Unintelligent Design, or Do We Come From Viruses?

In the discussions of intelligent design, one hears a yearning for an old-fashioned creation story, in which some singular, inchoate entity stepped in to give rise to complex life-forms—humans in particular. Now the viruses appear to present a creation story of their own: a stirring, topsy-turvy, and decidedly unintelligent design wherein life arose more by reckless accident than original intent, through an accumulation of genetic accounting errors committed by hordes of mindless, microscopic replication machines. Our descent from apes is the least of it. With the discovery of Mimi, scientists are close to ascribing to viruses the last role that anyone would have conceived for them: that of life's prime mover.

Many theists are willing to admit that evolution is at least possible, but remain convinced that the formation of our very first ancestor was too improbable to have happened by chance. Indeed it seems impossible that something as complex as a cell could have formed by chance and it's unclear what the precursor to a cell could be. However, if we start from a sea of amino acids and try to figure out the simplest possible replicator which could have eventually evolved into... well, us, than we might come up with something that looks a lot like a virus -- basically a strand of genetic material wrapped in a protective protein shell.

According to this fascinating article, some scientists are starting to believe that viruses may in fact be our ancestors. Also, even if the first replicator wasn't something like a virus, viruses may have played a key role in the development of the first cell nucleus.

Now, with the recent discovery of a truly monstrous virus, scientists are again casting about for how best to characterize these spectral life-forms. The new virus, officially known as Mimivirus (because it mimics a bacterium), is a creature "so bizarre," as The London Telegraph described it, "and unlike anything else seen by scientists . . . that . . . it could qualify for a new domain in the tree of life." Indeed, Mimivirus is so much more genetically complex than all previously known viruses, not to mention a number of bacteria, that it seems to call for a dramatic redrawing of the tree of life.

"This thing shows that some viruses are organisms that have an ancestor that was much more complex than they are now," says Didier Raoult, one of the leaders of the research team at the Mediterranean University in Marseille, France, that identified the virus. "We have a lot of evidence with Mimivirus that the virus phylum is at least as old as the other branches of life and that viruses were involved very early on in the evolutionary emergence of life."

That represents a radical change in thinking about life's origins: Viruses, long thought to be biology's hitchhikers, turn out to have been biology's formative force.

This is striking news, especially at a moment when the basic facts of origins and evolution seem to have fallen under a shroud. In the discussions of intelligent design, one hears a yearning for an old-fashioned creation story, in which some singular, inchoate entity stepped in to give rise to complex life-forms—humans in particular. Now the viruses appear to present a creation story of their own: a stirring, topsy-turvy, and decidedly unintelligent design wherein life arose more by reckless accident than original intent, through an accumulation of genetic accounting errors committed by hordes of mindless, microscopic replication machines. Our descent from apes is the least of it. With the discovery of Mimi, scientists are close to ascribing to viruses the last role that anyone would have conceived for them: that of life's prime mover...

Now, with the recent discovery of a truly monstrous virus, scientists are again casting about for how best to characterize these spectral life-forms. The new virus, officially known as Mimivirus (because it mimics a bacterium), is a creature "so bizarre," as The London Telegraph described it, "and unlike anything else seen by scientists . . . that . . . it could qualify for a new domain in the tree of life." Indeed, Mimivirus is so much more genetically complex than all previously known viruses, not to mention a number of bacteria, that it seems to call for a dramatic redrawing of the tree of life.

"This thing shows that some viruses are organisms that have an ancestor that was much more complex than they are now," says Didier Raoult, one of the leaders of the research team at the Mediterranean University in Marseille, France, that identified the virus. "We have a lot of evidence with Mimivirus that the virus phylum is at least as old as the other branches of life and that viruses were involved very early on in the evolutionary emergence of life..."

Even as Darwinism has come under attack from the theology of the intelligent design movement, scientists have never been closer to divining life's origins. With DNA evidence as solid as that used to convict criminals, researchers can trace the shared genetic lineage of life's different branches back to the very base of the tree, some 4 billion years ago, when the interaction between primordial bacteria and viruses culminated in the "mother cell," the common ancestor of all life on Earth. Although the remoteness and complexity of those events makes them difficult to piece together, viruses like Mimi are emerging as the key players in the picture...

How the first nucleus came to be is a question that has intrigued scientists ever since Scottish botanist Robert Brown first detected a cell nucleus while peering at orchids under a microscope one day in 1824.

