Michael J. Behe's Blog, page 590

Winston Churchill on possible alien civilizations

The original Nature article is here. From Sarah Lewin at LiveScience:

Winston Churchill was known for his leadership during World War II, but a newfound essay on alien life reveals another side of him, one that was deeply curious about the universe.

“I, for one, am not so immensely impressed by the success we are making of our civilization here that I am prepared to think we are the only spot in this immense universe which contains living, thinking creatures,” he wrote in the newly uncovered essay, “or that we are the highest type of mental and physical development which has ever appeared in the vast compass of space and time.” More.

Churchill’s opinions sound cogent, though not a history-making contribution to astrobiology, a discipline that lacks a subject. That said, if the United States is actually into space exploration, it was right to bring back Churchill’s bust to the White House.

Oh, you didn’t know about that?:

The Jacob Epstein sculpture was given to President George W Bush by Tony Blair.

It was displayed in the Oval Office but was removed by President Barack Obama and replaced by a bust of Martin Luther King in 2009.

The former president’s decision to send the bust back to the British embassy in Washington was greeted with outrage on both sides of the Atlantic.

The bust is back now. And Dr. King remains suitably honoured, we are told, despite rumours to the contrary.

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[Off Topic] The Shack, a Review

UPDATE:  Dear readers, the movie version of The Shack will be out soon, so I thought it might be a good time to dust off my December 2009 review of the book.

The Shack by William P. Young is an unlikely publishing phenomenon.  The book was first conceived as a private gift to the author’s children and a few friends.  Young’s friends were so thrilled with the manuscript they encouraged him to find a publisher, but after several publishers rejected the book, Young and his friends self-published.  Propelled almost exclusively by word-of-mouth in the evangelical Christian community, sales skyrocketed, and the book has been firmly ensconced in the best seller lists for many months now, with sales topping one million copies.  The Shack has also been a phenomenon in the evangelical Christian community, spawning websites and seminars and breathless blurbs such as the one by a theology professor comparing The Shack to Pilgrim’s Progress.

This Thanksgiving my wife and I took a trip to visit family in Clear Lake, Iowa, and we decided we would use our time on the road to see what all the fuss was about.  We popped an audio copy of the book into the CD player, and by the end of the trip we had finished the book, and I was deeply troubled.

The Shack is the story of Mackenzie Phillips, known as “Mack” to his friends.  Mack grew up in the Midwest, the son of an abusive Bible-thumping alcoholic father who beat him and his mother regularly.  Mack left home at an early age and after spending several years wondering the globe and attending seminary, he settles in the Pacific Northwest with his wife Nan and their five children.  On a weekend camping trip a serial killer abducts Mack’s youngest child, Missy, and takes her to an abandoned shack, where he murders her.  Mack is devastated by the loss, and sinks under “the great sadness.”  All of this back story is recounted in flashback.  The book’s narrative begins four years after Missy’s death, when Mack receives an invitation from “Papa” to visit him at the shack where Missy died.  Mack reluctantly accepts the invitation and travels to the shack where he meets God, who appears to him in three persons, God the Father in the form of a large black woman who invites him to call her “Papa,” God the Son in the form of a Jewish handyman, and God the Holy Spirit in the form of a small Asian woman named Sarayu.  Most of the rest of the book is a dialogue between Mack and these persons, in which Williams explores themes of the problem of evil (what theologians call the “theodicy”), the incarnation, the trinity, free will and determinism, forgiveness and relationships.

I can understand why The Shack has become such a phenomenon.  Williams is a talented story teller, and he weaves his theological discussions into the narrative deftly without allowing the story to get bogged down in dry theory.  Williams treats us to a profound discussion of the problem of evil.  How can a loving God allow such evil to befall His creation?  How can He allow innocents like Missy to suffer so horribly?  Surely He could have prevented Missy’s death, and by not preventing it when he could have done so easily, is He not in a sense responsible for it?  Papa tells Mack that evil is the inevitable result of free will.  God chose to limit Himself by giving man the ability to choose.  Man chose evil, and this has led to immense suffering, even by those who have not yet chosen evil themselves.  At one point Jesus says, “To force my will upon you is exactly what love does not do.”  And at another Papa says, “If I take away the consequences of people’s choices, I destroy the possibility of love.”

God allows evil because He allows love, which requires Him to allow us to choose.  God’ heart breaks at the evil His children have caused, but He will not intervene now in a direct way.  Instead, He will use all things, even man’s evil, to accomplish His purposes in the end, and in the mean time, Papa says, “You’ve just gotta trust my love.”

