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God and Nature, the online magazine of the ASA which arose as an expansion of this blog, is now live! The new open-access publication features a broad range of content with essays, poetry, cartoons, feature articles, stories, and more about the intersection of science and faith.

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Toad Prince Proteins and the Chemistry of Evolution

In the onset of diseases like Parkinson’s and Alzheimer’s, they’re the usual suspects. Inside cells, amyloid proteins have a tendency to amass like frogspawn and grab on to one another until their gluey corpus begins to block important pathways and cause vital processes to falter. While not everyone who possesses amyloid proteins suffers because of them—recent studies suggest they may have helpful roles in the body, as well—their sticky quality is dangerous, and as a result, amyloid proteins are generally perceived as personae non gratae by the bodies they’re part of.

However, according to a recent paper by ASA member David Andreu, professor of chemistry at Pompeu Fabra University in Barcelona, Spain, amyloids may be something like the toad princes of the protein world. Although they’re mostly seen as undesirable, amyloid proteins possess certain features in their amino acid structure (amino acids is what proteins are made of) that could potentially transform them into proteins with beneficial rather than hazardous properties.

All it would take is a wave of the evolutionary wand (over a few million years, that is).

David explains, “This tendency that some proteins have of sticking to each other is called ‘aggregation,’ and in general, it’s bad news. The proteins per se aren’t bad, but once they begin to stick to each other, it becomes harmful. This is for instance the case with the amyloid proteins causing Parkinson’s and Alzheimer’s diseases. When these proteins start to form aggregates, it triggers an alarm mechanism and cells try to get rid of them by a process called apoptosis. Apoptosis refers to programmed cell death, a normal part of the life and death cycle of cells in which cells commit what one could call ‘cellular suicide’ rather than go along with the aggregation taking place within them.”

While it’s better for cells to kill themselves upon recognition of the danger they pose when potentially harmful processes such as are taking place within them, David and his team propose a potential “win-win” situation in which cells experiencing protein aggregation might evolve to respond in a more positive way than jumping off the proverbial building.

As the workhorses inside every living cell, proteins perform the various tasks that make all living things functional. They’re made up of chains of amino acids arranged into singular shapes. “What we showed is that there are certain positions in the amino acid structure of amyloid proteins that are, so to say, privileged,” says David. “Privileged in the sense that if an adequate rate of mutation occurred over the course of evolution, some of these amino acids could potentially transform the protein’s three-dimensional structure into the alpha-helix shape characteristic of antimicrobial proteins (AMPs), one of the main players in innate immunity, the body’s first line of defense against infection. These changes would transform the amyloid protein from one that’s offensive to cells to one that’s defensive of the entire organism.”

 

If that sounds like the all-too-happy ending of a myth or fairy tale, for any skeptics out there, David also explained the finding via negativa, “If someone came along who didn’t believe in evolution or who was suspicious of these results, he or she might point out that in showing it’s chemically possible for an amyloid protein to become an AMP through evolutionary means, we’re introducing a lot of human intelligence into the process that doesn’t exist in nature. Any experiment we do in the 21st century can be done in a few months with the help of sophisticated machines and algorithms, so it’s not random and time-consuming like evolution in the wild. But what we’ve done is to show how this particular transformation would be a relatively uncomplicated process, and as every evolutionary biologist knows, it’s possible that this kind of thing can happen over many millions of years.”

While David’s lab primarily works on the protein chemistry of AMPs, not their evolution, the team’s hypothesis yielded such conclusive predictions that it was published in one of the world’s most prominent chemistry journals, Angewandte Chemie. “Mostly, our lab is interested in developing synthetic versions of antimicrobial proteins and peptides into biomedical tools. Our approach, when looking at a protein with AMP features, is to try and cut it down, trim the fat (so to speak), and make it into a useful machine with therapeutic potential,” says David. “The intuition for this experiment came to me and a postdoc of mine when we were both intrigued by recent reports mentioning that some amyloid proteins may have antimicrobial properties, and some AMPs have a tendency to aggregate. There seemed to be a cross-talk between the two groups. While scientists who deal with amyloids are obviously concerned about their aggregation, people like us are interested in what the AMPs are programmed to attack. Our intuition when the two sides came together showing each other’s properties was that—wow, perhaps these two groups are more related than we thought.”

Since there’s no physical record of how amyloids and AMPs evolved, David and his colleagues wondered which came first: Is one group the parent of the other? Did nature eventually ‘decide’ that it could develop new features in proteins and make something useful out of them?”

The evidence is that amyloid proteins are, in fact, older than AMPs, which appear to have developed later (i.e., they exist in more “highly evolved” organisms, whereas amyloids are more common throughout the biological world).

Andreu and his team chose 25 of the most abundant human amyloid proteins and, using bioinformatic algorithms, identified the regions more likely to be involved in aggregation. Then, using these regions as templates, they introduced certain types of mutations in particular places (in this case, increasing positive charge), which turned an inactive stretch of amino acids into an active antimicrobial site. As controls, the team also took random sequences of amino acids, as well as regions with low predicted scores of aggregation, and attempted to do the same, but found that only when they started with an amyloid protein did they end up with an AMP.

“It was really exciting,” says David, “You need the amyloid-prone sequence as a starting point. Applying the same strategy to a non-amyloid stretch doesn’t lead to antimicrobial properties. The referees at Angewandte Chemie were very demanding about negative controls, and the fact that such controls were so clearly negative was a strong support for our hypothesis that, over the course of years and years of evolution, it’s possible that some amyloid proteins might have evolved into AMPs and thus given their organisms an evolutionary advantage.

“Of course some people, particularly some creationist Christians, may take issue with this particular path of evolution we’re proposing,” David continues. “But it’s really quite unassuming. We’re just showing that there are fairly simple ways in which proteins can acquire new features…”

David pauses for a moment, perhaps weighing the significance of the slow and plodding, two-steps-forward-one-step-back universe that human research suggests against the thought of instantaneous, divinely compelled creation.

“As a scientist and a chemist, I am happier with the first option,” David then says. “As a Christian, I believe God is all-powerful—but I have no problem with the idea of the Creator working through evolutionary change. I don’t see any conflict in being a theist and at the same time believing that God used physical and chemical processes in creation. Rather than having God intervening at this or that step, I think God endowed His creation with robust mechanisms that can explain quite satisfactorily the universe and the amazing diversity of our world in particular. That there is a Creator underlying something so powerful as the genetic code and the intelligence behind it all—is absolutely wonderful.”

In addition to research in protein chemistry, David is also interested in faith-science questions. He was particularly motivated by the 2010 issue of Perspective on Science and Christian Faith, the academic journal of the ASA, dedicated to “The Search for the Historical Adam.” So provocative and controversial were the ideas explored in that issue that two contributors had to defend their faith to an investigative panel, and one ended up resigning his job teaching science at a Christian college. Concerned by the lack of awareness on these subjects among in the Spanish-speaking protestant community, David and Pablo de Felipe, a Madrid-based molecular biologist member of Christians in Science and the Faraday Institute, have taken up the task of extracting the controversial articles in PSCF and translating them into Spanish.

“We are doing this as a service to the Spanish readers so they, too, can enjoy, criticize, and start the same kinds of discussions they’re already having in the English-speaking world,” says David. “I have lived in the US for extended periods of time, and the science/faith debate is completely different to that in countries like Spain. In the US, people who don’t identify as Christians tend to give philosophical, theological, or scientific reasons for why they don’t believe in God. Here, it’s more historical and sociological than intellectual. We have the added historical dimension of a domineering Catholic church, which still casts a powerful shadow on many areas of our society and culture. So the Spanish (and to some extent the Latin American) scene is quite different from that of the US, the UK or other European countries. Here, faith-science issues interest a minority within a minority.

“Within this minority (i.e., the Spanish evangelicals), creationist viewpoints are practically unchallenged,” David continues. “The protestant denominations that grew up in the 20th century in Spain were largely the outcome of missionary work by Southern Baptist, Pentecostal, and other fundamentalist denominations, mostly from the US. Most of the missionaries who came were opposed to evolution, and this was the only position available in our churches as I and others in my generation were growing up. By God’s grace some of us have managed to challenge these views without losing our faith in the process, but many casualties have taken place along the line.

For years, they’ve been concerned about the situation, but David thinks they’ve probably been overcautious about not rocking the boat. “I think that now the time is ripe to bring these issues to the forefront,” says David. “In most seminaries training people for ministry in Spain, chances are that faculty will either refuse to give an opinion of theistic evolution, or, more likely, be openly critical of the idea. Many pastors are still convinced that evolution and faith don’t mix well, and that’s a pity, because it confines meaningful dialogue to very small circles. Eventually, though, they will realize they can’t ignore the issue any longer, because churches keep losing young people who go to college and can’t relate what they learn in science classes to what they were told in Sunday school.”

