Of course they did: a group of scientists intelligently designed a complex creature and brought it into being. Isn’t that what creationists say that God is supposed to have done?  So the answer to this question, which is being raised all over the internet (see here, here, and here, for example), is “yes.”

But whether Craig Venter and his colleagues created a synthetic bacterium in order to play God is doubtful.  Over at the Guardian, where for some reason Andrew Brown is allowed to continue injecting nonsense into the ether, he sees the synthetic organism as “another triumph of the only major scientific programme driven from the beginning by explicit atheism.”

This is remarkably stupid, even for Brown.  Yes, Venter is an atheist, and so was Francis Crick, who Brown sees as the father of the synthetic life program.  But it’s clear that the work culminating in today’s remarkable paper in Science was driven not by an idea to disprove God, or replace him, but by two other factors.

The first is simple curiosity—to see if we really could synthesize a working genome.  H. L. Mencken described this as the strongest motivation of the scientist:

What actually moves him is his unquenchable curiosity–his boundless, almost pathological thirst to penetrate the unknown, to uncover the secret, to find out what has not been found out before. His prototype is not the liberator releasing slaves, the good Samaritan lifting up the fallen, but the dog sniffing tremendously at an infinite series of rat-holes.

And, really, think of what we’ve done: using only the 3 pounds of jelly in our heads, and materials wrested from the Earth and laboriously transformed, we’ve been able to make a genome—one that can completely direct a living organism.  This is not the same as creating life, for that’s still a way off.  But it’s nevertheless amazing, and we don’t grasp how truly amazing it is because we’re inured to the miracles of biotechnology.  But think: how close is a chimp to doing this? They don’t even have PCR machines!

But Venter and his team are no fools, and they know that their methodology, which took a decade to perfect, can have enormous payoffs.  We can now make genomes to our desire, and put in them any genes we want, and then use them to build organisms.  We’ll have to start with simple ones like bacteria, but even there the social benefits are immense: the use of artificial bacteria to produce biofuels, for example.  Accompanying all this must be stringent government and public oversight, of course—even Venter recognizes that.  But still, even if this project simply stopped here, it would be a triumph of the human imagination, like putting men on the Moon.

But enough.  I won’t go over the technical details of this achievement: the background has been discussed by Carl Zimmer at The Loom (he’ll undoubtedly do a big post today), and the research by Elizabeth Pennisi at Science and P. Z. at Pharyngula.

I’ll just post a Quick Guide (apologies again to Current Biology):

What is Mycoplasma?

Mycoplasma is a type of bacterium that lacks cell walls (thereby rendering it impervious to antibiotics like penicillin, which work by hindering cell-wall synthesis, preventing bacteria from dividing).  M. mycoides causes lung disease in cattle and other ruminants.

Why did they use this group of bacteria?

Because it’s the creature with the smallest genome that can still grow independently in the lab.  A small genome makes synthesis easier, and it has to grow independently in the lab because under all definitions that is a living creature. (There is still a controversy about whether viruses, whose genomes have already been synthesized, qualify as “living” creatures, for they parasitize the genomes of other creatures for replication and coat synthesis, and cannot grow by themselves in the lab.)

What did Venter’s team do?

They synthesized the chromosome of one bacteria, Mycoplasma mycoides, from scratch, and injected that artificial chromosome into dead cells of a related species, Mycoplasma capricolum.  The artificial chromosome worked properly, reviving those dead cells and giving them the ability to grow, metabolize, and divide.  In effect, they artificially built the entire genome of a species and showed that it could work in a manner similar to that of the naturally-occurring genome.

What’s so great about that?

First of all, it’s a stunning technical achievement.  The M. mycoides genome is a million base pairs long, and getting that all correct, and putting the DNA together in the proper linear order, took a decade of work.  (A much smaller viral chromosome had been synthesized a few years ago.)  The chromosome was assembled in yeast, and in several stages, each of which was fraught with problems.  Finally, the assembled chromosome was put into the recipient cell. Each of these steps required developing a new technology.  And of course, as I mentioned above, there is the potential of enormous benefits of genetically engineered organisms.

Couldn’t this kind of tinkering cause big problems?