Here Williams echoes Dostoevsky in Brothers Karamazov.  The atheist, Ivan, spews at his Christian brother Alyosha:   ” Listen! if everyone must suffer, in order to buy eternal harmony with their suffering, pray tell me what have children got to do with it? It’s quite incomprehensible why they should have to suffer, and why they should buy harmony with their suffering.”

The problem of innocent suffering nearly drove Dostoevsky mad, and his Alyosha never attempted to rebut Ivan with a theoretical Christian apologetic; for Dostoevsky knew that all attempts at theodicy are ultimately unsatisfying, and in the end all we can do is confess that in this age we see through a glass darkly, and while we are waiting for the time when we shall see face to face, the best we can do is hope and trust in God’s love demonstrated to us at the Cross.

Williams’s discussion of the incoherence of relativism is spot on.  Sarayu asks Mack “what is good?” and Mack responds with a standard “the good is the desirable and the desirable is what I actually desire” relativist answer.  Sarayu responds that Mack’s standard is no standard at all, because things he once found desirable he no longer desires.  Therefore, if the standard shifts even within Mack, how could it possibly by used to judge among others, and any attempt to use a shifting standard must result in chaos.

Mack asks “Why do I have so much fear in my life?”  God answers:  “Because you don’t believe.”  Truly, if we believe what we say we believe – that we serve the all powerful and loving God who spoke and the universe leapt into existence at the sound of His voice – then why do we fear?

Williams’ discussion of forgiveness is perhaps the best I have ever read.  Forgiveness does not mean forgetting (how can it); nor does it mean that we cannot be angry and hurt at the wrong we have suffered.  Nor is it a once and for all event.  It is a process that begins with the choice to relieve the other from condemnation and judgment (to “take your hand off of their throat” as Williams puts it).  That choice must be followed by successive choices.  Every time the matter is brought to mind we must choose to forgive yet again.  Forgiveness is the choosing of the other, and in that sense it is little different from love.  And forgiveness is powerful.  Williams writes:  “Every time you forgive, the universe changes.”  Indeed.

But for all of its powerful insights and provocative images, at the end of The Shack I was deeply troubled, and I cannot recommend it, because The Shack is rife with error.  Indeed, the error in The Shack is perhaps the most powerful kind of error because it is mixed with powerful truth, which makes the error all the more attractive to the undiscerning.

Before turning to the book’s shortcomings, let me first say a word about a criticism of the book that I do not share.  Some commentators have attacked Williams’ use of the “Papa” metaphor as flippant or even sacrilegious.  This attack is not entirely fair, because Williams is careful to explain that his images of God are strictly metaphorical.   Any attempt to capture the character of God must necessarily be incomplete and metaphorical.  Nevertheless, if the author is able to use the metaphor to express more clearly some aspect of God’s character in a way that helps people understand, then it is a good thing.  There are plenty of reasons to be disturbed by The Shack, but its provocative use of metaphor is not one of them.

Now to the parts of the book I found troubling.

There are numerous technical heresies in the book, which others have documented, and I see no reason to replicate that technical discussion here.  Instead, I will point you to Norman Geisler’s excellent summary here.

Williams’ many doctrinal failures, troubling as they may be, are not, for me at least, the main problem with the book.  The main problem with The Shack it is that it is so completely infused with the zeitgeist, the spirit of our age.  It is no wonder The Shack is so popular.  Far from challenging the biases and preconceptions of our time, Williams panders to and reinforces them.  He tells people what they have been preconditioned to want to hear, and it is little wonder they are lining up in droves to hear it.  Let me give a few examples:

Emasculating God.  In our postmodern age manliness and masculine virtues are under attack.  Far from challenging that bias Williams gives us a feminine, even an emasculated, God.  It is no accident that two of the three images Williams uses for God are women.  Now the metaphor of God as a kindly black woman who bakes scones is not necessarily wrong in itself.  God is kind and tender.  But Williams errs when he suggests that is anything close to a complete picture, that God is only tender and kind.  God is also a consuming fire, powerful beyond our imagining, and fearsome.  When Isaiah encountered God he fell on his face and cried “Woe is me; for I am undone!”  Williams’ effete God is not the God of the Bible.

Anti-Church.  In his website Williams declares that he is not a member of any church.  This is consistent with his statements in The Shack in which he declares that God hates religion and has no use for churches.  This is absurd.  God clearly ordains and establishes the church in Scripture.  Leave it to Williams to suggest that Paul and Augustine and Martin Luther and Charles Wesley all had it wrong, that we need to throw out Scripture and 2,000 years of tradition and do it his way.  The spirit of our age tells us that traditional institutions – including marriage and the church and the family – must be changed to suit our more enlightened preferences.  Williams does not challenge that spirit; he bows to it.