The discovery of Mimivirus lends weight to one of the more compelling theories discussed at Les Treilles. Back when the three domains of life were emerging, a large DNA virus very much like Mimi may have made its way inside a bacterium or an archaean and, rather than killing it, harmlessly persisted there. The eukaryotic cell nucleus and large, complex DNA viruses like Mimi share a compelling number of biological traits. They both replicate in the cell cytoplasm, and on doing so, each uses the same machinery within the cytoplasm to form a new membrane around itself. They both have certain enzymes for capping messenger RNA, and they both have linear chromosomes rather than the circular ones typically found in a bacterium.

"If this is true," Forterre has said of the viral-nucleus hypothesis, "then we are all basically descended from viruses..."

We have been looking for our designer in all the wrong places. It seems we owe our existence to viruses, the least of semiliving forms, and about the only thing they have in common with any sort of theological prime mover is their omnipresence and invisibility. Once again, viruses have altered the way that we view them and, by extension, ourselves. As it turns out, they are not the little breakaway shards of our biology—we are, of theirs.

(via digg)

Bedrock of a Faith Is Jolted

From the time he was a child in Peru, the Mormon Church instilled in Jose A. Loayza the conviction that he and millions of other Native Americans were descended from a lost tribe of Israel that reached the New World more than 2,000 years ago.

"We were taught all the blessings of that Hebrew lineage belonged to us and that we were special people," said Loayza, now a Salt Lake City attorney. "It not only made me feel special, but it gave me a sense of transcendental identity, an identity with God."

A few years ago, Loayza said, his faith was shaken and his identity stripped away by DNA evidence showing that the ancestors of American natives came from Asia, not the Middle East.

"I've gone through stages," he said. "Absolutely denial. Utter amazement and surprise. Anger and bitterness."

For Mormons, the lack of discernible Hebrew blood in Native Americans is no minor collision between faith and science. It burrows into the historical foundations of the Book of Mormon, a 175-year-old transcription that the church regards as literal and without error...

Critics want the church to admit its mistake and apologize to millions of Native Americans it converted. Church leaders have shown no inclination to do so. Indeed, they have dismissed as heresy any suggestion that Native American genetics undermine the Mormon creed.

Yet at the same time, the church has subtly promoted a fresh interpretation of the Book of Mormon intended to reconcile the DNA findings with the scriptures. This analysis is radically at odds with long-standing Mormon teachings.

Some longtime observers believe that ultimately, the vast majority of Mormons will disregard the genetic research as an unworthy distraction from their faith.

"This may look like the crushing blow to Mormonism from the outside," said Jan Shipps, a professor emeritus of religious studies at Indiana University-Purdue University Indianapolis, who has studied the church for 40 years. "But religion ultimately does not rest on scientific evidence, but on mystical experiences. There are different ways of looking at truth."

Interestingly, the person who made the discovery is a former Bishop in the church.

In the 1990s, DNA studies gave Mormon detractors further ammunition and new allies such as Simon G. Southerton, a molecular biologist and former bishop in the church.

Southerton, a senior research scientist with the Commonwealth Scientific and Industrial Research Organization in Australia, said genetic research allowed him to test his religious views against his scientific training.

Genetic testing of Jews throughout the world had already shown that they shared common strains of DNA from the Middle East. Southerton examined studies of DNA lineages among Polynesians and indigenous peoples in North, Central and South America. One mapped maternal DNA lines from 7,300 Native Americans from 175 tribes.

Southerton found no trace of Middle Eastern DNA in the genetic strands of today's American Indians and Pacific Islanders.

In "Losing a Lost Tribe," published in 2004, he concluded that Mormonism — his faith for 30 years — needed to be reevaluated in the face of these facts, even though it would shake the foundations of the faith.

The problem is that Mormon leaders cannot acknowledge any factual errors in the Book of Mormon because the prophet Joseph Smith proclaimed it the "most correct of any book on Earth," Southerton said in an interview.

"They can't admit that it's not historical," Southerton said. "They would feel that there would be a loss of members and loss in confidence in Joseph Smith as a prophet."

Echoes of Orthodox Jews reinterpreting Genesis abound:

Officially, the Mormon Church says that nothing in the Mormon scriptures is incompatible with DNA evidence, and that the genetic studies are being twisted to attack the church.

"We would hope that church members would not simply buy into the latest DNA arguments being promulgated by those who oppose the church for some reason or other," said Michael Otterson, a Salt Lake City-based spokesman for the Mormon church.

"The truth is, the Book of Mormon will never be proved or disproved by science," he said.

Unofficially, church leaders have tacitly approved an alternative interpretation of the Book of Mormon by church apologists — a term used for scholars who defend the faith.

The apologists say Southerton and others are relying on a traditional reading of the Book of Mormon — that the Hebrews were the first and sole inhabitants of the New World and eventually populated the North and South American continents.