Although it’s tempting for scientifically minded Christians to wish all their brothers and sisters could simply understand and appreciate the challenging ideas science brings to their faith, the greater body of the Christian church isn’t going to evolve all at once. But perhaps those same places and congregations where science is currently most discouraged and understanding at its weakest are in some ways similar to the “privileged positions” David and his group studied in chains of amino acids. With the simple influence of patience, love, and respectful conversation with those who may have never heard from a sympathetic scientist before, the fundamentalist Christianity around the world could transform from a religion that’s at best suspicious of scientific knowledge to one that promotes and most ardently defends it.

Like the existence of life in the universe, such a reality appears highly unlikely, even unbelievable—but it’s certainly not impossible.

 

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Giving It up — Giving It All up — for Reason

Before he even opened his mouth, most of the 1,600 people in the audience were on their feet. Hands flew together and a chorus of shouts and whoops filled the large Richmond, Kentucky, auditorium, which had reached capacity well before that warm October night’s Chautauqua lecture was scheduled to start.

In three separate viewing rooms in buildings just steps away from the assembly hall at Eastern Kentucky University’s Brock Auditorium, video screens had been erected to simulcast the event to the 600+ disappointed fans turned away at the door.

Who was responsible for this adoring, zealous support in a small college town in rural Kentucky? Whose most recent book did this throng of mostly young adults clutch in their hands, hoping to see his autograph scrawled upon its title page?

A great British evolutionary biologist—a man hailed for his skill at communicating science to the masses—Richard Dawkins.

While event organizers at EKU made apologies to those watching via video screen and expressed their surprise at the overwhelming turnout, I mused that it probably had less to do with Dawkins’s knack at making the complexities of biology, cosmology, physics, et al. coherent to nonscientists (there are plenty of excellent science writers out there who’ve never drawn a 2,000-deep crowd) than his famously caustic attacks on religion, especially Christianity.

My own presence in the audience that particular evening was something of a coincidence. Just hours before Dawkins’s lecture was scheduled to start, I completed two days of travel from Boston, Massachusetts, to Richmond, Kentucky. My purpose there was twofold:

1. Make the final preparations for my wedding

2. Get hitched

Yet upon arriving home and hearing that Richard Dawkins just happened to be gearing up to speak less than a mile away, my parents and I decided to take the night off from ribbon-tying and veil-making. I had a few strong, timely reasons not to miss his talk.

For one, I’d just published a long article here on God and Nature called “Clearing the MiddlePath,” exploring the social, spiritual, and intellectual merits of focusing on fostering productive dialogue rather than razing the road to mutual respect and appreciation between religion and science. My article featured theologian Peter Hess, who works at the National Center for Science Education (NCSE) helping Christians and other people of faith understand why evolution (and the ancient age of the earth, the possibility of alien life, etc.) can enhance instead of threaten their worldview. Likewise, Peter helps reduce the level of religious intolerance held by some scientists by showing them that most mainstream denominations try and are successful at incorporating scientific theories into their respective theologies.

Peter related that in performing his work, it’s become very clear that neither the so-called  “new atheists” (sometimes referred to as  “evangelical atheists” for their fervor that parallels that of some evangelical Christians) nor fundamentalist Christians know nearly enough about what they’re rejecting, or whom.

To illustrate, Peter described a personal meeting he had a few  years ago with an atheist biologist. In the course of a conversation about a project Peter was consulting on (helping the religion department at a nearby Catholic high school organize a series of lectures and discussions on evolution, called the “Darwin Project”), the biologist—who happened to be Professor Dawkins—expressed surprise not only that the Catholic school was enthusiastically pursuing public dialogue about what many assume to be a controversial theory, but that the religious studies department was instrumental in helping to organize it. Professor Dawkins demonstrated unawareness about the openness of Christians to engage with scientific culture. Like their non-theistic neighbors, many Christians are searching, curious people who want to learn more about the universe, how it was formed, and why thinking beings exist in it.

After my article went up on God and Nature, vitriolic comments from atheist defenders surged onto the NCSE’s Facebook page. Some were directed at the NCSE, accusing the organization of being “accomodationist” for having a Catholic theologian on staff. Others were ad hominem insults regarding Peter’s personal beliefs and how they affect the level of his intelligence:

~[Peter is] trying to shoehorn his fantasies and delusions into reality. He’s still trying to prove that all his childish beliefs work in the grown up world. Religion is fundamentally a magical world view; magic has no place in science.

~Courting the crazies and having them defend sanity is not a good call on our part. And as crazies go, give me a good, honest fundamentalist any day, at least they really BELIEVE. This guy is just another fence straddler without the courage to make up his mind.

~Truth and belief are not even close to the same thing and Peter knows this. To treat belief, not just Christian belief, with the same respect as knowledge is insane. I hate philosophy, [because] it seems like if you can’t win an argument with the facts, [and] it is a last resort for credibility.

~Both [Peter] and his position are negative acts in the very positive, supposed, goal to which NCSE claims to be dedicated, and the organization seriously needs to rethink.

Some of the most hateful posts were deemed unconstructive by the site’s administrator and removed. At several points throughout the 40+ comment stream, the NCSE stepped in to defend the importance of Peter’s job and why such derogatory, polarizing behavior should be avoided by those struggling to illuminate modern science for the public, “The primary objective of NCSE is to defend and promote the teaching of evolution in public schools. We do this by dealing with local flareups, by speaking at local, regional, and national meetings of professional organizations, and by communicating with various communities … We find that when we approach these communities with respect and sensitivity to the beliefs they regard as important, we are more likely to be successful in our goal of defending and promoting acceptance of evolution.”

More simply put, only those who give respect get respect. If we use hate speech, we should expect to receive it in kind—or at least, to have our message ignored by the people we target and/or deride. For those of us trying to advance knowledge and truth in the way Professor Dawkins does in his public communication about science, insulting someone who doesn’t automatically accept the validity and importance of our own views isn’t just impolite, it’s illogical. It harms, rather than helps, the advancement of scientific understanding.

A month ago in Richmond, Kentucky, I traded some of the only time I had left as a single woman to attempt to understand just what it is Dawkins and his cadre of atheists have against people like Peter Hess—one of the wisest and most intelligent men I’ve had the pleasure of interviewing—and that most pursued of all scientific questions: why?

My second reason for attending the lecture was more personal than professional. I wanted to see how the residents of my hometown would react to what Dawkins had to say.

While the so-called halcyon days of my childhood were spent scampering through the backyards of suburban Maryland, I entered that trial of sanity and reason known as “middle school” in Kentucky. Like most middle-schoolers, I was utterly dismayed at my luck in life—dismayed by the prospect of growing up, in general, and specifically dismayed by the thought of doing it in Kentucky. For starters, at all of eleven years old, I was certain that I’d never, ever make friends in my new home. I’d also heard somewhere that Kentucky schools were ranked pretty badly, so I could say goodbye to frequent field trips and the Magnet Program for advanced learning. Finally, so far as I could tell, Kentucky wasn’t full of cool stuff—just horse farms and regular farms. (I didn’t know about bourbon yet).

Throughout those years, my family attended a small Episcopal church on the edge of town, where I faithfully went to Sunday services, youth group, Bible school, acolyte training, and Confirmation classes before graduating high school. Had anyone asked, I’d have reported being just as true and good a Christian as the next, since I’d never really questioned the fact. It was around that time, however, that I started taking a long, hard look down my nose at Jesus Christ, his seemingly contradictory teachings, and his followers.

My temporary departure from faith resulted in no small way from experiences I had growing up in Kentucky. In high school science class, I learned to abhor how fellow Christians attempted to dismiss themselves from lectures in modern biology with the snide declaration, “I’m not a monkey.” Outside of class, I saw Christians my age standing in the middle of the mall and “witnessing” to passersby about the horrors of eternity in Hell. And it didn’t take a genius to figure out that many social leaders of our school’s Fellowship of Christian Athletes were also some of its most notorious partyers and drug abusers.

In the four years I was a member of FCA and Campus Life, neither supposedly interdenominational club once dedicated a meeting to exploring what Christianity means to believers of varying backgrounds, nor how to question reality while taking a “leap of faith,” nor what one should and shouldn’t accept as interpretations of biblical truth. All those minutes were taken up teaching what I felt was a rather scripted, vacant version of Christian evangelism.

In a short-sighted reaction to the actions of a few, I allowed those unsavory encounters to color my opinion of the whole Christian community. By the time I went off to college, I, too, was jeering at Jesus and joking that he wasn’t much but a rebellious spiritual leader who could perform magic tricks.

I, too, would have adored Richard Dawkins, if I’d known about him.

Ten years, two university degrees, and one recommitment to Christianity later, I was sitting in the same auditorium where my high school band used to play end-of-year concerts, and near the spot onstage where I once sat, soloed, and counted out rests, Richard Dawkins was giving a speech called “The Magic of Reality.” The audience, which I later learned included folks from every major city in Kentucky, as well as the states of Illinois, Indiana, Ohio, Virginia, West Virginia, and Tennessee, (not to mention Massachusetts), didn’t hear the bold religious attack many of us were anticipating.

What we did hear was a 45-minute commercial for Dawkins’s recently released book, also called The Magic of Reality. Targeted for teenagers about the same age I was when my family moved to Kentucky, the new work walks readers through several ways of thinking about difficult or misunderstood scientific topics. Dawkins’s mission in writing the book, he said, was to teach young people how to think critically, not what to think.

