection; only the way it was expressed in a phenotype experienced a shift within a single generation.

All right, so the newsies got it wrong.  Is it a big deal in the scheme of things?  I would say so.  Evolution itself is confusing enough as it is, and most people don’t understand it.  That’s why it is easy for creationists to make headway in the political realm.  They take stories such as these, and make hay not over the science itself, but the misunderstanding of science.  Uncommon descent was quick to jump in with a “See we have been right all along and Darwinism is doomed.”  Here’s Paul Nelson:

While Darwin argued for a single Tree — probably the most powerful image he introduced into biological perception — he was always cagey about the structure of its root. Life was “originally breathed ['by the Creator,' added in the 2nd edition of the Origin] into a few forms or into one” (1859, 490). There’s a world of (inferential / phylogenetic) difference, however, between divinely created first life and naturally arising first life, when the single most important question in the latter scenario concerns the probability of abiogenesis. “A few forms” that independently evolved (say) ribosomal structure, versus a single origin for the ribosome, would entail radically different consequences for phylogenetic reconstruction.

Move the red bead of the probability of abiogenesis down its wire, away from zero and towards one, and funny things happen to the structure of the monophyletic tree of life. The tree comes apart from the bottom, and the fracturing process rapidly climbs up into the branches.

And Abbie Smith at ERV catches John West using the cover:

West just plastered this New Scientist cover on the screen and read a line or two from it. I asked him about this during the Q&A, and he responded appropriately– its a web/net of life at the beginning, not ‘one’ LUCA. So I was like ‘So why did you say DARWIN WAS WRONG if you knew the information in that article was decades old?’ He just dirped on stage, I told everyone to go online to read the article. He tried to dirp back ‘Or go on your BLAGS LOL!’ and I was like, ‘Yeah, we talked about this weeks ago. Idiot.’

Darwin was wrong and he was right.  He first published 150 years ago, so it is not strange nor is it unheard of for an understanding of evolution or of any scientific concept to be modified as people work and study and explore.  These pop articles were put out so that magazines and newspapers had something sensational to “scoop,” to grab attention in the growing frenzy over Darwin’s birthday.

Are they scamming us?  They may not believe it, and they may even be sincere in thinking that they are publishing “news.”  But they are publishing misleading, sensational claims and making money from it while we pay an additional price in the general understanding of science.

Are they scamming us?  You tell me.

The Great Leap Forward for Energy Metabolism

Abiogenesis has been a sticking point for naturalists and creationists in the argument over the necessity for a creator. Biologists are often careful to point out that evolution and natural selection begin where abiogenesis sets the table, and I disagree on that. I have maintained that the process of abiogenesis was a matter of a continuum of change in chemistry over a period of millions of years way back about 4 billion years ago and that the whole process wavered back and forth over some threshold before natural selection, adaptation and flow among proto-life and life finally took hold.

It was all an evolutionary process, as various means of energy metabolism proved stronger and more successful than others, leading to a strategy that allowed self-sufficiency and the maintenance of individual self-contained cells that we would all agree are living. The definition of “life” is fuzzy, so much so that the argument belongs as much to philosophers of science as it does to biologists.

So when did life begin? We will never be able to pinpoint a fossil or genetic “first life,” but we can say a few things about what is common to all life here and now. Cells have membranes to contain all of their functioning parts, filter those molecules that should enter from those that should stay outside. Cells have DNA, which provides the framework for the proteins and organelles which make up the cells. Cells have RNA, which carries the message from the DNA through the cytoplasm to determine the characteristics of the organelles within the cytoplasm. This, of course, is a very general description.

Cells also contain mitochondria, and this is one of the puzzles of early evolution. Mitochondria are symbiotic, originally a form of self-sufficient bacteria, which when integrated with eukaryotic cells, gain and provide benefit to the host cell. Mitochondria have their own set of DNA, and this DNA provides the basis for some of its key structures, and the unique tools that the mitochondria use to convert sugar into the energy it shares with its host.