Flirtation with Universalism.  “Inclusiveness” may be the only sacred tenet of postmodernism, and the spirit of our postmodern age simply cannot abide the gospel’s claims of exclusivity.  Jesus said that he is the Way and that no one can approach the Father except through him.  Now Jesus’ claim may be true and it may be false, but one thing it is not is inclusive.  Jesus did not say he is one way or, as Williams puts it, the “best way” to God.  Jesus said he is THE WAY.  “Christian” means literally “little Christ” and by extension a follower of Christ.  Williams’ God, who declares he has no interest in making people into Christians, is not the God of the Bible.

Ranting Against Hierarchy.  Postmodern theorists tell us that all narratives are about power relationships, and Williams keys off of this concept when he says that all hierarchies are evil.  Scripture tells us just the opposite, that God has ordained hierarchy in government, in the church and in the family.

I could multiply examples of Williams’ frothy postmodern platitudes, but you get the point.  Williams is a man of his times and he has no interest in challenging the spirit of his age.  In summary, I believe Geisler’s conclusions are apt and quote them at length here:

The Shack may do well for many in engaging the current culture, but not without compromising Christian truth. The book may be psychologically helpful to many who read it, but it is doctrinally harmful to all who are exposed to it. It has a false understanding of God, the Trinity, the person and work of Christ, the nature of man, the institution of the family and marriage, and the nature of the Gospel. For those not trained in orthodox Christian doctrine, this book is very dangerous. It promises good news for the suffering but undermines the only Good News (the Gospel) about Christ suffering for us. In the final analysis it is only truth that is truly liberating. Jesus said, “You shall know the truth and the truth shall set you free” (John 8:32). A lie may make one feel better, but only until he discovers the truth. This book falls short on many important Christian doctrines. It promises to transform people’s lives, but it lacks the transforming power of the Word of God (Heb. 4:12) and the community of believers (Heb. 10:25)

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But it can’t really be Fake Physics because humans did not evolve to perceive reality

Peter Woit comments at Not Even Wrong on his review (paywall; no paywall) at Wall Street Journal of A Big Bang in a Little Room: The Quest to Create New Universes by Zeeya Merali:

My concern about the topic of the book is that it’s Fake Physics, not that religion is motivating the author (and likely motivating the Templeton Foundation to fund this project). A book about the religious views of physicists would be an interesting one that I’d certainly read, and the material in this book on that topic is quite interesting. One of the odder twists here is that the two blurbs from physicists promoting the book are from Sean Carroll and Martin Rees, with Carroll writing

So you want to make your own universe. Zeeya Merali’s new book won’t quite give you an instruction kit—but it’s the closest thing we have at the moment. A fun and mind-expanding ride through modern ideas of how universes come to be.

I don’t see how you can be devoted to fighting for science against religiously-driven pseudoscience, and think that this book is one you’d like to see be the public face of what “modern ideas” about cosmology are. More.

But what is the solution? If they give up all the nonsense, they must face fine-tuning as a fact. There is no use blaming “religion” or “Templeton” or even the crackpot cosmologists who make a living off fronting weird new stuff.

No, from the point of view of naturalist atheism, the facts are wrong. Worse, a new shipment of authentic facts that supports the multiverse cosmology that would save them seems to be unaccountably delayed in transit (in this universe). And humans here did not evolve to perceive reality anyway.

See also: Multiverse explains why progress in fundamental physics is slow? It’s not a blip actually. It’s a trend toward de-emphasizing fact, evidence, and truth in favour of narrative, spin, and talking points.

Atheist cosmologist warns “deeply religious” people not to put their faith in “apparent” fine-tuning Why are atheists so solicitous about theists who, they fear, will lose their faith? The reality is that the only faith many of us are rapidly losing is in government of science by atheists. Take the unstoppable crises of peer review, for example.

and

Evolution bred a sense of reality out of us

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Multiverse explains why progress in fundamental physics is slow?

Further to “Atheist cosmologist warns “deeply religious” people not to put their faith in “apparent” fine-tuning” (Nature), Columbia mathematician and string theory skeptic Peter Woit (of Not Even Wrong) offers a review at Wall Street Journal of the same book, A Big Bang in a Little Room: The Quest to Create New Universes by Zeeya Merali, “Searching for God at the Centre of the Big Bang,” in which h notes,

…

Mr. Guth was initially fascinated by the idea of baby universes getting produced and making up a multiverse, though he imagined these other universes would all have the same physics as ours. Ms. Merali relates that he quickly lost interest: Why care much about cosmological models producing not just our universe but other copies we can never observe? Over the past 15 years, however, Mr. Linde’s slightly different argument—for a multiverse of universes, each with different physics, has become very popular. Such a multiverse even provides an explanation for the lack of progress in recent decades toward a better understanding of where fundamental laws of physics come from: The laws we observe are just artifacts of where various inflaton fields happened to randomly end up after our Big Bang; in other universes, the laws are different. Ms. Merali gives a disturbing version of this, contemplating the possibility that “string theory and inflation may be conspiring against us in such a way that we may never find evidence for them, and just have to trust in them as an act of faith.”