All 12 of the book’s chapters have questions for titles, like, “What is reality? What is magic?,” “Who was the first person?,” “When and how did everything begin?,” “What is an earthquake?,” and “What is a miracle?” Each of them starts out by describing myths that humans have used or still use to explain the topic at hand. Dawkins draws these from the religious traditions of Christianity, Buddhism, Hinduism, Native American and Greco-Roman mythology, among others. The chapters then explain, “What is it really?” in more rational, scientific terms.

Dawkins began both the book and his EKU lecture by dashing the idea of magic against the masthead of reality. Miracles, magic, and other supernatural beliefs are incompatible with scientific truth, he said, using the fabrication of Cinderella’s carriage by her fairy godmother as an illustration of how such fanciful stories are simply contrary to nature. According to Dawkins, anything humans call a “miracle” is really just a mistake, a hallucination, or a scientific shortcoming—that is, something for which we don’t yet have an explanation.

For someone to decide that a mysterious event or feeling isn’t capable of being explained with existing or revolutionary science, Dawkins said, is cowardly and dishonest. “We should teach our young people to think critically,” he said.

“I don’t want to give the impression that science knows everything,” Dawkins admitted, “far from it. Science is constantly asking new questions, constantly opening new doors, constantly searching and changing and admitting mistakes. Not even the best scientist of today knows everything. But I don’t think that means we should block off all investigation by resorting to phony explanations by invoking magic or the supernatural, which don’t explain anything at all.”

Throughout the lecture, Dawkins illustrated the irrationality of such beliefs with an array of metaphysical stories that he claimed could be just as easily explained using logic. One of them was Portugal’s “Virgin of Fatima,” a Christian miracle reported in the early 20th century after a ten-year-old shepherd girl claimed to have seen a vision of the Virgin Mary on a hill. The Virgin said she would return to the site and perform a miracle on an appointed day. This caused quite a stir, and some 70,000 people gathered to observe the event, which was described in an array of colorful ways by witnesses.

Some said that the sun began to dance and twinkle in the sky. Others said that it whirled around and around. The most dramatic interpretation had the sun crashing down from the heavens toward the “horrified multitude” and just before destroying them all, the miracle kindly ceased.

“What really happened at Fatima?” asked Dawkins. He gave three possibilities:

  1. The sun really did come crashing down. “The first possibility,” Dawkins said, “would have involved not just people in Portugal, but everybody in the daylight half of the world would have seen it and what’s more, it would have been the end of the world.”
  2. 70,000 people experienced a mass hallucination.
  3. The whole thing was misreported, exaggerated, or made up.

Favoring the latter explanation as being the most probable, Dawkins dismissed the others and explained that the purpose of this chapter on miracles is to encourage people to think critically and evaluate evidence, rather than just to believe what they’re told. “Don’t ever be lazy enough, defeatist enough, cowardly enough to say, ‘There’s something I don’t understand. It must be supernatural—it must be a miracle,” Dawkins encouraged his audience. “Say instead, ‘It’s a puzzle, it’s strange, it’s a challenge that we should rise to.’ Whenever we rise by questioning the truth of the observation or by expanding our science in new and exciting directions, the proper and brave response to any such challenge is to tackle it head-on … The truth is more magical in the best and most exciting sense of the word than any myth or made-up mystery or miracle. Science has its own magic—the magic of reality.”

With that, Dawkins concluded his talk.

Walking home from the lecture through Richmond’s quiet, small town dusk, I kicked at early-fallen leaves and talked with my parents about what the famous scientist had and hadn’t said that night. Rounding the corner into our neighborhood, my mother looked up at the clouded moon and mentioned something I’d completely missed.

“You know, Richard Dawkins may be a great academic and argue with intelligence and authority on some topics,” she said, “but tonight, every time he reasoned for something by logically eliminating all other possibilities, he didn’t do it logically at all. He just made assumptions about what ‘reality’ is, and left out all but the most extreme choices. Among the three explanations he gave for the miracle at Fatima, for instance, he didn’t choose to include the option that it really happened, but in a less ridiculous way than the sun crashing down. If you believe in God or miracles, then it’s just as probable that the saint appeared to the crowd in a beautiful, magnificent way—so what did he actually prove? You can’t claim you’ve eliminated a choice you never presented.”

She had a point. In the way that humble, rational people experience their faith, it doesn’t threaten our collective pursuit of scientific truth, it encourages it. As my mother pointed out, Dawkins only described and deconstructed the easiest types of beliefs and believers to denounce as antiscientific.

Maybe he was just playing to the crowd. Even the Richmond Register’s report on Dawkins’s talk the following day commented on the overwhelmingly homogenous audience, “Most in the crowd, which often applauded and cheered Dawkins and fellow speaker Sean Faircloth, seemed thrilled to see and hear Dawkins, even if he failed to deliver any ringing denunciations of religion … no one asked a hostile question or offered any protest the evening of his appearance.”

Nothing. Nada. Going into the lecture, I was pleased by the gap on the stairs where I assumed there’d be a throng of protestors and picket signs, thinking that the lack of outright antagonism from fundamentalists was an indication that real discourse was about to take place. Alas, those who’d come had either come with Dawkinsian reverence or tacit curiosity. Dawkins spent his hour illuminating scientific reality, critical thinking, and the need for judicious skepticism to an audience that already accepted the merits of each.

Standing in my family’s oak-tree-studded backyard, drinking a homebrew and trying not to feel a bit rooked by the whole experience, I thought,

Surely, somewhere among the 2,000 people attending this popular EKU lecture series was a believing Christian, Jew, or Muslim who was on the fence about evolution, the ancient age of the earth, anthropogenic climate change, or some other controversial mainstream scientific theory. Someone who merely needed to hear the facts in a well-thought out, inviting way to be able to say that she could start accepting the science behind them.

Yet Dawkins’s unsubtle insinuation that this believer’s irrational, lazy worldview must be sacrificed at the knees of science before apprehending “the magic of reality” would probably have sent her shrugging in the opposite direction. My thoughts rounded down to a single, regretful impression: What a waste.

Because it doesn’t have to be that way. Not at all. Not every brilliant scientist spends his or her off hours verbally tackling “the crazies” in defense of science as the only acceptable path to truth.

During my tenure in the graduate program in science writing at MIT, I studied with noted author and theoretical physicist Alan Lightman. Alan taught me many difficult lessons about the well-turned essay—the properly examined question whose elusive answer really is worthy of trying to write about. In his classes, Alan delved into what some professors consider unteachable territory: how to perform this work well, with literary style … (i.e., … don’t overuse ellipses … or Latin abbreviations … etc., etc. …). Alan also strived to instill in his students a sense of how to write with grace and humility before your topic and your readers.

In a recent essay for Salon.com, “Does God Exist?,” Alan explores a question that’s probably familiar to God and Nature readers. Subtitled, “The case for reconciling the scientific with the divine—and against the anti-religion of Richard Dawkins,” Alan’s essay was published the day before we posted “Clearing the Middle Path.” Both pieces explore what it means to successfully reconcile science with religion, and why it’s important and even practical to do so.

Alan isn’t a Christian, Jew, Agnostic, Buddhist, Transcendentalist or any other kind of religious believer. He doesn’t have a dog in the fight, so to speak. As a scientist and atheist, Alan is not a defender of faith in God nor of religion, itself—yet he is a defender of respect for the people who practice religion and believe in something beyond what we can explain using the scientific method. Alan writes,

I believe there are things we take on faith, without physical proof and even sometimes without any methodology for proof. We cannot clearly show why the ending of a particular novel haunts us. We cannot prove under what conditions we would sacrifice our own life in order to save the life of our child. We cannot prove whether it is right or wrong to steal in order to feed our family, or even agree on a definition of “right” and “wrong.”

We cannot prove the meaning of our life, or whether life has any meaning at all. For these questions, we can gather evidence and debate, but, in the end, we cannot arrive at any system of analysis akin to the way in which a physicist decides how many seconds it will take a one-foot-long pendulum to make a complete swing. These are questions for the arts and the humanities. These are also questions aligned with some of the intangible concerns of traditional religion.

Whether or not we think about it every day, our shared reality is an almost unbelievable balance of space and time, mass and matter, energy and gravity. A few faint measures nearer the sun and we’d all be up in a blaze of heat. A few tweaks in the laws of physics and the universe as we know it simply wouldn’t work at all.

The magic of reality is that this dance of atoms and space in such careful balance actually exists. Obviously, it’s up for debate who or what is responsible for initiating all of it, and when, and how. Somehow Earth ended up having not too much and not too little of any one thing. Maybe other planets are like that, too.

Whether or not you believe that it’s all very intentional and that there’s a loving God somewhere watching over it, no human consensus will actually change reality, whatever that happens to be. No matter what brand of consensus we subscribe to and would like other people to subscribe to, as well—we can’t help anyone, anywhere, change anything they trust and believe while simultaneously engaged in shredding their intelligence in front of them.

If each one of us could value human dignity as much as we value our personal brand of truth, we’d not only be as wise as we are intelligent, we might also get our adversaries to see things from a different point of view. At the very least, they might consider it, which would be a giant leap in the right direction. Times seven billion.