As a symbiotic feature, mitochondria have safe homes inside the cells, and they pay rent by using the Krebs Cycle to provide much more energy than the hosts would be able to produce without them. Mitochondria are perhaps the most successful example of how cells work in tandem to assure mutual survival. Mitochondrial DNA is also passed, in sexually reproducing life, through the female’s DNA line, which yields data on lineage. This is unique and helpful, but not the issue in this post. I only mention it here because this is the way that mitochondria have entered the vernacular. I am sure that my readers are aware of the “Mitochondrial Eve,” a woman who lived on the order of 200,000 years ago and is thought to be the ancestor of all humans now alive.

My question remains on the origin of the mitochondrial integration with eukaryotic cells. A recent commenter made the claim that evolution can’t explain how mitochondria came to be included in the cellular structure of eukaryotes, and I did some checking. Guess what I found with a quick search through PubMed? Don’t sweat it too much, cause I’ll just blurt it out. I found a paper from 2001 that explains the likely integration. I just wish creationists wouldn’t get so cocky, because it is so easy to burn down their strawmen.

The paper I found is The Origin and Early Evolution of Mitochondria. The chief authors are Michael W. Gray, Gertraud Burger and B. Franz Lang. ¹

Here is the abstract:

Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial (specifically α-proteobacterial) ancestor but raise questions about the evolutionary antecedents of the mitochondrial proteome.

Recent debates about eukaryotic cell evolution have been closely connected to the issue of how mitochondria originated and have evolved [1,2,3,4,5,6,7]. These debates have posed such questions as the following: Did the mitochondrion arise at the same time as, or subsequent to, the rest of the eukaryotic cell? Did it originate under initially anaerobic or aerobic conditions? What is the evolutionary relationship between mitochondria and hydrogenosomes (H₂-generating and ATP-producing organelles that are found in eukaryotes lacking mitochondria)? Is the amitochondrial condition in these organisms a secondary adaptation or is it evolutionarily primitive – or, in other words, did any organisms diverge from the main line of eukaryotic evolution before the advent of mitochondria? Whereas the issue of how the eukaryotic cell arose remains controversial [8,9], current genomic data do allow us to make a number of reasonably compelling inferences about how mitochondria themselves originated and have since evolved.

Now, I have a confession to make on this paper. Because I am not a trained biologist, I only understood portions of the study. I read through it and ran into many concepts with which I am not familiar. So why would I write about this?

I wanted to point out that an important pathway leading to the emergence of eukaryotes from their prokaryotic ancestors includes the integration of mitochondria, and in this study, the authors examined the relationships between the genomes of yeast and mitochondria to show how this integration likely occurred. Examination of genomic sequences has become nearly as important as the study of fossils into determining the early pathways of evolution, and it will likely assist biology in answering these questions to a degree that paleontology can’t match.

I don’t mean to say that examining genomes can replace paleontology. I mean that they are complementary tools of science.

Further, since we all as eukaryotic beings carry mitochondria in all of our cells (even sperm cells carry a tiny fragment of mitochondrial DNA), we have an answer to the creationist objection, “Were you there?”

We can answer, “Yes, we were there. Almost. We were there sometime shortly after abiogenesis.” Yes, it was likely some hundreds of millions of years after life passed the abiogenesis threshold once and for all, but in the geological timeframe, it was a very short time indeed.

Okay, so today is Charles Darwin’s birthday. The claim is that natural selection only earned its wings once the first cell arrived and began its differential reproductive success. This “natural selection” thing and the publication of On the Origin of Species are well worth celebrating, because although there had been sketches and inklings prior to Darwin’s formulation, there was no serious explanation for how evolution could work. Darwin broke the ice, so to speak, and encouraged biologists to explore natural means of species creation.

This is why we celebrate Darwin. His work was not the beginning of the idea of evolution, and more importantly his work was not the end nor the summit of evolutionary thought. We celebrate because he took the first steps of serious investigation into the pathways of evolution. He showed us the tools that we could use to explore our common heritage in a way that provides answers—and questions.