The latest scholarship, they argue, shows that the text should be interpreted differently. They say the events described in the Book of Mormon were confined to a small section of Central America, and that the Hebrew tribe was small enough that its DNA was swallowed up by the existing Native Americans.

"It would be a virtual certainly that their DNA would be swamped," said Daniel Peterson, a professor of Near Eastern studies at Brigham Young University in Provo, Utah, part of the worldwide Mormon educational system, and editor of a magazine devoted to Mormon apologetics. "And if that is the case, you couldn't tell who was a Lamanite descendant."

Southerton said the new interpretation was counter to both a plain reading of the text and the words of Mormon leaders.

"The apologists feel that they are almost above the prophets," Southerton said. "They have completely reinvented the narrative in a way that would be completely alien to members of the church and most of the prophets."

The church has not formally endorsed the apologists' views, but the official website of the Church of Jesus Christ of Latter-day Saints — http://www.lds.org — cites their work and provides links to it.

Reactions have varied among the faithful. One said, "There's not very much in life — not only in religion or any field of inquiry — where you can feel you have all the answers. I'm willing to live in ambiguity. I don't get that bothered by things I can't resolve in a week." Phil Ormsby, a Polynesian who grew up believing he was a Hebrew had a different reaction: "Some days I am angry, and some days I feel pity. I feel pity for my people who have become obsessed with something that is nothing but a hoax."

(Bedrock of a Faith Is Jolted, via digg)

Truth, Beauty, Meaning, Morality

How is it that smart people with similar values can come up with such different worldviews and belief systems? What makes one person become an atheist while another becomes a deist and still another turns towards a more traditional religion? I've written before about the powerful influence of inertia on religious affiliation -- the single most predictive factor in religious choice is the religion of one's parents and a close second is the religion of one's country, if different than the parents'.

In this post, I'd like to look at what might be the next most important factor. That is, what is the question that most informs your choice of worldview? People who ask different questions will reach different answers. I think each of us has a primary question, although it may be unconscious. Everybody asks pretty much all of the questions, but the order in which we rank their importance will inform our most important decisions.

What is true?

This is the question of the skeptic, who wants to know the truth regardless of its consequences. If her entire life has been a lie, if her husband has been cheating, if she's got six months to live, she wants to know. Ignorance is never bliss as long as she's aware that she's ignorant. The skeptic doesn't do denial. These are the atheists, the agnostics, the religious skeptics, some of the theologians and philosophers.

What is beautiful?

This person prefers the beautiful answer, even if it's not necessarily the literal truth. He prefers the dramatic response over the most effective one, the storybook version of history over the nitty-gritty details, the poetic description rather than the reductionist one. He thinks of the flower turning towards the light as an act of love or worship rather than an unfeeling response to stimulus. These are the religious mystics, the wiccans, the blissed-out holy men.

What is meaningful?

This person craves purpose. She's not satisfied with the how but demands to know the why. She doesn't do anything for its own sake but rather for its part in some larger project. She finds meaning in the shulkhan aruch's instructions on how to tie one's shoes. These are the ones who "talk" to God, the millenialists, the eschatologists, the Purpose-Driven Life readers.

What is moral?

This is the rule-abider. He believes that every action must be guided by morality, that we must live by strict rules. These are the people adopting the latest stringencies, the fans of Dr. Laura, the judgemental of others.

What makes me feel safe?

(Edited to add.)

Conclusion

Maybe we talk past each other because we're answering different questions. People searching for morality won't be touched by evolution while people searching for truth will be mystified by the "beautiful sunset" proof of God. People looking for meaning won't like scientific materialism while those looking for beauty won't be moved by legalistic or nit-picky argumentation.

The Search for Religious Truth

People don't realize religion is never a search for truth. Religion is a search for security. Now, we have theological enterprises that try to shape truth. But the bedrock of our religion is a search for security. And that comes out of the very dawning of self-consciousness. --Bishop John Shelby Spong

Religion, being primarily theoretical rather than empirical, generally raises more questions than answers. This in itself is perfectly okay -- questions can be valuable tools to understanding. The problem is twofold: (1) there is no sure-fire method for testing candidate answers, and (2) people aren't satisfied with questions; they want answers.

It's interesting to see the various ways different religions (and other non-empirical thought systems like many branches of philosophy) go about satisfying the thirst for answers.

Biblical "Literalists"

Philosophy is questions that may never be answered. Religion is answers that may never be questioned. --Unknown.

First, you have the Biblical literalists who, uncomfortable with the fact that no text can be completely unambiguous, pretend that the Bible always says exactly what it means and no more. The problem they face is that the Bible is at times ambiguous, self-contradictory, or in defiance of the facts. Literalists generally either ignore such problems or develop convoluted apologetics to explain them away.