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Clearing the Middle Path

Two years ago, ASA member Peter Hess participated in a colloquium on Intelligent Design at the University of St. Thomas in Minneapolis. He argued that science can neither discover nor rule out the existence of God. A few days later, in the online discussion sparked by this event, a blogger labeled him the Anti-Christ.

A practicing Catholic with a master’s degree in philosophy from Oxford and a doctorate in historical theology from the Graduate Theological Union at Berkeley, Peter found the accusation amusing rather than offensive. As he and other ASAers are aware, those who dedicate their lives to learning about the delicate issues at the interface between science and religion don’t expect applause after every attempt to reconcile what some folks regard as approaches to truth standing in rigid opposition.

Peter works at the National Center for Science Education (NCSE), a nonprofit organization dedicated to defending and promoting the teaching of evolution in public schools, so he is neither afraid to defend the Christian worldview from militant atheists nor the evolutionary perspective from anti-scientific fundamentalists.

As the resident theologian on the NCSE staff, Peter’s job is twofold: to reach out to religious groups and suggest how they might reconcile scientific truth with the teachings of their respective denominations, and to communicate with scientists — who are understandably fed up with the anti-scientific attitude of fundamentalists — the fact that most mainstream Christian denominations have already come to accept evolution.

In the course of doing so, Peter has been labeled a “stupid theist,” an “accommodationist,” and he recently received a formal denunciation of heresy (lodged with the Bishop of the diocese of Yakima in Washington).

While Peter believes that neither science nor religious belief are fundamentally threatened by either one’s constantly evolving understanding of the cosmos, he recognizes that neither side has a monopoly on good will. Numerous people he encounters for the first time would just as soon toss a verbal bomb across the fence than question their own interpretation of scripture or nature.

“The apparent conflict between the scientific and religious world views is in part a hermeneutical problem — that is, a matter of interpretation,” he says. Scientists often lack the perspective to communicate science to people of faith in a way that is intelligible and non-threatening to the spiritual truths that those people hold dear. And religious believers are often woefully uneducated in science, such that they cannot perceive how scientific discoveries offer exciting new perspectives on their faith.”

For Peter, it’s as important for religious communities to regularly re-think and re-articulate their beliefs as it is for scientists to test and re-test every emerging theory. “Both cherished formulations of faith and seemingly solid ‘laws of nature’ are subject to revision,” says Peter. “In my theological understanding, it’s not a matter of God being either always in process or always static and immutable; rather, it’s a matter of the human experience of God being constantly shifting. We humans inhabit an ancient, dynamic and evolving cosmos, and yet we’ve constructed most of our Abrahamic theologies within the rather temporary window of a very comfortable universe that is hospitable to life.

When asked to explain what comfort and hospitality have to do with theology, Peter says, “Even setting aside climate change, Earth’s future environment may be far less hospitable, and therefore less transparently reflective of the blessing of God. If humans last another few million or tens of millions of years, what will the ‘love of God’ mean when we’re suffering in a resource-degraded environment, or in a period of earth-scouring glaciation, or when the increasing solar winds begin to strip away our atmosphere? What will be the texture of our theology of creation when creation no longer seems particularly welcoming of plant or animal life?”

 

As a lifelong outdoorsman and mountain climber, it’s understandable why the kinds of questions lying at the interface between science and religion would appeal to Peter’s adventurous nature. “These questions probe at the heart of everything, asking not just how the universe works and how human beings evolved on earth, but why the universe exists at all — a question Steven Hawking also posed (perhaps rhetorically) at the end of A Brief History of Time.”

After earning his master’s degree in philosophy and theology at Oxford, Peter took a job teaching in an inner city Catholic high school for girls in San Francisco’s largely Hispanic Mission district. “This was a real culture shock for me, having just returned from the historic heart of the English-speaking world. I spent four very challenging and gratifying years trying to communicate global history, ethics, philosophy and theology to young women, many of whom were struggling to learn English.”

Embarking on his doctoral studies at the Graduate Theological Union at Berkeley, Peter probed more deeply into the ways in which science and religion have influenced each other throughout history. He focused on the development of natural theology from its medieval role, which at that time was essentially a preparation for the discussion of revealed theology, to a role it would assume in modernity as a free-standing apologetic.

“Before and during the Enlightenment, the impulse to demonstrate the being and attributes of God evolved into an increasingly urgent project to actually prove the existence of God, Peter says. “As one scholar once said (ironically but with some exaggeration), ‘Nobody doubted the existence of God until someone tried to prove it.’”

In his doctoral dissertation, Peter examined how Anglicans, nonconformists, and Catholics all engaged in the project of natural theology for their own confessional reasons, variously appropriating and misappropriating perspectives from the developing scientific revolution. They used these emerging scientific ideas for their own purposes, adapting astronomy and physics, natural history and geology, well into the nineteenth century to demonstrate the being and wisdom of God.

“Of course, the project of natural theology as a proof for the existence of God foundered in the nineteenth century, but the engagement of religion with science by no means ended,” says Peter.

He notes that the rift we now observe between science and spirituality began perhaps early in the eighteenth century, around 1725, when a small but vociferous faction of scientists within the Royal Society started to scoff at references to Adam and Eve, or to Noah and the flood.

The fissure grew with the gradual discovery over the next century of the ‘deep history of time,’ and with the professionalization of the various sciences. In the nineteenth century, the room for amateur clergy-philosophers in the academy was rapidly diminishing — ‘natural philosophy’ had been transmuted into physics, astronomy, and chemistry, and ‘natural history’ was becoming archeology, paleontology, and biology.

“Still, the variation in responses to Darwin’s theory of natural selection reveals that there wasn’t a clear split between scientists who accepted it and the theologians who rejected it,” says Peter. “Some scientists rejected Darwin’s theory on scientific grounds, and a number of theologians welcomed it on theological grounds as offering further testimony of divine creative wisdom. It was not until the twentieth century that an increasing number of scientists began to express either an indifference or a deep hostility to religion, and this arose in part as a result of the increasing hostility of Fundamentalist Christians to what they perceived as the threat of science.”

According to Peter, the roots of the evolution-creation conflict are multiple, reflecting scientific, philosophical, theological, academic, and cultural differences. But one of the most significant roots is epistemological — that is, it lies within the theory of knowledge and its foundations.

“The problem with Biblical literalists is that they are ignorant of exegetical history,” says Peter, “and are generally

unaware that an insistence on a woodenly literal understanding of scripture is a relatively recent invention imposed on the Church’s traditional four-fold interpretation. They’re as ignorant of theology as they are of the sciences they presume to critique…

“On the other hand, the issue with some scientists who are atheists is that they fail to see that they are actually making a theological claim by declaring that there is nothing to believe in. Scientists who feel they are qualified to comment authoritatively on religious faith because they have apprehended some of the truths of the natural world are putting on a very ill-fitting philosophical hat.”

It is this meeting of reason with faith that lies at the heart of Peter’s work with the National Center for Science Education. Leaving the immediate task of handling anti-scientific “flare-ups” (as NCSE calls them) to other experts on the staff, he regards his particular duty as endeavoring to change hearts and minds and open channels of communication between factions that are often at loggerheads.

In 2008, Peter was contacted by a theology teacher at the Convent of the Sacred Heart Catholic High School in San Francisco. Convent wanted to celebrate the Darwin bicentennial year by creating a program called “The Darwin Project,” which would integrate evolutionary thinking across the curriculum in a dozen different departments. The year involved frequent class lecture visits by Peter to the senior students and a fantastic conference on evolution to which parents and the public were invited.

Around that time, Professor Richard Dawkins happened to be in Berkeley for a lecture and came into the NCSE office for a visit. He sat through a staff meeting, at which everyone was invited to introduce themselves and describe the most interesting project they were currently working on. “When I brought up Convent High School’s ‘Darwin Project,’” Peter says, “Richard Dawkins showed moderate interest, and then remarked,

‘I imagine the religion department had to be dragged kicking and screaming into this.’

“When I told him that quite on the contrary, the religion department had initiated the project, Dawkins looked stunned — as if he couldn’t quite comprehend why a theology teacher would be interested in evolution, much less why they would accept the theory.”

It’s amazing to Peter how Professor Dawkins — who is well-known for his criticisms of creationism and intelligent design as well as for being an excellent communicator of scientific knowledge — could be so uninformed of contemporary intellectual currents within the Christian community.

“The idea that Christians as a group are opposed to science is plainly ludicrous,” says Peter. “The Vatican has had its own astronomical research observatory and has funded scientific study and discussion for hundreds of years — and Protestant theologians in most denominations both in the last century and today have been and continue to be vigorously involved in the theological assessment of the evolutionary perspective.”

Curious to know more about the debate? Check out Peter's book, Catholicism and Science

While some Christians would argue that the theoretical strivings of religious communities should be toward improving and strengthening their faith, alone, (rather than on contemplating theories of the natural world), Peter feels that a theology that is not challenged and transformed as the scientific culture changes around it is not really a living theology at all, but only the fossilized relic of a once-living tradition.