This geologist was the Newton of biology. Just as our understanding of physics has grown immensely since Newton, so to our understanding of biology has bloomed since Darwin. His was the seed that led to the flowering and the study of such tools as genomics. Funny that he wasn’t even aware of genetics, but there you have it. And so do we.

1. Genome Biol. 2001; 2(6): reviews1018.1–reviews1018.5. Published online 2001 June 5.

   PMCID: PMC138944

   Copyright © 2001 BioMed Central Ltd
   The origin and early evolution of mitochondria
   Michael W Gray,¹ Gertraud Burger,² and B Franz Lang²

   ¹Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada

   ²Département de biochimie, Université de Montreal, Montreal, Quebec H3C 3J7, Canada

   Correspondence: Michael W Gray. E-mail: M.W.Gray@dal.ca
   Corresponding author.

   Michael W Gray: M.W.Gray@dal.ca

We’re partying all over the world!
A year ago March, Richard Dawkins was in town as a guest of Minnesota Atheists. That was the first I heard about making the anniversary of Darwin’s birth (200 years ago) and publication of his book (150 years ago) into a time of celebration. Dawkins said Britain was already gearing up—taking this opportunity to educate as well as to have fun with science. I wondered what my hometown would be doing to celebrate evolution. Whatever it was, I wanted to be a part of it.

PZ Myers thought it was a cool idea.
March flowed into April and spring. Nobody I talked to knew of anybody who wanted to think about an evolution party. I knew one scientist who would, so I called PZ Myers. He said, “Great! Let’s talk.” I visited him in Morris in May for a delightful afternoon walking around the campus, talking science, art and evolution. We both love the Bell Museum’s science-for-the-people series, Café Scientifique, and thought it would be the perfect venue for Darwin Day. PZ holds the Café in Morris, too. So we decided we’d do a presentation of art and science and evolution in both locations. (The Morris event will be held February 24.)

Talking evolution with insight, humor—don’t forget outrageous sex!
Shanai Matteson and Don Luce at the Bell Museum expanded the evening to include other scientists, who will present rapid-fire, media-rich presentations about Darwin and evolution with good storytelling and controversy. If you haven’t heard some of them speak before, you are in for a treat:

• Dr. Mark Borrello, history of science
• Dr. Sehoya Cotner, professor of biology
• Dr. Greg Laden, biological anthropologist
• Dr. PZ Myers, evolutionary biologist
• Dr. Keith Olive, particle physicist

Mitochondrial Eve by Lynn Fellman
Party Details
Where: The Bell Museum of Natural History (map and parking information)
When: Feb 12 from 7 to 9 p.m.
Cost: $10/free to museum members and U of M students
There will be a cash bar, and cake will be served.

Before and after the presentations, you’ll want to see Frans Lanting’s North American premier of “LIFE: A Journey Through Time.” On display in the Bell’s gallery, these large-format photographs interpret the evolution of life on Earth. Also displayed are my DNA Portraits.

Do us all a favor and bring along someone with 19th-century thinking. A little cake, a little vodka and hearing some great storytelling may just be the thing to kick them into the 21st.

Lynn is a Minneapolis artist and blogger, as well as an interviewer for Atheists Talk radio and one of science’s most enthusiastic cheerleaders. For Lynn’s interview with Don Luce, the curator of the exhibits, and Greg Laden, one of the guests, a podcast is available.

Charles Darwin believed that no matter who thought of an idea first, it was really the first person to articulate it clearly and convincingly who should get the credit for it. Darwin believed that Wallace’s version of natural selection, published together with Darwin’s version of natural selection, was much better stated and more logical than his own. He also felt somewhat pressured to write The Origin (which is considered his quintessential work by most) in the short time he wrote it in (several decades!?!?) because he really had a lot more to say than space (600 pages) allowed.

These facts reveal, I’m sure, that Darwin was a total dork!

But how do we know all these things? Because he tells us in his autobiography, which is a truly delightful read. Darwin’s autobiography is one of a handful of writings that I’m recommending to you in order to do your part in celebrating, through the reading of the original texts, Charles Darwin’s two hundredth birthday.