…

In an era where “post-truth” was the word of the year, scientists and science writers need to make clear that science is not a species of theological or philosophical speculation and not about belief or entertainment value. Legitimate scientific claims are those that can be backed up with evidence, and unfortunately the wonderful and exciting story told well here contains none at all. (paywall; no paywall) More.

It’s not a blip actually. It’s a trend toward de-emphasizing fact, evidence, and truth in favour of narrative, spin, and talking points.

See also: The war on falsifiability in science continues

Atheist cosmologist warns “deeply religious” people not to put their faith in “apparent” fine-tuning Why are atheists so solicitous about theists who, they fear, will lose their faith? The reality is that the only faith many of us are rapidly losing is in government of science by atheists. Take the unstoppable crises of peer review, for example.

2016 as the worst year ever for fake physics

and

Multiverse cosmology at your fingertips

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New evidence for the universe as a hologram?

Big Bang/NASA

From astrophysicist Brian Koberlein at Nautilus:

New Evidence for the Strange Idea that the Universe Is a Hologram

One of the great mysteries of modern cosmology is how our universe can be so thermally uniform—the vast cosmos is filled with the lingering heat of the Big Bang. Over time, it has cooled to a few degrees above absolute zero, but it can still be seen in the faint glow of microwave radiation, known as the cosmic microwave background. In any direction we look, the temperature of this cosmic background is basically the same, varying by only tiny amounts. But according to the standard “cold dark matter” model of cosmology, there wasn’t enough time for hotter and cooler regions of the early universe to even out. Even today we would expect parts of the cosmic background to be much warmer than others, but that isn’t what we observe.

So rapid early inflation, despite lack of direct evidence, is a “widely supported idea.”

What if everything around you, from the distant stars to your very hands, were a hologram? Like Plato’s cave, our world of solid objects and three-dimensional space would simply be a shadow of a two-dimensional reality. On the human scale a holographic universe would be indistinguishable from the reality we expect, but on a cosmic scale there could be subtle differences we might be able to detect.

Flatland.

In their paper, published last month in Physical Review Letters, the team report the holographic model fitting the Planck satellite data slightly better than the standard model. The results don’t prove the universe is holographic, but they are consistent with a holographic model.

But the results could be consistent with a variety of explanations, including unreplicated error. Why, exactly, should their explanation have precedence?

The idea comes from string theory: “Although string theory hasn’t been proven experimentally, its mathematical structure has an elegance and power that makes it appealing as a theoretical model. ”

To say that string theory has not been proven experimentally is to shower it with praise. It is simply a way of sneaking in a variety of non-evidence-based theses like the multiverse.

The fact that both the standard and holographic models can account for early inflation supports the idea that the holographic principle applies to our universe. Cosmic inflation remains a mystery, but by viewing the universe as a hologram we might just be able to solve it. More.

Why? How? There is no pressing reason whatever to consider the holographic model. Whatever Koberlein and others are trying to talk their way around, that causes them to think up this stuff, must be pretty powerful. In this case, it turns the unsupported theory into evidence.

See also: Universe refuses to discuss whether it is a hologram Larger question: Is the reason that a lot of this stuff is classed as “science” the fact that the researchers are playing around with the tools of science? Nothing the matter with that, but it would be good to make the situation clear.

“Substantial evidence” claimed for universe as a hologram: Researchers: “However, this time, the entire universe is encoded!” Encoded? Funny that.

Universe is not a hologram after all?

Oh, not this again… Is the universe a hologram?

We are living in a giant hologram, or a giant trailer filled with poop, or whatever Stephen Hawking says we are living in

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Atheist cosmologist warns “deeply religious” people not to put their faith in “apparent” fine-tuning

In “Physics: A cosmos in the lab,” a review of A Big Bang in a Little Room: The Quest to Create New Universes by Zeeya Merali, cosmologist Andreas Albrecht writes at Nature,

The question of cosmic origins, and the possibility that humans might create new universes, can connect with religious concerns. These form a substantial thread through A Big Bang in a Little Room that significantly reduced the book’s appeal to me. I am an atheist. I respect that many people are deeply religious (some are very close to me) and that religion can have a positive, even beautiful, role. And I know many religious people who do superb science. But I find most attempts to connect religious questions with the fundamental questions of physics and cosmology (or vice versa) deeply unsatisfying.