“When theology fails to recognize that the contemporary scientific view of the world is in a constant state of change and development, and refuses to adapt accordingly, then it is doomed to insignificance,” he says.

When asked which side in this debate is harder to talk to — rigid atheists or fundamentalist Christians — and who loses the most from an inability or refusal to dialogue, Peter pauses. “I’m not sure,” he says. “It’s different every time. I never use the same kind of language and arguments to approach either side. I count it a success if I can at least get people to consider viewpoints that are dissimilar to their own.”

Simply talking about the pursuit of science versus the pursuit of faith is a misnomer in Peter’s opinion, since they are orthogonal descriptions of the universe — that is, one doesn’t cancel out the other. “There is a faith dimension to science, in that scientists trust that the world is knowable,” says Peter, “and there is an empirical dimension to the doing of theology, because a theological doctrine that does not in any way resonate with human experience in the world is vacuous.”

An example of this, Peter goes on to explain, is the fundamental misconception of asking whether someone believes in creation or evolution.

“In my classes, I frequently use an analogy to describe what I mean,” says Peter. “I hold up a grapefruit. Then I ask my students to tell me whether it is yellow or roughly spherical. Usually, a student will say that it’s both, that color and shape are not contradictory but complementary ways of describing this fruit. Analogously, creation and evolution are complementary ways of talking about the world. Creation is in a metaphysical category, and describes a relationship — but it need not imply a particular fashion or order in which the universe came to be or even a specific event in time. Evolution, on the other hand, is a theory to explain both the diversity and the relatedness of all life on earth. Properly interpreted, evolution implies nothing about the existence or nonexistence of God.”

Peter believes that when practitioners of science and religion invade each other’s sphere of competence, conflict is inevitable. While it’s challenging to constantly be caught in the cross-fire, it’s also exciting to watch when people in opposition learn to think past their own prejudices and strive towards a point where they can take in the view from every side.

Of course, for some, summiting one mountain might happily reveal just how many there are to climb.

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Shooting the Red Planet

Mars as seen through the Hubble Space Telescope.

If the old expression “shooting the moon” means taking on a risky challenge, just imagine what “shooting Mars” might imply.

Perhaps even more than that heavenly body illuminating our nightly strolls and tugging on ocean tides, Mars looms large in our collective imagination. Pictures of the red planet liven up the walls of almost every grade school science classroom in the country. There’s no dearth of movies, cartoons, and novels in which bulbous-headed Martians descend to Earth in coin-shaped ships to help us humans achieve our own demise.

And when we wander outside of night-sky-dulling city lights, we often see Mars with our own eyes — although most of us mistake its rubicund glow for a brighter-than-average star.
Even when he was a little boy, ASA scientist Roger Wiens wouldn’t have made that mistake. For him, Mars isn’t as much a distant, alien object as it is an old acquaintance. He knows where it lies on a map of the skies at any point in the calendar year, and could probably draw a pretty accurate map of the surface of Mars, itself.

Roger grew up in an exciting time for stargazers and aspiring NASA scientists, especially those with an affinity for the red planet. Roger’s interest was ignited along with the Mariner 9 mission, the first spacecraft to ever orbit Mars, and grew when the planet passed closer to earth than it had in many years.

But unlike the majority of kids who lit out for the nearest field at night with a telescope in tow, Roger’s red planet passion followed him past adolescence — pushed him, even, to where he is now: leading the team of researchers at Los Alamos National Laboratory that just put the finishing touches on a machine that’s being taken to Mars.??The rock-vaporizing, element-identifying laser gun that Roger and his team developed will be an important part of the Mars Science Laborator rover, Curiosity, scheduled to launch this fall. Their instrument, called the ChemCam (http://www.msl-chemcam.com), will be “interrogating” its Martian home by boring through the dust and outer layers of rocks on the planet’s rusty surface and analyzing their composition.

The Curiosity rover, on the red planet with ChemCam, starting in 2012 (NASA/JPL/Caltech).

“Knowing just what a rock is made of and what other types of rocks are around it can tell you a lot about the conditions in which it formed,” says Roger. “It’s pretty clear that Mars was full of water at one time, but the planet has been relatively dormant for billions of years. We’re trying to understand what the environment of Mars was like in the distant past, including whether life ever developed there, by doing just what we do on earth when we’re searching for ancient life forms — looking under the surface.”

Roger added, “ChemCam will be able to analyze the presence of elements like carbon, nitrogen, oxygen, and hydrogen — the ‘building blocks’ of life, as well as take higher resolution, close-up images of Martian rocks than any camera NASA has yet deployed. The surfaces of these rocks, the grooves and knobs and bumps on their faces, give us clues as to whether they formed in the presence of water.”

Artist depiction of the ChemCam instrument interrogating a rock outcrop on Mars.

ChemCam is the first instrument being taken to Mars that can actually determine the elemental composition of rocks without having to deploy an arm or use scooping and grinding mechanisms, which are energy-depleting and wear down over time. Instead, the laser Roger and collaborators in France and the U.S. developed can point to an area of interest up to twenty feet away without any physical touch besides its pulsing beam of photons.

As these pinpoint-focused light beams zap the surface of a rock, they excite atoms within it and emit light of different colors depending on what elements are present. This light is seen by a telescope that’s built into ChemCam, which then transfers the colored light, or spectra, through an optical fiber into the body of the rover. Inside the rover, a spectrometer sees the colors as if they were flags representing the elements themselves.

“Every element has its own associated wavelengths of light,” Roger explains. “If you think about the distinctly yellow color of sodium vapor streetlamps, you’ll get the idea. Those streetlamps look yellow because that’s the wavelength at which sodium fluoresces. So if there were sodium in our sample, it would appear as a thin yellow line among many other colored lines in the spectrum, each one telling us something about the elements that make up the rock.”

The ChemCam project first entered Roger’s mind over ten years ago when a colleague at Los Alamos Lab gave a demonstration of a laser technique similar to the one he and his team later built for Curiosity. In the past, Roger had done research on the chemical make-up of Martian meteorites as well as of particles in solar wind, so when he saw a laser the size of a cigar powered by a 9-volt battery cause a spark on a sample across the room, he knew the technique could be developed for use on another planet.

The Curiosity rover touches down on Mars almost nine months after lifting off. For the makers of the many machines that comprise Curiosity, that pregnant wait will be well worth it when the lab opens its shutters to the Martian landscape for the first time.

Dr. Wiens and instrument manager Bruce Barraclough don protective goggles as they prepare to test ChemCam’s laser (LANL photo).

“It’s been so exciting to see the ChemCam finally perform exercises and collect data,” says Roger. “I can hardly imagine what the feeling in our lab will be a year from now, once Curiosity starts sending information back from Mars.” Roger has already given special lectures on Mars and on the ChemCam instrument in a number of countries and across the US.

While much of that data will be used to determine what Mars looked like in its youth, NASA scientists are also keen on learning what might still be lurking just below reach of past Mars rovers and of Curiosity, itself.

Giving an interview with BBC Radio during the landing of NASA’s GENESIS capsule.

“We’re taking baby steps,” says Roger. “We won’t be able to explore more than a few inches deep for quite some time, maybe not until we actually put a human on Mars. But data taken by ChemCam will also be instrumental in planning for a human mission, since we need to know what astronauts can expect when they get there, like whether the soil is toxic and where to look for water.”
In terms of challenges, imagining a future in which we humans stride across Mars might be quite a stretch for some. But it was the same for folks at the turn of the last century who, shifting their gaze to the moon, simply assumed it was unreachable.

Roger embraces Christianity, which he sees as a statement of scientific humility. Just over a century ago the Physics community had a strong sense that there was relatively little left to discover. A statement widely attributed to Lord Kelvin at that time implies that the only remaining job of science was to make increasingly precise measurements. Roger points out that little more than a hundred years later we already see how wrong that idea was! The existence of galaxies, the big bang, nucleosynthesis, relativity, quantum mechanics and band-gap theory of semiconductors, the structure of DNA and the human genome were all unknown at the time of these statements.

Projecting a century from now, who knows what new dimensions, either literally or figuratively, will be discovered? So while science needs to remain skeptical of things not yet proven, it also needs to remain humble and open to what the future will illuminate.
Roger points out that the new discoveries of the 20th century, such as the ancient age of the Earth and human origins, also influence our understanding of scripture, just like the discoveries of the previous centuries caused people to abandon archaic ideas like the geocentrism or “the firmament” and heaven as physical locations in our three-dimensional sky. “But the core message of scripture is timeless. It still gives the best description of the human condition and of how we ought to live,” Roger adds.

Roger feels that his involvement in science hasn’t just been the result of lucky coincidences — rather, he senses the hand of God’s providence in his work. For those Christians who grow nervous seeing once-deep mysteries laid open by scientific study, Roger feels sympathy as well as a desire to help them appreciate the glory of God more fully throughout creation — which, of course, extends beyond our own horizon.

Roger and his wife, Gwen, pose in front of an instrument display in the cleanroom (LANL photo).