People Followers

[Many of my students] act like children and experience religion like children. This is why they accept all types of fanaticism and superstition. --Rabbi Joseph B. Soloveitchik

Others try to resolve the problem by finding a person and treating every word he utters as "the gospel truth." The biggest such group are Catholics who have made their Pope infallible. Also included in this category are various Hasidic groups as well as most cults.

Tradition Followers

Traditionalists are pessimists about the future and optimists about the past. --Lewis Mumford

Many people believe that weight should be given to authority figures of the past. As a bonus, there are always many authority figures to choose from, so this neatly overcomes the problem of self-contradiction. If Rabbi Hillel's students disagreed with Rabbi Shamai's students, they can accept both traditions as valid and just pick one to run with. Obviously a great many Orthodox Jews take this path, leading to a great diversity of opinions and practices. As they say, "Two Jews, three opinions." However, even the richest of traditions can't contain answers for all questions (particularly new ones) so people in this camp must be in other ones as well.

Personal Truth Followers

With the rise of the self in the West, combined with the advent of widespread literacy and the move away from the Catholic Church, many people have turned inward for answers. Some believe that they can speak directly with God via intuition (and sometimes voices in their heads, presumably) and others are comfortable with interpreting the various holy texts for themselves. Many of these people take another practical approach, picking and choosing cafeteria-style aspects of various religions and philosophies which resonate with them.

Theologians

And Jesus said unto them, "And whom do you say that I am?"

They replied, "You are the eschatological manifestation of the ground of our being, the ontological foundation of the context of our very selfhood revealed."

And Jesus replied, "What?" --Unknown

Theologians are much like the literalists in that they engage in tortured apologetics. However, being better educated, they can usually arrive at religious philosophies which are unfalsifiable. They will generally redefine terms so that they are completely at odds with the common understanding of them. This last group is perhaps the least objectionable of contemporary religious thinkers since they keep working until their beliefs are at least internally consistent and usually consistent with the world as well. However, their explanations are unsatisfying to the (fictional, of course) objective observer since they violate Occam's razor. Moreover, considering themselves members of their religion rather than members of a distinct one provides cover for all the believers in the other groups. Many a lay-person will take pride in the fact that a religious theologian is nominally of the same religion, but more often than not, the only similarity is in the label. In fact, if some of these theologians spoke their true views to the people, they would likely be kicked out of their communities.

Skeptics

Skeptics exist within religious traditions as well as with atheism and agnosticism. Religious skeptics are content to live without some answers, but either believe that the answers they do have are sufficient to act upon or simply choose to be religious in the absence of evidence.

Conclusion

In a recent thread, Orthoprax told me, "If Judaism were the ideological 'search for God' rather than a dogmatic assertion of the same, it could much more easily retain people like you, I think." I think that this is correct and, moreover, that such a Judaism would be a much more meaningful and thoughtful religion. However, it would also be much smaller and would run the risk of dying out within a few generations.

I believe that we must always choose to accept uncertainty over false truths and that we should encourage others to do the same. We must teach people that it's okay not to know the answer to every question and that saying "I don't know" is preferable to saying "I know" when they don't.

Evangelical Leaders Join Global Warming Initiative

Despite opposition from some of their colleagues, 86 evangelical Christian leaders have decided to back a major initiative to fight global warming, saying "millions of people could die in this century because of climate change, most of them our poorest global neighbors."

Among signers of the statement, which will be released in Washington on Wednesday, are the presidents of 39 evangelical colleges, leaders of aid groups and churches, like the Salvation Army, and pastors of megachurches, including Rick Warren, author of the best seller "The Purpose-Driven Life."

"For most of us, until recently this has not been treated as a pressing issue or major priority," the statement said. "Indeed, many of us have required considerable convincing before becoming persuaded that climate change is a real problem and that it ought to matter to us as Christians. But now we have seen and heard enough."

I've got to give credit where credit is due. I've long complained about prominent Christians focusing on stupid issues like preventing civil unions and boycotting t.v. shows, but these guys are stepping up to the plate.

Not all the evangelical leaders are on board, though:

Some of the nation's most high-profile evangelical leaders, however, have tried to derail such action. Twenty-two of them signed a letter in January declaring, "Global warming is not a consensus issue." Among the signers were Charles W. Colson, the founder of Prison Fellowship Ministries; James C. Dobson, founder of Focus on the Family; and Richard Land, president of the Ethics and Religious Liberty Commission of the Southern Baptist Convention.

All quotes from the New York Times.