Charles Darwin and Abraham Lincoln were born within minutes of each other on Sunday, February 12, 1809. February 12 is therefore Darwin Day as well as some form of presidential holiday for Americans. I find it interesting that there is a substantial amount of hype regarding Darwin’s 200th birthday but almost none regarding Lincoln’s birthday. Interesting but virtually inexplicable.

Anyway, my purpose here and now is to make a few recommendations to you as to what you should read from the Charles Darwin canon. This is not from the perspective of True Darwin Scholarship. Technically, I’m not a Darwin scholar, so I would not know how to recommend the more erudite approach to this literature, and if you are a Darwin scholar, then you certainly don’t need my advice. I’m not suggesting this from the perspective of an educator in the life sciences, either. Rather, I’m suggesting specific readings (in a specific order) because I believe that this approach will captivate you and provide the most meaningful sampling of Darwin’s work with the least effort on your part.

And it will be some effort, because Darwin was writing two centuries ago and they talked funny back then, and modern English speakers (not to mention non-English speakers) may have a hard time relating to the style. But I’ve taken this into account as well, and my specific suggestions are designed and presented to smooth the process.

You should begin with a book called The Voyage of the Beagle by Charles Darwin. If you go back to the original publication of this book, you won’t find it mentioned by this name in the early manuscripts for a couple of reasons. The clear distinction between the names of books vs. series vs. other published entities was not maintained in Victorian England in the same exact way it is now, and this volume underwent a complex and confusing history of publication, having started out as part of a different, larger work. But today, modern publishers have smoothed over all the early strangeness, and you can go to the bookstore, or Amazon.com, or wherever, and find a book called The Voyage of the Beagle by Charles Darwin and read it. (Example: The Voyage of the Beagle: Charles Darwin’s Journal of Researches (Penguin Classics)
. Also, you can also read my extensive blogging about The Voyage here.)

Don’t bother trying to find the most original version. Read any version you can lay your hands on, but any recently published version will likely be one of the revised editions. You want the revised edition, and you want to make sure to read the footnotes when you read the book (much of the revision is in the footnotes). Always read the footnotes when reading Darwin.

The Voyage (the book) starts before the voyage (the voyage) itself and chronicles Darwin’s travels over a five-year period. Because it is written retrospectively, Darwin’s experiences are to some degree placed in the broader context of Darwin’s later research and writing but not to the extent that you will find annoying.

You will learn a lot of things about Darwin, like his attitude towards slavery; his eye for ethnography; the fact that he was, above and beyond all else, a geologist rather than a biologist; and so on. Read it in a leisurely fashion. Skip around if you like. That won’t damage the story too much. By the time you are done with the book, even if you’ve really only focused on two-thirds of it or so, you’ll be totally accustomed to the nature of the language, and you will have learned a lot about Darwin, boats, the nineteenth century, and South America.

The next book you should read is Darwin’s monograph, Coral Reefs. You will not easily find a copy of this, but you can read it online. You can also skip around a bit with this volume. Let me tell you why I think you should read this book. Then you’ll know how to approach it. You can probably get everything you need out of this book in about an hour or two of perusal, once you know what you are looking for.

Darwin was a total geology nerd and, prior to his voyage, was only beginning to become recognized by his British colleagues as a young scholar with potential. And he looked up, in a big way, to the ultra-famous, imposingly famous, super-big-shot-famous geologist, Charles Lyell. As you will see a bit later on with my next selection, Lyell influenced Darwin and Darwin’s approach to science more than any other individual. Darwin respected Lyell and was afraid of Lyell.

Meanwhile, Lyell had this theory about how coral reefs formed. Darwin was quite excited to be going on this voyage, in part, because he was going to get to look at these reefs firsthand, and combining these observations with Lyell’s theoretical descriptions of the reefs was going to be cool. As  I said, he was a total geology nerd.

But something went differently than originally planned. When Darwin started to observe coral reefs “in the wild,” he quickly started to notice things that were unexpected. Lyell’s model for how coral reefs formed did not fare well under the test of observations that Darwin was making in the field.