As such, Roger is the author of a well-read paper on radiometric dating and the ancient age of the Earth from a Christian perspective (one of the first such writings to be published online) that is available on ASA’s website at http://www.asa3.org/ASA/resources/wiens.html. He’s also working on a book about his experiences in space called Getting to Mars.

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Going Algae-Green

Algae.

Even the word sounds slightly slimy. “Al-gae” — especially when articulated slowly, is a sort of squishy, guttural utterance —and when one imagines the subject of these syllables, themselves, they seem a rather fitting appellation. To accompany their aural ooziness, many visual and somatic properties of algae make them organismae-non-gratae for anyone with whom they come in contact. A lot of folks frankly dislike the idea of the green stuff murking up their decorative Kio ponds, lining their local swimming holes, or even staring up at them from the label of their daily vitamins bottle.

Not biologists. Or chemists, or environmental scientists, for that matter. To them, algae are one of the most useful and versatile organisms in the universe — especially on this planet, which is so full of animals breathing the oxygen algae pump into the atmosphere and drinking the water that algae help strip of excess carbon dioxide and inorganic nutrient waste.

Especially on this planet, whose sovereign species is at the dawn of a global energy crisis.

Over the past century, algae have gone from being a vastly under-appreciated ecological and nutritional resource to becoming recognized for all of their redeeming qualities, and thus (of course) put to work as a health supplement, as an eco-friendly fertilizer, as an energy source, and as a no-engineering-needed air and water purifier.

And now scientists, small companies, and even big fuel giants are studying algae for their potential to produce one of the most successful biofuels in the world.

Not only are algae more efficient than current renewable fuels in terms of the amount of material needed for substantial product yield, they are also more carbon-reducing and could be less problematic for farmers to find the time, energy, and space to grow.

According to ASA member and biofuel researcher John Korstad, “Algae are a far more effective source of fuel than corn ethanol, diesel from corn stover (the inedible part of the plant), or promising fuel-producing weeds like switchgrass, because the kinds of lipids that algae store when they photosynthesize utilizing carbon dioxide and nutrients in water are a more efficient source of energy than cellulose and starch. Pound for pound, even switchgrass doesn’t approach the percentage of fuel that scientists have been able to extract from the same amounts of algae so far.”

John, a biologist and the head of the honors program at Oral Roberts University, became interested in biofuels while on sabbatical in the fall of 2009. After spending a year talking to scientists around the world involved in algal biofuels research, John decided to go back to the field to study them, and has already co-authored four papers on the subject. With a B.A. in Geology, a B.S. in Biology, an M.S. in Environmental Science and an M.S./Ph.D. in Zoology, John sees algal biofuels as, “A way to make many, many lemons into lemonade…” Maybe not lemonade that most people would want to drink, at first — but promotion of the algae and its potential is one of the hurdles scientists currently have to overcome.

The unnerving fact for investors is that biofuels have been around for years, successfully brewed from the sugars in plants like corn, sugarcane, and soy. But these “first generation” biofuels also compete with food crops for arable land, water, and processing energy, which has mitigated their success both environmentally and economically. “Second generation” biofuels, on the other hand, are those sources that don’t compete with food crops, including cellulosic, corn stover, switchgrass, jatropha, unused fruit pulp, and other types of organic industry waste.

According to John, the idea of converting algae into energy isn’t a new one, but only in the past few years have studies shown that the process of producing algal biofuels can be orders of magnitude more efficient than making similar power-supplying products from algae’s corn and switchgrass cousins. “Algae grow faster if there are adequate nutrient and CO2 sources,” says John. “They then store CO2 as carbohydrates, proteins or lipids. This makes them a great source of the kinds of fatty acids that can be converted to methyl-esthers (i.e., biodiesel). What’s more — algae actually capture the excess carbon dioxide released through combustion of fossil fuels. Algal biofuels aren’t just carbon-neutral, they’re carbon-negative.”

Many of the big companies that predict great things from algal biofuels (like BP and Exxon) are looking large and trying to perfect the craft of algal fuel production with large and expensive laboratories before going global, which could take years and years of work. While John sees such “big picture” efforts as being a great leap towards sustainability and a needed effort to get algae to produce large quantities of fuel, he’s also focusing his attention on the “little picture,” as it were.

One of John’s major projects is to help local businesses and farmers start to benefit from algal fuels right now, quite literally in their own backyards.

John’s desire is to connect various industries that produce CO2 and nutrient wastes, which includes local oil refineries, electrical power

plants, cement factories, waste management landfills, agricultural land, animal feed lots, and city sewage treatment plants, and use this waste to cultivate algae for biofuels. The algae would improve the air and water quality by taking up the waste CO2 and nutrients, and then be of further benefit by providing a feedstock for biodiesel and chemicals used for nutritional and pharmaceutical products like omega-3 fatty acids.

The thing about algae is that they naturally produce more of the lipids you need for biofuels, but it’s hard to expand this to the commercial level where you can produce thousands of barrels all year long,” says John. “My dream is to have basically half and half — greenhouse photo-bio-reactors (closed systems in which algae can be harvested daily) in winter and open-pond systems cleaning up waste water in the summer.”

John started his scientific career as a limnologist, or one who studies freshwater ecosystems (lakes, ponds, rivers, streams, wetlands, even underground springs — in short, every water feature that isn’t the ocean or the sea). His vision comes from a long history examining nutrient and phytoplankton (microalgae) interactions in the laboratory and in the field.

If you think on the level of a smaller system,” John says, “third world countries, for instance, where people need clean water and energy, or the small farmer who has a pond that’s collecting fertilizer runoff and who could set up a biofuel-generating station to become self-sustainable… that’s where I think the inspiration is right now. I personally feel that all of the entrepreneurial companies looking solely at making money are missing the more important thing — but then again, those folks who have great ideas to do something good for the environment but which aren’t economically viable — well, that’s not good in the long term, either. I really think the thing to work toward now is finding out how it can be both at once.”


John also sees the potential of algal fuels as a bit of a God-given revelation. “To me, as a Christian,” he says, “God gives us witty ideas and insights all the time — and I think Christians should be more proactive about using those insights to help find solutions to the problems that face human beings and the environment (Creation) in which we live. That’s good stewardship!”

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Infinity’s Holding Cell

Da_Vinci_Studies_of_Embryos_Luc_Viatour

Hundreds of years ago, under cover of darkness. Shrouded in secrecy. Breaking the law.

This is what human biological science used to look like. Once upon a time, seekers of knowledge in the natural world (Leonardo Da Vinci among them) risked their careers and lives digging up cadavers to peek inside them and try to discern how the human body functions. At the time, this act was seen as a violation of human dignity, immoral, and, of course, illegal.

That was then. This is now: biologists are once again caught in a moral dilemma that threatens their scienceand puts them under constant legal crossfire. While the dissection of a dead, thus de-souled, human body is no longer viewed as a scientific travesty, the disassembly of human embryos has for years been generating enormous controversy for researchers, politicians, and the public.

In 2001, President Bush signed a law restricting the use of federal funding for embryonic stem cell (ESC) research to cell lines that had already been extracted from unwanted IVF (in vitro fertilization) embryos in fertility clinics. In March 2009, President Obama issued an order destrictifying Bush’s policy so that new embryo lines could be opened up to researchers. But in August 2010, a federal judge made a preliminary ruling against the more lenient policy in court, citing a 1996 ban on federal funding for any project that destroys human embryos. And this May, a federal appeals panel overturned the judge’s temporary injunction restricting federal funds from being used while the judge makes a final ruling.

Physician and ethicist William Hurlbut was on the President’s Council on Bioethics when lawmakers were considering whether to open up new embryonic stem cell lines for research purposes. “Contrary to what’s printed in the press, the group advising President Bush was not a ‘rubber stamp’ council,” said Hurlbut recently via phone, pausing to clarify that his position on the council was not a political appointment, “I thought it was clear that the science was worth investigating—stem cells are what naturally give rise to cells of every other type (cell, tissue, and organs), and many scientists then saw ESC research as the fast-track to lifesaving cures and technologies. But I also felt like it raised a lot of troubling issues. Traditional stem cell research—even research that might result in needed cures for the dying and infirm—also means relegating millions of living human embryos to the status of raw materials.”

The issue is far more complex than most defenders and supporters of ESC science make it out to be, Hurlbut says. Even he didn’t know his own mind until he was on the President’s council and really had to think about why dismantling unwanted embryos should give scientists (and the public) pause. “Embryos are microscopic,” Hurlbut said, “an eight-celled embryo can easily rest on the sharp tip of a pin, and they certainly don’t look like unique individuals… it’s kind of hard for people to relate to a tiny clump of dividing cells. But there’s a big difference between living embryos and every other type of cell in the human body.”

Explaining that difference required about an hour of poignant discussion of what it means to be human, in the first place. Fortunately, the essential distinction Hurlbut illustrated can be whittled down to a single elegant word: potential.