Does your favourite interpretation of quantum mechanics or apparent fine-tuning of the fundamental constants provide evidence for or against a divine creator? Deeply religious people know better than to leave something so important to them to fads in physics. And when people do engage in these debates, they seem to find a reason to believe what they want to believe, regardless of how the science unfolds.

More.

Rubbish. Fine-tuning is the most obvious fact of the universe and efforts to undermine the evidence for it have driven crackpot cosmology for decades. The crackpots now turn on the very idea of evidence to protect their position.

First, no one cares what Dr. Albrecht finds “deeply unsatisfying”; he can find himself another universe if he likes, and take his fads in physics with him.

Second, “deeply religious people” feel constrained by facts, evidence, and truthfulness, not by the view—attractive to so many Darwinian atheists—that “evolution” bred a sense of reality out of us.

The choice matters to science and we fear we know which one most of them have made.

By the way, why are atheists so solicitous about theists who, they fear, will lose their faith? The reality is that the only faith many of us are rapidly losing is in government of science by atheists. Take the unstoppable crises of peer review, for example.

Why are we better off with science’s affairs run by people who believe that if they win they survive and that none of us evolved so as to grasp reality anyway?

Note: We confess we don’t know why all this sounds like BioLogos on steroids either.

See also: Evolution bred a sense of reality out of us

Ethan Siegel tackles fine-tuning at Forbes

and

Copernicus, you are not going to believe who is using your name. Or how.

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One Small Step Sideways, Two Huge Steps Back

Recently a new paper by Richard Lenski and colleagues (Meyer et al 2012) appeared in Science ( http://www.sciencemag.org/content/335/6067/428.short ) with, as usual, commentary in the New York Times. ( http://tinyurl.com/7xthu7q ) (Lenski's lab must own a red phone with a direct line to The Gray Lady.) The gist of the paper is that a certain bacteriophage (a virus that infects bacteria) called "lambda" gained the ability to bind a different protein on the surface of its host, the bacterium E. coli, than the protein it usually binds. The virus has to bind to the cell's surface as a prelude to invading it. The protein it normally binds is called LamB. Lenski's lab, however, used a bacterial strain that had turned off the production of LamB in 99% of E. coli cells but, crucially, 1% of cells still produced the protein. Thus the virus could still invade some cells, reproduce, and not go extinct. Under these conditions the viral binding protein (called "J") underwent several mutations, apparently to better bind LamB in the fewer cells that produced it. Then, surprisingly, after the viral gene gained a fourth mutation, the viral J protein acquired the ability to bind a different protein on E. coli, called OmpF. Now the virus could use OmpF as a platform for invading the cell. Since all cells made OmpF, the virus was no longer restricted to invading just the 1% of cells that made LamB, and it prospered. The workers repeated the experiment multiple times, and frequently got the same results.

As always, the work of the Lenski lab is solid and interesting, but is spun like a top to make it appear to support Darwinian evolution more than it does. As the authors acknowledge, this is certainly not the first time a lab has evolved a virus to grow on a different strain of host. In a recent review (Behe 2010) ( http://tinyurl.com/25c422s ) there is a section entitled "Evolution Experiments with Viruses: Adapting to a New Host" discussing just that topic. In general, viruses have been shown to be able to adapt to bind to related host cells which have similar surface features. In almost all cases the virus uses the same binding protein, and the same (mutated) binding site to attach to the new host cell. This seems to also be the case with Lenski's new work. As stated above, the first several mutations apparently strengthen the ability of the J protein to bind to the original site, LamB, while the fourth mutation allows it to bind to OmpF. As the authors state, however, the mutated viral J protein can still bind to the original protein, LamB, which strongly suggests the same binding site (that is, the same location on the J protein) is being used. It turns out that both LamB and OmpF have similar three-dimensional structures, so that strengthening the binding to one fortuitously led to binding to the other. In my review (Behe 2010) I discussed why this should be considered a "modification of function" event rather than a gain-of-function one. The bottom line is that the results are interesting and well done, but not particularly novel, nor particularly significant.

To me, the much more significant results of the new paper, although briefly mentioned, were not stressed as they deserved to be. The virus was not the only microbe evolving in the lab. The E. coli also underwent several mutations. Unlike for lambda, these were not modification-of-function mutations — they were complete loss-of-function mutations. The mechanism the bacterium used to turn off LamB in 99% of cells to resist initial lambda infection was to mutate to destroy its own gene locus called malT, which is normally useful to the cell. After acquiring the fourth mutation the virus could potentially invade and kill all cells. However, E. coli itself then mutated to prevent this, too. It mutated by destroying some genes involved in importing the sugar mannose into the bacterium. It turns out that this "mannose permease" is used by the virus to enter the interior of the cell. In its absence, infection cannot proceed.