Now, the next part of the story is conjecture on my part, but reasonable conjecture. While on the voyage, Darwin wrote letters back home, sometimes including his scientific observations. One such letter, it seems—a letter about coral reefs and how Lyell was seemingly wrong in his theory about them—was passed around back home and impressed people sufficiently that it was read at a scientific meeting and published, unbeknown to Darwin. I suspect that this embarrassed Darwin a great deal, because it was a sidelong attack on Lyell or, at least, could be seen that way.

As it would turn out, Lyell did not get mad at Darwin and accepted Darwin’s new understanding of coral reef formation and development. But Darwin was still a scholar who leaned towards caution. In his monograph on coral reefs…the book I’m suggesting you have a look at…he developed a method of making scientific assertions that was based in part on methods he had learned from Lyell, but which I believe was taken by Darwin to a greater height. Darwin would assemble all the prior writings and facts about a topic, catalog all the explanatory models, develop falsifiable hypotheses which he would then, in turn, try very hard to falsify and, in the end, present what was left: some descriptive and some explanatory theory about what something was and how that thing worked.

I believe that while this approach was shown to Darwin by Lyell, and may have been part of Darwin’s nature, that it was sharpened and underscored by the fact that Darwin’s first real contribution, his first real bit of novel research with new results destine to change the way we think about a certain natural phenomenon, was in conflict with the theories of his hero Lyell, the man he feared.

The monograph on coral reefs was his first run at this approach. It’s all in one neat little not-too-long volume. Go online and have a look at it, enjoy the prose, peruse the volume, pay attention to the structure of the argument, and read it as carefully or as casually as you like. You won’t be able to avoid enjoying it.

The third Darwin book you should read is Darwin’s autobiography. This is a great companion volume to The Voyage of the Beagle because it focuses on Darwin’s life before and after The Voyage. There are notes throughout added by Darwin’s son, clarifying or correcting here and there. It is roughly written, like a first draft, and could be a bit unfocused and wandering except that, since it is a chronological memoir, it has a natural structure that holds the “plot” together. Darwin’s autobiography is short, engaging, and includes at least half the famous “Darwin stories” you’ve heard in college lectures or read in the writings of Stephen Gould. This is where we learn Darwin’s attitude towards medical school, for instance.

That’s it. Read The Origin if you want, but even though Darwin saw it as an abstract, it is mind-numbingly long. Same with Descent. His other books are highly specialized or a bit quirky, though all are fun. I won’t dissuade you from exploring all of Darwin’s other work, but I strongly recommend the plan I lay out above.

Enjoy.

Brownsnout Spookfish

Les yeux sont le miroir de l’âme (The eyes are the mirror of the soul.)  I am not sure what the late James Brown would have said about that, but a recent discovery that a unique adaptation for vision evolved in the brownsnout spookfish has captured the fascination of evolutionary biologists.

This the first time that a vertebrate has been found to use crystals to reflect light onto the retina of the eye in order to aid vision.  It illustrates the wonder of the eye and the multitude of ways in which evolution has solved two issues critical to the survival of metazoan creatures:

1. What’s available for me to eat?
2. What wants to eat me?

Among all the senses, vision was the trickiest question that Charles Darwin sought to resolve in developing the theory of natural selection for evolution.  While he did allow that it is difficult to imagine a giant leap from sightlessness to clear vision in a single bound, he was able to propose processes by which sight developed in minute stages to the eyes that humans, raptors, dogs, cephalopods and, um, lots and lots of animals use from the humble beginnings of eyespots in planaria.

To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree. (Darwin 1872)

It does seem absurd to think that nature can do what man was unable to do until the invention of the camera:  to interpret changes in light in ways that provide meaningful data to the beholder.  The above passage from Darwin has been used in quotemines to cry triumphant defeat of evolution, admitted to by the scientist most closely associated with natural processes of biological evolution.  Darwin admitted no such thing, and it is important to understand his method of presentation.