“When scientists discuss the ‘building blocks’ of life in terms of DNA, amino acids, proteins, etc., none of these materials, when stripped from their surrounding elements, have the potential to become organisms that have the indwelling powers to develop as a human organism,” Hurlbut said. “Even gametes—the sperm and the egg—are alive in a body as cells, but they aren’t living beings. Only when they join together to create something that has a special kind of organization—an organization that will eventually give rise to a fully formed, living, breathing baby with fingers, toes, a heart, a brain, and reproductive organs of its own—can a single cell be considered a living thing. It’s this active power to develop in a human way that endows the human embryo with its unique moral status’. This simple 1+1 of sperm and egg creates the infinity and eternity of a human being.”

The moral controversy over embryonic stem cells is based on the fact that to get these cell lines a living human embryo is destroyed. However, to get the true equivalent of embryonic stem cells, and to keep from having to destroy human embryos, in 2006 scientists proposed a way to modify the nuclei of adult cells so that they functionally double-back to a state of pluripotency (or the prenatal ability to give rise to a wide array of cell types). To do this, they modified a technique known as SCNT (Somatic Cell Nuclear Transfer), in which the nucleus of the adult cell, which contains its DNA, is removed from the cell body and implanted into an egg cell that’s had its own nucleus removed. The egg then has a full set of DNA and, after some electrical stimulation, starts to divide like an IVF egg and forms an embryo.

This embryo creation method is also called cloning, and as Hurlbut points out, it’s exactly the same method that was used to create Dolly the Sheep, but scientists haven’t yet gotten it to work with human cells. If someday they can get adult cells to produce embryos, these may be more promising than IVF embryos in some technical ways (like medical applications in which cures made from a person’s own DNA would be favorable over a stranger’s), but the process still creates and destroys a viable embryo that could have gone on to become a human. So for both sides of the stem cell debate, this, too, may be stalemate.

What Hurlbut wants to do is help researchers plot a path around all the ethical tripwires. To do that, he’s designed and proposed a morally sound method for stem cell research called Altered Nuclear Transfer (ANT). Using ANT, all scientists have to do is insert an extra step into the standard cloning procedure. This extra step is to silence mRNA in the cytoplasm of the egg so that when the nucleus is transferred into the egg no embryo is produced. Although the embryo still produces pluripotent stem cells, it doesn’t have the organization—that precious potential—to create life.

While Hurlbut’s solution could be a way to move stem cell science out of the courtroom and back into the lab full time, Altered Nuclear Transfer needs more research, more support, and of course, more funding before it can become a standardized method of stem cell production. In the meantime, (for now at least), ESC research has the federal thumbs up, so scientists may feel less urgency to pursue ANT and other alternatives.

 

“My whole orientation and alignment is to help extend the circle of agreement on this topic, and ANT has been found morally acceptable by some of the most conservative religious leaders in the country,” says Hurlbut. “I just don’t think we’re ever going to solve the debate over embryo destruction, and having this moral and political tug of war is damaging to our nation’s need for unity—as well as a sense of nobility in science.

“The fact is, morality is essential for our society to exist, and most people will agree that human beings are an exceptional kind of creature, endowed with a sense of love, justice, and beauty, and that these things set us apart from the rest of the animals on earth,” Hurlbut says. “But humans aren’t just a species, they’re individuals. And if we believe that all human individuals have the right to live good, meaningful lives, then we must have a way to recognize those individuals. So where and when does our love for each other, and our love from God, actually start? You and I were once a clump of two, four, eight cells in a fallopian tube in your mother. Can we really say that there’s a single point in the dividing, implanting, and diversifying of embryonic cells that an unrepeatable human is endowed with morality and dignity? Human life is anunbroken continuity from fertilization to natural death. I believe that once we are initiated as living human organisms, we are worthy of full respect, protection and nurture as the image of God.”

Fortunately for embryonic stem cell researchers, they don’t live in a time at which any of them have to meet for midnight digs through the dumpsters behind fertility clinics, nor even duck their heads in public concerning the nature of their work. But the laws that govern the funding they need to pursue this work are being written with erasable ink. Hurlbut hopes that more of them will want to look for ESC alternatives, if for no other reason than they’ll be building their labs on higher, more solid moral ground. The big shift hasn’t happened yet—but there’s potential.

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A Ladder to the Protein Moon

by Monica Slinkard

Since the announced completion of the human genome project in April 2003, the scientific community has been working to decipher the meaning of the approximately 24,000 genes in the human genome. In case you don’t remember from high school biology (or chemistry), genes are specific sets of DNA unique to every single organism, and the code contained in a person’s DNA is part of what makes them who they are, for better or for worse.

But when it comes to understanding the exact ways in which DNA differences define unique characteristics of a person at the cellular level, in the way cells function and malfunction, even the most learned academics agree that the science of genomics has a very long way to go.

Dr. Liskin Swint-Kruse, an ASA member and a professor of biochemistry at the University of Kansas Medical Center, has high hopes. Really high — Liskin compares the quest for mastering genomics to the challenge of putting a man on the moon at the turn of the century (the last century). To an early 1900’s stargazer, the impossibility of walking on the dark side of a glowing orb in space is a fitting comparison to the distance scientists must travel before they unlock the subtleties of how DNA works.

The fact is, after decades of work, the functions of ~98% of the human genome are still poorly understood, and even for the ~2% of the genome that codes for the amino acid sequences of proteins, understanding is limited. Amino acids are the building blocks of proteins, which are the molecules that perform many of the functions in every living cell. Each DNA gene specifies a precise combination of amino acids, which in turn gives each protein a specific shape.  Each unique protein shape allows it to bond to specific molecules or carry out a specialized task. Although the ability to “read” amino acid sequences from DNA sequences is robust, there is still a huge gap in understanding as to when polymorphisms (changes in gene and protein sequences alter a protein’s function.

For any given protein, some amino acids are essential to maintain the integrity of the protein’s structure and function, and most research has focused on studying amino acids that have this critical impact. In general, these amino acids do not tolerate polymorphisms well — for example, a mutation could cause a genetic disease. However, other regions of the protein can tolerate polymorphisms. Some of these “nonconserved” amino acids have little biological effect, whereas changes at other nonconserved amino acids can give rise to important functional variation (and ultimately, unique individuals).

Several algorithms have been written that attempt to identify important amino acid positions. Unfortunately, the algorithms require several assumptions about proteins that are not yet confirmed by — or sometimes do not agree with — actual experiments.

According to Liskin and colleagues at KUMC, one possible resource to identify the functionally-important amino acid positions is to compare the amino acid sequence of related proteins (homologs) that are found within and between different species. These protein “families” have similar sequences of amino acids and similar gross structures and functions, but each protein in the family differs at the nonconserved amino acid positions and can have a unique variation of the common function. The algorithms were created within the realm of working knowledge regarding protein structure and function, but some of the current working knowledge is based on limited experimental data.

The goal of Liskin’s research is to fill this gap.  Using a protein family common to bioinformatics studies, her group has engineered synthetic family members that allow systematic experimental studies of amino acid changes. Using these proteins, they have demonstrated that many more amino acid positions have biologically significant roles than previously thought. For example, Liskin’s team demonstrated that amino acids don’t have to be in direct contact with a binding partner to make a large functional contribution, and that “conservative” changes between chemically-similar amino acids can have a much bigger impact on protein function than expected. These results reveal the imperfect assumptions underlying interpretation of genetic change — as is often the case with God’s creation, little of what we take for granted is actually insignificant.

Liskin’s work is exciting, but it highlights how the scientific community is just beginning to comprehend the complexitiesandnuance that arise from variations in DNA sequence. Liskin notes that when she presents her breakthrough research at conferences, scientific colleagues are sometimes discouraged by the reality that we are still far from fully understanding protein function. Given the complexity, some colleagues have even suggested that we will never be able to predict the functional outcomes for many amino acid changes.

Then again, if everyone had listened to the naysayers of space travel, there wouldn’t be an American flag on the moon right now.

This  research may not be as visibly heroic as moon-walking, but it is of great importance to doctors, biological engineers, and other scientists who want to both understand how genomic changes evolve new protein functions here on earth, to use genomic differences to improve medical diagnostics, and to engineer new protein functions for biotechnology.

In Liskin’s spare time, she shares her passion for science at her children’s schools and at her church. She runs hands-on science activities at “Science Night” at her kids’ elementary school and leads discussions for an international women’s education organization. She encourages children to pursue the delight of science in the religious context at her United Methodist church by developing various activities (which she would be happy to share with anyone interested), which bring Bible teachings to light through science. Liskin shares, “I hope the kids will feel that science and religion have always been integrated in their lives and not be pushed into the ‘either-or’ position.”

If you have more questions for Liskin, you can reach her at lswint-kruse@kumc.edu

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Logic, Time, and the Divine

Ask anyone in ASA—becoming a scientist while remaining a Christian requires a lot of questioning.

Most Christians in science have to find a way to reconcile what the Bible literally says with what science tells us about God’s creation, but Bob Geddes has faced the opposite challenge. He became a minister after working for fifteen years as a geologist, and upon entering seminary, he had to wonder whether his logical, scientific method-based approach to answering questions and solving problems would be compatible with the more mysterious, subjective role of a spiritual guide and counselor.

Fortunately, God works in mysterious and logical ways, and Bob found that the methods of research and inductive reasoning that he acquired as a scientist were just as useful when he switched from studying minerals to being a minister.