Yes, of course.  If this kind of work was done without the proper guidelines and oversights, pathogenic or destructive bacteria could accidentally wreak havoc.  Nobody, including Venter, claims that scientists should be allowed to do this kind of work willy nilly. In the case of the Science report, the researchers were careful to disarm all the genes in M. mycoides that were pathological.  But clearly new guidelines are in order.

Did Venter’s team create life?

No.  They created an artificial genome that was able to direct a living organism.  But that stretch of DNA would have been absolutely useless had it not been injected into a cell that already had the proteins and protein-synthesizing system that could take the DNA and use it to assemble new cells and proteins, as well as to allow the DNA to divide and make new cells. (This is a complicated process that requires many enzymes and other proteins.)  After a few generations, all the protein-synthetic, metabolic, and DNA-replicating machinery finally derived from the synthetic genome, so in that sense there was now synthetic life.  But it could not have started without enzymes, ribosomes, and other biological material from the “dead” recipient species, M. capricolum.

Indeed, this is the whole problem of how life appeared in the first place.  The biggest obstacle in understanding how life evolved is that DNA needs proteins in order to build a cell and to replicate itself,  but those proteins can’t be made without DNA in the first place. It’s a chicken-and-egg problem.  The problem of the origin of life is the problem of how the DNA/protein system coevolved.  Venter’s team circumvented this problem by providing the starting materials: the proteins and cellular matrix that helped the artificial DNA start replicating and making proteins.

Is real artificial life around the corner, then?

Probably not for a while.  We have to solve the chicken-and-egg problem first. That is, we need to synthesize a DNA or RNA molecule that can, out of a vat of supplied but simple chemicals, construct a cell that has the proteins and other materials necessarily to make the whole thing a self-contained organism that can grow and divide in the lab.  That is a long way off. I don’t know if I’ll see it in my lifetime, but I am confident that my students will in theirs.

When we do that, will we then be playing God?

I don’t like this whole notion of “playing God” because I don’t believe in one.  If that question means, “Can we create life from off-the-shelf chemicals?” then the answer is “almost certainly yes.”  But we must add that this creation of life in a high-tech lab bears no resemblance to how scientists think life originated four billion years ago.  That happened in some “warm little pond,” using chemicals much simpler than the ones Venter used. It was a process that took eons, and resulted in an organism much simpler than a Mycoplasma.  We should not think that Venter’s group was somehow mimicking the origin of life.  They weren’t, and didn’t intend to.

Will we ever be able to figure out, then, how life began?

I don’t think so.  The traces of that life are long gone, although remnants exist in things like the genetic code of modern organisms. But those first replicating creatures left no fossils, and there are many ways they could have originated. We’re gradually developing an understanding of how they might have come into being—RNA, for example, seems to be a better candidate than DNA for the first “replicator”—but we’ll never know for sure.  There are some questions that science simply can’t answer, because the substrate for our understanding isn’t there.  But that does not mean that God did it!

How will creationists react to this achievement?

I predict several responses. First, that it doesn’t mimic the creation of life the way that God did it (either poofing complex species of organisms into being ex nihilo or, if you’re a theistic evolutionist, evolving the first cell).  Or, they’ll say that this proves intelligent design because the Venter creature was, after all, intelligently designed. But, as I said, this experiment was not conducted to mimic the evolutionary origin of life.

But what creationists cannot get around is the increasing demonstration that life is merely an immensely complicated chemical reaction.  Venter’s team made a genome able to direct and support life using off-the-shelf nucleotides and some other reagents.  Eventually, in a few decades, they’ll be able to make a fully living bacterium in the same way.  And then we will have played God, at least the way religious people mean it.  And maybe, before our own species gets incinerated by the Sun in five billion years, we may even make conscious creatures.  That will be the final blow to mind-body duality.

Life is just complex chemicals—nothing more, nothing less.  Venter and his team have gone a long way toward showing this.  And I’m very glad that I was alive to see it.

UPDATE:  Carl Zimmer has put up a post about this, noting (and I didn’t know this) that one of the “watermarks” Venter’s group put in the synthetic DNA was a line from James Joyce!  Of course I would have preferred the last line from “The Dead,” the finest prose piece ever written in English: “His soul swooned slowly as he heard the snow falling faintly through the universe and faintly falling, like the descent of their last end, upon all the living and the dead.”