So at the end of the day there was left the mutated bacteriophage lambda, still incompetent to invade most E. coli cells, plus mutated E. coli, now with broken genes which remove its ability to metabolize maltose and mannose. It seems Darwinian evolution took a little step sideways and two big steps backwards.

Literature Cited

Behe, M. J., 2010 Experimental Evolution, Loss-of-function Mutations, and "The First Rule of Adaptive Evolution". Quarterly Review of Biology 85: 1-27.

Meyer, J. R., D. T. Dobias, J. S. Weitz, J. E. Barrick, R. T. Quick et al. 2012 Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335: 428-432.

More Darwinian Degradation

Recently a paper appeared by Ratcliff et al. (2012) entitled "Experimental evolution of mulitcellularity" and received a fair amount of press attention, including a story in the New York Times. ( http://tinyurl.com/6va4fpp ) The authors discuss their results in terms of the origin of multicellularity on earth. The senior author of the paper is Michael Travisano of the University of Minnesota, who was a student of Richard Lenski's in the 1990s. The paper, published in PNAS, was edited by Lenski. The gist is as follows. The authors repeated three steps multiple times: 1) they grew single-celled yeast in a flask; 2) briefly centrifuged it; and 3) took a small amount from the bottom of the flask to seed a new culture. This selected for cells that sedimented faster than most. After a number of rounds of selection the cells sedimented much faster than the beginning cells. Examination showed that the fast-sedimenting cells formed clusters due to incomplete separation of replicating mother-daughter cells. The cell clusters also were 10% less fit (that's quite an amount) than the beginning cells in the absence of the sedimentation selection. After further selection it was seen that some cells in clusters would "commit suicide" (apoptosis), which apparently made the clusters more brittle and allowed chunks to break off and form new clusters. (The beginning cells already had the ability to undergo apoptosis.)

It seems to me that Richard Lenski, who knows how to get the most publicity out of exceedingly modest laboratory results, has taught his student well. In fact, the results can be regarded as the loss of two pre-existing abilities: 1) the loss of the ability to separate from the mother cell during cell division; and 2) the loss of control of apoptosis. The authors did not analyze the genetic changes that occurred in the cells, but I strongly suspect that if and when they do, they'll discover that functioning genes or regulatory regions were broken or degraded. This would be just one more example of evolution by loss of pre-existing systems, at which we already knew that Darwinian processes excel. The apparently insurmountable problem for Darwinism is to build new systems.

Literature Cited

Ratcliff, W. C., R. F. Denison, M. Borrello, and M. Travisano, 2012 Experimental evolution of multicellularity. Proc. Natl. Acad. Sci. USA doi/10.1073/pnas.1115323109

A Blind Man Carrying a Legless Man Can Safely Cross the Street

I never thought it would happen but, in my estimation, Richard Lenski has acquired a challenger for the title of "Best Experimental Evolutionary Scientist." Lenski, of course, is the well-known fellow who has been growing E. coli in his lab at Michigan State for 50,000 generations in order to follow its evolutionary progress. His rival is Joseph Thornton of the University of Oregon who, by inferring the sequences of ancient proteins and then constructing (he calls it "resurrecting") their genes in his lab, is able to characterize the properties of the ancestral proteins and discern how they may have evolved into more modern versions with different properties.

I have written appreciatively about both Lenski and Thornton before, whose work indicates clear limits to Darwinian evolution (although they themselves operate within a Darwinian framework). Thornton's latest work is beginning to show a convergence with Lenski's that greatly boosts our confidence that they both are on the right track. In a recent review (Behe, 2010) I pointed out that all characterized advantageous mutations that Richard Lenski has observed in his twenty-year experiment have turned out to be degradative ones — ones in which a gene or genetic control structure was either destroyed or rendered less effective. (Random mutation is superb at degrading genetic material, which sometimes is helpful to an organism.) In his latest work Thornton, too, shows evolution of a system by degradation, although he speculates that the changes were neutral rather than advantageous.

In Finnegan et al (2012), "Evolution of increased complexity in a molecular machine", Thornton and colleagues study a ring of six proteins in a molecular machine (that also has many other parts) called a V-ATPase, which can pump protons (acid) across a membrane. The machine exists in all eukaryotes. In most eukaryotic species, however, the hexameric ring consists of five copies of one protein (let's call it protein 1) and one copy of another, related protein (call it protein 2). In fungi, however, the ring consists of four copies of protein 1, one copy of protein 2, and one copy of protein 3. Protein 3 is very similar in sequence to protein 1, so Finnegan et al (2012) propose that proteins 1 & 3 are related by duplication of an ancestral gene and subsequent modification of the two, originally-identical duplicated genes.