Bob grew up in the Presbyterian church and fell in love with rocks on the stony beaches of Lake Huron, where his family sojourned in the summers. He went to college at the University of Western Ontario for geology, and after obtaining his master’s degree with a specialty in glacial deposits, Bob worked for the Minerals Division of Gulf Oil using glacial materials to trace out substances like uranium, gold, and base metals.

After a number of years, Bob went on to do geological surveying and research in Ontario for the Provincial government there. Most of the work with Gulf and the Ontario Geological Survey was done outside, in the harsh, beautiful wilderness of the north. Bob loved it.

Bob also loved God, and though work often took him far from his home church, he started thinking more about his role in the Christian church when an old professor from Western asked him to come explore evolution from the Presbyterian perspective at Knox College, which was near his office.

This was in the 1980’s, when a surge of interest in creation versus evolution was running through the public and academic arenas. While holding conversations on science/faith issues in his spare time, Bob started thinking about how people learn things, especially with regard to how they use and interpret the information in the Bible.

“The more we learn about creation, the more we learn about God and how much God loves us. Some of the debate that goes on between science and faith regarding the age of earth, evolution, etc., all comes down to how people use holy scripture. The more we learn about subjects like geology, the more it frees us up to get to the heart of the message behind the stories that are in the Bible,” Bob said over the phone.

“For example, take Genesis 1—if we try to tie that too literally to the seven days, we end up in debate, which is not whats its all about. If Jesus wanted to get to the heart of truth, he told a parable, so it makes sense that God’s truth would come to us in that form. There are some intriguing parallels between Genesis 1 and what science tells us about how the earth developed and humanity’s place in it. So if we accept Genesis as something that has truth behind it, we can learn that not only is creation good, but it’s a step-like process, which God put into motion and which took a very long time,” Bob said, then added, “God has a great, great patience…”

During those conversations, Bob realized that not only were the topics stimulating and important, he even felt called to switch the arena in which the talking took place. Instead of peering from science into Christian issues, Bob wanted to start from faith and work outward. His church was without a pastor at the time, which provided Bob with opportunities to get involved with congregational leadership. Feeling a general call to service, Bob went back to school (seminary) in 1987.

After 20 years as the pastor of South Gate Presbyterian Church in Ontario, Bob Geddes has retired and spends much of his freetime working as secretary treasurer of CSCA (the Canadian sister of ASA). Bob describes the role of the two organizations as “self-help groups” for aspiring and working scientists. “When it comes to controversy, scientists are getting it from both sides,” he explained, “There’s pressure from Biblical literalists on how to interpret scripture, so they have to restrict what they say about their work in church… but there are also colleagues in the university setting who may be atheistic or see no role for God in the scientific endeavor, and they have to clam up about their faith.”

In organizations like ASA, however, people can talk openly about both their work and their Christian life. They can share frustration over prejudiced viewpoints as well as talk about how to unite Biblical teachings with scientific scholarship. “I’m always interested in how people end up working it out for themselves,” Bob said of these discussions, “For instance, there are many ways of reconciling Genesis with old earth geology, and over the years, I’ve continued to develop my thoughts on the matter. I’m intrigued that many, many people have worked it out in their minds, and it’s always an individual thing. They compare and take inspiration from the things they read, but they also learn through their own intuiton and a love of nature.”

Certainly, the greatest scientists in the world would be remiss if they didn’t attribute some of their talent at discovery not just to intellectual rigor, but to little leaps of faith and logic that never make it into their published papers. Einstein, himself, once said, “On the path to discovery, the intellect has little to do. There is a leap in consciousness—call it intuition or whatever you like—and the solution comes to you, and you do not know how and why.”

The how and why of all creation deepens in meaning when studied from a Christian perspective, since everything scientists learn helps them reflect on God and God’s purpose. Bob illuminated his own wonder, “When we learn what geology is telling us about the age of the earth, in comparison to how long humans have been on the planet—it’s a humbling perspective—but at the same time, it’s kind of strengthening that we know God came to earth to be with us humble humans and come stay with us. I think about it as a Psalm 8 kind of thing, in which the speaker is looking at the heavens and pondering humanity’s existence and how much God loves us.”

Admittedly, I had to look up Psalm 8 to get the full effect of Bob’s comparison:

“When I look at your heavens, the work of your fingers, the moon and the stars that you have established,

what are human beings that you are mindful of them, mortals that you care for them?

O Lord our Sovereign, how majestic is your name in all the earth.”

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Calculating Mystery

Doug Lauffenburger looks like the kind of guy who might love a good mystery.

Or be in one.

His bone white hair falls just short of thick round glasses as he folds his hands and ponders the best way to answer a question. In his office, light from slatted windowpanes stairsteps across the large L-shaped desk behind him, where neatly organized stacks of paper await Doug’s attention.

The question he’s currently turning over in his mind: What inspired you to combine your lifelong training as a chemical engineer with your love of biology? After a few moments, Doug responds, “In contrast to engineering, biology has always been very mysterious. It’s unpredictable.”

CC-BY-SA FR; CC-BY-SA-2.0-FR.

But, he says, it can be more predictable now that he and scientists like him have been studying the most basic components of life not as biologists, but as engineers.

Doug is head of the Department of Biological Engineering at MIT, one of the newest and fastest growing scientific fields, which marries the elusive, hypothesis-driven elements of the life sciences with the more data-based, analytical fields of engineering and technology.

According to Doug, not a lot of people even know what biological engineering really is—including top-level academics and researchers at MIT. Many people incorrectly assume bioengineers spend their time creating gadgets that incorporate technology into biology (like MRIs and mind-controlled prosthetics that help scientists study or solve a specific problem), but typical bioengineering actually reverses the arrow from life science to engineering. Instead of trying to make a tool or machine to meet a biological need, bioengineers apply the methods of engineering (math, physics, chemistry, computer science) to biology, itself, by developing models to make predictions and create useful things from the elements of nature.

By Rfch, via Wikimedia Commons

“We want to understand biology in our own terms,” says Doug. “Where traditional biology is hypothesis driven, systems biology (a sub-field of biological technology), is data-driven. The notion is that biology is so complex it’s kind of vain to think you can formulate hypotheses based on single observations. With a data driven mindset you use the data available to turn what’s there into a computational model.”

Unlike most traditional biologists, bioengineers don’t study just one piece of a natural puzzle at a time—rather, they take all those pieces and plug them into a network of 1’s and 0’s.  The computer takes over from there, rearranging the whole thing into a predictive picture.

To illustrate, imagine you’ve been living with a life-threatening cancer. Once recognized, doctors might only have one round of treatment to fight the disease effectively, and the odds of killing all the cancer before it kills you are about as good with any one drug as they are with another. Hopefully, your doc’s got good intuition, and chooses the right one. I repeat: hopefully.

Doug is working to reduce this kind of uncertainty. In his office at MIT, many of the tidy stacks of paper on his desk contain data that will someday be used to help doctors of the future make better decisions about what their patients need based on each one’s unique physiology, not just their ailments. “People would tell you you’re crazy if you said you wanted a treatment that’s specific to your own genetic makeup, but creating that kind of system is exactly what we want to do,” says Doug.

While computational models of living cell behavior have already been successfully applied to the unnatural environment of a petri dish, Doug and a team of researchers from MIT and Massachusetts General Hospital recently completed the first ever attempt to apply systems biology “in vivo,” that is, in a living animal. In March, they successfully modeled (predicted) the behavior of mouse intestinal cells in the presence of the natural chemical TNF (tumor necrosis factor). Knowing how the thousands of proteins inside cells will behave in a dish is one thing, but adding the involvement of a body’s own complex chemistry is a huge step towards creating better, more predictive therapies in the medical field.

“Organisms don’t behave according to laws, like particles do in physics; you can’t ever predict with certainty what’s going to happen when a drug or bacteria is introduced into an animal or human body,” says Doug. “But my work is focused on improving those odds, and we can do that now that molecular biology has isolated for us all the basic elements of life. So now what we can do is think like an engineer and build things—computer models and tangible products—from those parts.”

“The best science is going to be when both biology and technology are working together,” he says.

Just like some human couples, whose differences make them a perfect pair, the disparate fields of biology and engineering have only just recently grown up enough to benefit from each other in similar ways.

“As technology in the 20th century was influenced by chemistry and physics, in the 21st century it’s going to be influenced by biology. That may sound philosophical on a high level, but it really is that profound.”

For Doug, the profundity of his scientific work doesn’t end at the cell or the human level. As intrigued as he is by natural phenomena, Doug also directs his time and attention at MIT to exploring the holy mysteries. Doug is a faculty advisor for MIT’s Graduate Christian Fellowship and frequently councils students as they grapple with issues of science and faith. “I think as a Christian, you have to treat the biological sciences as real, because they are. Evolution happens. As a scientist, you have to work a little harder to reconcile what the Bible says with what science has shown us, and get used to being viewed as kind of the ‘crazy uncle’ by colleagues”

Crazy uncle doesn’t mean mad scientist—although, as Doug might tell you, having something of a split personality certainly holds a few academic advantages…

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