________

Gibson, D. G. et al. 2010. Creation of a bacterial cell controlled by a chemically synthesized genome. Science DOI: 10.1126/science.1190719

Voila! Kittehs beat Boobquake any day!

We’re taking a very short break from evolution, cats, and atheism to follow America as it gets taken over by bigoted morons who, reflexively, elect other bigoted morons to public office.

Here’s the new face of racism in America: Rand Paul, Tea Party (Republican) nominee for Kentucky’s senate seat.  His tactic: pay lip service to Dr. King while claiming that business owners have the right to discriminate on the basis of race.  After all, that’s just free speech for racists.

If you lived in America during the 1960s, and witnessed the long struggle for the Civil Rights Act of 1964, you’ll remember that racists used all sorts of code words for segregation.  Back then it was “states’ rights.”  Now it’s “free speech.”

“I abhor racism.  I think it’s a bad business decision to ever exclude anybody from your restaurant.”  Bad business decision?

And here’s a transcript of part of Paul’s interview with Rachel Maddow yesterday:

Maddow: Do you think that a private business has a right to say that ‘We don’t serve black people?’

Paul: I’m not in favor of any discrimination of any form. I would never belong to any club that excluded anybody for race. We still do have private clubs in America that can discriminate based on race. Butdo discriminate.But I think what’s important in this debate is not getting into any specific “gotcha” on this, but asking the question ‘What about freedom of speech?’ Should we limit speech from people we find abhorrent. Should we limit racists from speaking. I don’t want to be associated with those people, but I also don’t want to limit their speech in any way in the sense that we tolerate boorish and uncivilized behavior because that’s one of the things that freedom requires is that we allow people to be boorish and uncivilized, but that doesn’t mean we approve of it…

Maddow:… How about desegregating lunch counters?

Paul: Well what it gets into then is if you decide that restaurants are publicly owned and not privately owned, then do you say that you should have the right to bring your gun into a restaurant even though the owner of the restaurant says ‘well no, we don’t want to have guns in here’ the bar says ‘we don’t want to have guns in here because people might drink and start fighting and shoot each-other.’ Does the owner of the restaurant own his restaurant? Or does the government own his restaurant? These are important philosophical debates but not a very practical discussion…

Maddow: Well, it was pretty practical to the people who had the life nearly beaten out of them trying to desegregate Walgreen’s lunch counters despite these esoteric debates about what it means about ownership. This is not a hypothetical Dr. Paul.

We all know Poe’s law: that any parody of fundamentalism is indistingishable from the real thing.  I want to supplement this with Coyne’s law, to wit:  any parody of campaign ads for Republicans or tea-party candidates is indistinguishable from the real thing.

When I first saw this ad, for Dale Peterson, a Republican running for the Alabama Agriculture Commission, I was convinced it was a joke, especially because he pulls out a rifle near the end.  Turns out it’s a real ad.  What’s even sicker is that this guy may win.

It’s this kind of thing that makes me proud to be an American.

On May 15, Eugenie Scott, director of the National Center for Science Education, got another—and well-deserved—honorary degree, this time from The University of Missouri, Columbia.  I can’t imagine giving a commencement address: what advice can you offer that hasn’t already been given?   But Eugenie did something clever: she elicited suggestions from her Facebook friends.  One of them gave her some really good advice, which became her theme:

Another of my Facebook friends had a suggestion that really resonated with me:

Trust your brain.

Now you’re talking. As you heard, I’m a scientist, and I believe strongly that reason, facts, and empirical evidence are essential for making not just scientific decisions, but other decisions as well. How can I encourage you to trust your brain? Well, as I was writing this talk, I read an article in the San Francisco Chronicle by a reporter who attended a psychic fair. He wrote:

A whole wonderful building full of miracles. Major credit cards accepted.

The reporter went on to describe these miracles, to wit:

It could be a magic bracelet (results not guaranteed), or a magic stick (your results may vary), or a magic meditation magnet (no refunds).  And indeed, there were people attending the fair who seemed not to be using their brains very much. One purveyor would, for $100, converse with a customer’s dead relatives. As the reporter commented, “her conversation seemed to be a trifle one-sided.”