How did protein 3 insinuate itself into the ring? The original protein 1, present in five copies in most organisms, already had the ability to bind to itself, plus an ability to bind to one side of protein 2, plus a separate ability to bind to the opposite side of protein 2 (see Finnegan et al's Figure 3). Thornton's results are consistent with the idea that, by happenstance, the gene for protein 1 duplicated and spread in the population. (These events apparently were neutral, the authors think, not affecting the organism's fitness.) Eventually one of the duplicates acquired a degradative mutation, losing the ability to bind one side of protein 2. This was not a problem because the second copy of the protein 1 gene was intact, and could bind both sides of protein 2, so a complete ring could still be formed. This also spread by neutral processes. As luck might have it, the second gene copy subsequently acquired its own degradative mutation, so that it could no longer bind the other side of protein 2. Again it's no problem, however, because the first mutant copy of protein 1 could bind to the first side of protein 2, bind a few more copies of itself, then bind a copy of protein 3, which still had the ability to bind the other side of protein 2. So a closed, six-member ring could still be formed. This apparently also spread by neutral processes until it took over the entire kingdom of fungi.

The work of Finnegan et al (2012) strikes me as quite thorough and elegant. I have no reason to doubt that events could have unfolded that way. However, the implications of the work for unguided evolution appear very different to me then they've been spun in media reports. ( http://tinyurl.com/7lawgpl ) The most glaringly obvious point is that, like the results of Lenski's work, this is evolution by degradation. All of the functional parts of the system were already in place before random mutation began to degrade them. Thus it is of no help to Darwinists, who require a mechanism that will construct new, functional systems. What's more, unlike Lenski's results, the mutated system of Thornton and colleagues is not even advantageous; it is neutral, according to the authors. Perhaps sensing the disappointment for Darwinism in the results, the title of the paper and news reports emphasize that the "complexity" of the system has increased. But increased complexity by itself is no help to life — rather, life requires functional complexity. One can say, if one wishes, that a congenitally blind man  teaming up with a congenitally legless man to safely move around the environment is an increase in "complexity" over a sighted, ambulatory person. But it certainly is no improvement, nor does it give the slightest clue how vision and locomotion arose.

Finnegan et al's (2012) work intersects with several other concepts. First, their work is a perfect example of  Michael Lynch's idea of "subfunctionalization", where a gene with several functions duplicates, and each duplicate loses a separate function of the original. (Force et al, 1999) Again, however, the question of how the multiple functions arose in the first place is begged. Second, it intersects somewhat with the recent paper by Austin Hughes (2011) in which he proposes a non-selective mechanism of evolution abbreviated "PRM" (plasticity-relaxation-mutation), where a "plastic" organism able to survive in many environments settles down in one and loses by degradative mutation and drift the primordial plasticity. But again, where did those primordial functions come from? It seems like some notable workers are converging on the idea that the information for life was all present at the beginning, and life diversifies by losing pieces of that information. That concept is quite compatible with intelligent design. Not so much with Darwinism.

Finally, Thornton and colleagues latest work points to strong limits on the sort of neutral evolution that their own work envisions. The steps needed for the scenario proposed by  Finnegan et al (2012) are few and simple: 1) a gene duplication; 2) a point mutation; 3) a second point mutation. No event is deleterious. Each event spreads in the population by neutral drift. Notice that the two point mutations do not have to happen together. They are independent, and can happen in either order. Nonetheless, this scenario is apparently exceedingly rare. It seems to have happened a total of one (that is, 1) time in the billion years since the divergence of fungi from other eukaryotes. It happened only once in the fungi, and a total of zero times in the other eukaryotic branches of life. If the scenario were in fact as easy to achieve in nature as it is to describe in writing, we should expect it to have happened many times independently in fungi and also to have happened in all other branches of eukaryotes.

It didn't. Thus it seems a good conclusion that such neutral scenarios are much rarer than some workers have proposed (Gray et al, 2010; Lukes et al, 2011), and that more complex neutral scenarios are unlikely to happen in the history of life.

Literature Cited

Behe, M. J., 2010 Experimental Evolution, Loss-of-function Mutations, and "The First Rule of Adaptive Evolution". Quarterly Review of Biology 85: 1-27.

Finnigan, G. C., V. Hanson-Smith, T. H. Stevens, and J. W. Thornton, 2012 Evolution of increased complexity in a molecular machine. Nature doi: 10.1038/nature10724.

Force, A., M. Lynch, F. B. Pickett, A. Amores, Y. L. Yan et al. 1999 Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.

Gray, M. W., J. Lukes, J. M. Archibald, P. J. Keeling, and W. F. Doolittle, 2010 Irremediable complexity? Science 330: 920-921.

Hughes, A. L., 2011 Evolution of adaptive phenotypic traits without positive Darwinian selection. Heredity (Edinb.) doi: 10.1038/hdy.2011.97.