1. Present an insurmountable problem.
2. Explain its resolution.

From the talkorigins.org Index to Creationist Claims (CA113.1, Isaak, 2004):

1. The quote is taken out of context. Darwin answered the seeming problem he introduced. The paragraph continues,
   

   Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real. How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated; but I may remark that several facts make me suspect that any sensitive nerve may be rendered sensitive to light, and likewise to those coarser vibrations of the air which produce sound. (Darwin 1872, 143-144)

   Darwin continues with three more pages describing a sequence of plausible intermediate stages between eyelessness and human eyes, giving examples from existing organisms to show that the intermediates are viable.

The process by which the brownsnout spookfish solves the food-finding and prey-avoidance problem is not yet fully understood, but the point is that there are many separate ways for vision to evolve. Spookfish use guanine crystals, layered into a mirror, to reflect din light from below. Their eyes look above them to see shadows and light streaming down from the surface to their deep habitat, in the depths to which light barely penetrates. The mirrors help them to avoid predators who may be attacking their vulnerable bellies from below. It’s this downward vision that may save them.

The spookfish were discovered and named in 1888, but the specimens captured were all dead at the time of recovery and had been mangled badly enough that until recently their eyes didn’t reveal their special adaptation. A new article in Current Biology¹

describes the process by which the fish were netted and then examined carefully using microscopes.

Tamara Frank took a series of pictures of the eyes and discovered that the flash from the camera reflected through the

Courtesy of Physorg

retina of the true eye in the way that she would expect.  The lower, “diverticular eye,” which appears as a “bump” on the head, instead reflected into the retina.  Professor Julian Partridge was curious as to why this happened, so he prepared slides of the lower eye and found the guanine crystals.  He discovered that the precisely layered crystals aimed light into the retina, giving the spookfish vision into the depths below.

The spookfish inhabit depths between 500 and 1,000 meters (1,500 to 3,000 feet.)  As I mentioned above, very little sunlight can penetrate this far down.  Many fish are clear, lacking the pigment in their skin to create color.  Bioluminescence is rather common at this depth, creating an additional source of light.

Any advantage that evolution can give a fish to see its predators and its prey is likely to survive.  As this is so far the only known vertebrate to possess this sort of eye (some crustaceans carry the trait). I am curious as to why fortune favored the fish in this way but the trait hasn’t been spread through other fish.

I would think it would pass an energy and mass cost advantage to the fish that possess the mirrored eye, because it reduces the need for muscular control of the eyes.  They needn’t pivot nor rotate their eyes to increase their field of vision.  Right there, we have an adaptive advantage.

This would seem to be such a plus for fish that we would expect to see more of them with this trait.  I am curious as to why they are unique, but this also illustrates another point of evolution.  Evolution doesn’t create optimal solutions to survival problems; it creates solutions that work.  It can only use the tools available to it.  Where this adaptation is found, its roots are still a mystery.  What were the first creatures in the spookfish’s ancestry to carry the genes to create the crystals?  What was the developmental pathway that led to those genes’ expressions?  What was the process that led to their development to mirrored eyes?

The fossil ancestors of the brownsnout spookfish may or may not be able to yield clues, if we can find them.  The remaining fossils could be buried deep below the ocean floor, and we may not have the technology to recover them for many years to come.  Genome sequencing of this fish and its cousins may help discover the genetic and mutational roots of this fabulous eye.

This is one solution to the vision problem.  Darwin would have loved it had he known, and likely would have included a grand description of it in his discussion on the evolution of the eye.  I venture to say that as marine biologists and divers continue to explore the depths, they will find more and stranger eyes.

Yahoo News India: “4-eyed Spookfish, first vertebrate to use mirrors for seeing.”
Zipcodezoo.com “Dolichopteryx longipes”
Phsyorg.com “Spookfish uses mirrors for eyes.“

1. subscription required: A Novel Vertebrate Eye Using Both Refractive and Reflective Optics, by Hans-Joachim Wagner, Ron H. Douglas, Tamara M. Frank, Nicholas W. Roberts and Julian C. Partridge. Current Biology 19, 1-7, January 27, 2009. DOI 10.1016/j.cub.2008.11.061