Trust your brain. It’s useful not just for surviving four years of university, but for deciding lots of things that are important. Like what brand of sunscreen to select, or what policies our elected representatives should follow, or whose fault the Deepwater Horizon oil spill is, as well as whether to believe someone can channel your dead relatives.

Excellent!  But why is it always the psychics, the homeopaths, and the astrologers who take it in the neck when scientists attack irrationality?  What about the most widespread form of irrationality?

Let’s rewrite this:

Another of my Facebook friends had a suggestion that really resonated with me:

Trust your brain.

Now you’re talking. As you heard, I’m a scientist, and I believe strongly that reason, facts, and empirical evidence are essential for making not just scientific decisions, but other decisions as well. How can I encourage you to trust your brain? Well, as I was writing this talk, I read an article in the San Francisco Chronicle by a reporter who attended a Catholic church:

A whole wonderful building full of miracles. Major credit cards accepted.

The reporter went on to describe these miracles, to wit:

It could be a rosary (results guaranteed), or a magic cracker  (your results won’t vary), or a magic goblet of Jesus’s blood (also guaranteed).  And indeed, there were people attending the church who seemed not to be using their brains very much. One purveyor would, for a few Hail Marys, ensure your entrance into Heaven.  Observing the congregation’s prayers, the reporter commented, “their conversation seemed to be a trifle one-sided.”

Trust your brain. It’s useful not just for surviving four years of university, but for deciding lots of things that are important. Like what brand of sunscreen to select, or what policies our elected representatives should follow, or whose fault the Deepwater Horizon oil spill is, as well as whether to believe that after you die a magical sky father will send you to live with the angels.

But of course you’ll never hear anyone from the National Center for Science Education, which has a Faith Project, or the National Academy of Sciences, or the American Association for the Advancement of Science, say anything of the kind.  It’s perfectly all right to go after people who peddle water as medicine, but not those who peddle wine as grace-providing blood.  By all means go after those who claim that the planets guide your life, but hands off those who think that it’s not the planets, but God.

Isn’t it weird that pro-science organizations gleefully take out after every form of superstition save the one that’s most pervasive?

This double standard about pseudoscience versus religion reminds me of a wonderful essay by New York Times science reporter Natalie Angier,  “My God Problem” (by all means read it):

Consider the very different treatments accorded two questions presented to Cornell University’s “Ask an Astronomer” Web site. To the query, “Do most astronomers believe in God, based on the available evidence?” the astronomer Dave Rothstein replies that, in his opinion, “modern science leaves plenty of room for the existence of God . . . places where people who do believe in God can fit their beliefs in the scientific framework without creating any contradictions.” He cites the Big Bang as offering solace to those who want to believe in a Genesis equivalent and the probabilistic realms of quantum mechanics as raising the possibility of “God intervening every time a measurement occurs” before concluding that, ultimately, science can never prove or disprove the existence of a god, and religious belief doesn’t—and shouldn’t—”have anything to do with scientific reasoning.”

How much less velveteen is the response to the reader asking whether astronomers believe in astrology. “No, astronomers do not believe in astrology,” snarls Dave Kornreich. “It is considered to be a ludicrous scam. There is no evidence that it works, and plenty of evidence to the contrary.” Dr. Kornreich ends his dismissal with the assertion that in science “one does not need a reason not to believe in something.” Skepticism is “the default position” and “one requires proof if one is to be convinced of something’s existence.”

In other words, for horoscope fans, the burden of proof is entirely on them, the poor gullible gits; while for the multitudes who believe that, in one way or another, a divine intelligence guides the path of every leaping lepton, there is no demand for evidence, no skepticism to surmount, no need to worry. You, the religious believer, may well find subtle support for your faith in recent discoveries—that is, if you’re willing to upgrade your metaphors and definitions as the latest data demand, seek out new niches of ignorance or ambiguity to fill with the goose down of faith, and accept that, certain passages of the Old Testament notwithstanding, the world is very old, not everything in nature was made in a week, and (can you turn up the mike here, please?) Evolution Happens.