Lukes, J., J. M. Archibald, P. J. Keeling, W. F. Doolittle, and M. W. Gray, 2011 How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 63: 528-537.

New Work by Thornton's Group Supports Time-Symmetric Dollo's Law

In the June 2011 issue of PLOS Genetics the laboratory of University of Oregon evolutionary biologist Joseph Thornton published ( http://tinyurl.com/3dsorzm ) "Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor", the latest in their series of papers concerning the evolution of proteins that bind steroid hormones. (Carroll et al, 2011) In earlier laboratory work ( http://tinyurl.com/3hevjzy ) they had concluded that a particular protein, which they argued had descended from an ancestral, duplicated gene, would very likely be unable to evolve back to the original ancestral protein, even if selection favored it. (Bridgham et al, 2009) The reason is that the descendant protein had acquired a number of mutations which would have to be reversed, mutations which, the authors deduced, would confer no benefit on the intermediate protein. They used these results to argue for a molecular version of "Dollo's Law", which says roughly that a given forward evolutionary pathway is very unlikely to be exactly reversed.

In my comments on this interesting work ( http://tinyurl.com/3cjm4gr ), I noted that there is nothing time-asymmetric about random mutation/natural selection, so that the problem they saw in reversing the steroid hormone receptor evolution did not have to be in the past — it could just as easily have been in the future. The reason is that natural selection hones a protein to its present job, with regard to neither future use nor past function. Thus, based on Thornton's work, one would not in general expect a protein that had been selected for one function to be easily modified by RM/NS to another function. I have decided to call this the Time-Symmetric Dollo's Law, or "TSDL".

But if there is such a thing as a TSDL, did the forward evolution of the steroid-hormone protein-receptor manage to avoid it? That question had not yet been addressed. Was the protein lucky this time, and encountered no obstacles to its evolution from the ancestral state to the modern state? If so, then maybe TSDL is occasionally an obstacle, but not so often as to rule out modest Darwinian evolution of proteins (as I had thought before reading Thornton's earlier work).

Well, thanks to the Thornton group's new work ( http://tinyurl.com/3dsorzm ), we can now see that there are indeed obstacles to the forward evolution of the ancestral protein. The group was interested in which of the many sequence changes between the ancestral and derived-modern protein were important to its change in activity, which consisted mostly of a considerable weakening of the protein's ability to bind its steroid ligands. They narrowed the candidates down to two amino acid positions, residues 43 and 116. Each of the changes at those sites decreased binding by over a hundred-fold. However, when the researchers combined both mutations into a single protein, as occurs in the modern protein, binding was not only decreased — it was for all intents and purposes abolished. Upon further research the group showed that a third mutation, at position 71, was necessary to ameliorate the effects of the combination of the other two mutations, bringing them back to hundreds-fold loss of function rather than essentially-complete loss of function.

Carroll et al (2011) conjecture that the mutation at position 71 occurred before the other two mutations, but that it had no effect on the activity of the ancestral protein. So let us count the ways, then, in which "fortune" favored the evolution of the modern protein. First, an ancestral gene duplicated, which would usually be considered a neutral event. Thus it would not have the assistance of natural selection to help it spread in the population. Next, it avoided hundreds of possible mutations which would have rendered the duplicated gene inactive. Third, it acquired a neutral mutation at position 71. Thus, again, this mutation would have to spread by drift, without the aid of natural selection. Once more, the still-neutral gene manages to avoid all of the possible mutations that would have inactivated it. Next, it acquires the correct mutation (either at position 43 or 116) which finally differentiates it from its parent gene — by reducing its activity a hundred-fold! Finally, somehow the wimpy, mutated gene (putatively) confers upon the lucky organism some likely-quite-weak selective advantage.

The need for passage through multiple neutral steps plus the avoidance of multiple likely-deleterious steps to produce a protein that has lost 99% of its activity is not a ringing example of the power of Darwinian processes. Rather, as mentioned above, it shows the strength of TSDL. Darwinian selection will fit a protein to its current task as tightly as it can. In the process, it makes it extremely difficult to adapt to a new task or revert to an old task by random mutation plus selection.

Dollo's law holds going forward as well as backward. We can state the experimentally based law simply: "Any evolutionary pathway from one functional state to another is unlikely to be traversed by random mutation and natural selection. The more the functional states differ, the much-less likely that a traversable pathway exists."

1. Carroll, S. M., E. A. Ortlund, and J. W. Thornton, 2011 Mechanisms for the evolution of a derived function in the ancestral glucocorticoid receptor. PloS. Genet. 7: e1002117.

2. Bridgham, J. T., E. A. Ortlund, and J. W. Thornton, 2009 An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461: 515-519.