Over at HuffPo (who knew?), Karl Giberson, Ph.D, vice president of the Templeton-funded BioLogos Foundation, discusses why intelligent design persists in America.  Here are his four explanations:

ID’s coffin is far from being nailed shut. Several things are propping it open:

1) The complex designs of many natural structures that have not yet been explained by science. As long as there are ingenious devices and intricate phenomena in nature (origin of life, anyone?) that we cannot understand, there will be ID arguments.

2) The remarkable, finely-tuned structure of the cosmos in which the laws of physics collaborate to make life possible. Many agnostics have had their faith in unguided materialism shaken by this, most recently Anthony Flew.

3) The widespread belief that God — an intelligent agent — created the universe. The claim that an intelligent God created an unintelligent universe seems peculiar, to say the least.

4) The enthusiastic insistence by the New Atheists that evolution is incompatible with belief in God. Most people think more highly of their religion than their science. Imagine trying to get 100 million Americans to dress up for a science lecture every Sunday morning — and then voluntarily pay for the privilege.

ID’s coffin will remain open — and empty — as least as long as these props remain. Science is working successfully only on the first prop above and is a long way from having explained all the mysteries of nature.

Well, we’re doing the best we can with #1, but of course a major reason for the persistence of creationism is #3.   Here’s what the Pew Forum says:

When asked what they would do if scientists were to disprove a particular religious belief, nearly two-thirds (64%) of people say they would continue to hold to what their religion teaches rather than accept the contrary scientific finding, according to the results of an October 2006 Time magazine poll. Indeed, in a May 2007 Gallup poll, only 14% of those who say they do not believe in evolution cite lack of evidence as the main reason underpinning their views; more people cite their belief in Jesus (19%), God (16%) or religion generally (16%) as their reason for rejecting Darwin’s theory.

The major impediment to acceptance of evolution in America is the persistence of faith.  It’s not the lack of outreach by scientists—many of us are reaching out (I do it all the time), and, as Carl Zimmer noted, there’s a veritable glut of information about evolution on television, in books, and on the internet.  There has never been a time, I think, when there has been so much popular writing on evolution.  And yet the statistics on American acceptance of evolution fail to budge.

That’s why winning over the public to evolution will be a long fight, for it involves loosening the grip of religion on our country. We may have to wait for decades.  But loosening that grip has ancillary benefits, for it also dispels much of the faith-based irrationality involved in opposing things like global warming, AIDS prevention, assisted suicide, and stem-cell research.  Compared to that, the rejection of evolution is small potatoes.

So what is Giberson’s solution?  Forget #3—let’s work on #4. Make those shrill New Atheists shut up!:

If the scientific community wants to dislodge ID, they need to start by admitting that their efforts have been an abysmal failure so far. And then they need to turn their considerable analytical skills on the problem of explaining that failure. If they do this, they might discover that enthusiastic pronouncements like “ID is dead” or “science has proven God does not exist” or “religion is stupid” or “creationists are insane” are not effective. They might discover that affirming that the universe is wonderful, despite our bad backs and the nonsense in our genomes, makes it easier for people to accept the bad design in nature.

And above all, they need to decide that it is OK for people to believe in God. For millions of Americans belief in ID is tied to belief in God. Unless people can find a way to separate them — and not be told by agnostic bloggers this is impossible — ID’s coffin will remain empty.

Our efforts have been an “abysmal failure” for one reason: up to now they have involved selling evolution rather than dispelling religion.  The New Atheists realize that fighting for evolution while leaving faith alone is doing battle with one hand tied behind their backs.

Giberson is simply wrong to assume that if we suddenly tell people, “Yes, you can be religious and accept evolution, too,” then millions of creationists will suddenly flock to embrace Darwinism.  There’s that little matter of 64% of Americans rejecting scientific fact if it contradicts their religious beliefs.  That’s data.  And it suggests that Giberson’s solution is nonsense.

I’m jealous of those of you who haven’t read this book, because you have immense pleasure in store.

I’m beginning to work my way through some of the books suggested in the spring book contest, and I started with the winner, Last Chance to See by Douglas Adams and Mark Carwardine (I suspect that most of the writing is Adams’).  After polishing it off last night, I agree completely with John TR’s winning review:

Most know of Adams through the Hitchhiker’s series and his wit and humour carry over brilliantly in narrating the journey to observe the world’s most endangered creatures. From the hilarious story of trying to buy condoms in China to the awe of patiently searching for white rhinos in Africa, Adams remains endearing and never condescending while educating the reader about such pressing environmental issues. This is the uproarious and enlightening story of an Englishman so far displaced from his clean and proper life.

As Adams would say, “Spot on.”  I would put this in the “must read” category for anybody who likes biology.  It’s more than just funny: it’s alternately sad, pensive, philosophical, and hilarious, and you’ll learn a fair amount of biology.  Although it was written 20 years ago, and Adams has since become an ex-Adams, it’s every bit as timely as it was back then.  The species that were endangered are still endangered, and one of them, the Yangtze River dolphin, is now gone (there’s a very nice new book on this creature, Witness to Extinction by Samuel Turvey).

Buy it or take it out of the library, but read it.  Adams has a unique voice (I confess that I’ve never read the Hitchhiker series), and the book is so good that it’s hard to single out one passage for praise.   Highlights are the horrific description of Komodo dragons eating a freshly-killed goat for the delectation of the tourists, and Adams and Carwardine’s arduous but ultimately successful search for the world’s only flightless parrot, New Zealand’s kakapo (Strigops habroptila).  There are only about 120 kakapos left, and they’ve all been moved to a predator-free island.  They once lived in the mountainous part of New Zealand called Fiordland:

Until 1987 Fiordland was the home of one of the strangest, most unearthly sounds in the world. For thousands of years, in the right season, the sound could be heard after nightfall throughout these wild peaks and valleys.

It was like a heartbeat: a deep, powerful throb that echoed through the dark ravines.  It was so deep that some people will tell you that they felt it stirring in their gut before they could discern the actual sound, a sort of wump, a heavy wobble of air.  Most people have never heard it at all, or ever will again.  It was the sound of the kakapo, the old night parrot of New Zealand, sitting high on a rocky promontory and calling for a mate.

I found one audio clip of kakapo booming, but my aged ears can’t hear it.  (Arkive has twelve short videos of the kakapo; the BBC has four.)

And I’ve put this up before, but it’s too good not to repeat: a clip from the BBC Last Chance to See television program, with Mark Carwardine and Stephen Fry.  Here Sirocco (the birds, being few, are all named) tries to bonk Carwardine’s head:

And one more passage from the book. Here, conservationist Richard Lewis goes out to feed a mouse to a hand-reared Mauritius kestrel (Falco punctatus) that has been released back into the wild. (This is a conservation bright spot: the species was once down to only four individuals but is coming back.):

“Okay, let’s feed the bird. You watching?”

Richard swung his arm back. The kestrel’s head followed his movement precisely.  With a wide underarm swing, Richard lobbed the small mouse high into the air. For a second or so, the kestrel just watched it, jittering its legs very slightly on the branch as it engaged in monumental feats of differential calculus.  The mouse reached the top of its steep parabola, its tiny dead weight turning slowly in the air.

At last the kestrel dropped from its perch and swung out into the air as if on the end of a long pendulum, the precise length, pivotal position, and swing speed of which the kestrel had calculated. The arc it described intersected sweetly with that of the falling mouse, the kestrel took the mouse cleanly into its talons, swept on up into another nearby tree, and bit its head off.

“He eats the head himself,” said Richard, “and takes the rest of the mouse to the female in the nest.”

It is natural selection, of course, that has instilled that wonderful and unconscious calculus into the bird.

If you have a biology maven on your Christmas list, this would make a great present.  But by all means get it for yourself, too.

Ah, Fox News is back to normal.  In a discussion of the Deepwater Horizon disaster, Brit Hume says it’s a lot of fuss about very little.

“Where’s the oil? It’s not on—except for little chunks of it, you’re not even seeing it on the shores yet.”

“But you know one of the greatest source of oil that seeps into the ocean is—is from natural seepage from underground, from subterranean deposits. That’s where most of it comes from—not from drilling accidents.  So what’s badly needed here is perspective on our energy policy, and also on the hard realities of what really goes on when it comes to oil spills.”

“The ocean absorbs a lot, a lot, the ocean absorbs a lot.”

I think he’s right about natural seepage, but it doesn’t come in huge gushers that befoul the shores and kill wildlife.