On the edge.

So, Michael Behe Was Right After All; What Will the Critics Say Now?

Casey Luskin July 16, 2014 1:30 PM

 

 

 

A new paper in Proceedings of the National Academy of Sciences USA has vindicated Michael Behe in one of the central controversies over his 2007 book The Edge of Evolution. Behe already reported here on the paper, which found that multiple mutations, at least two, are required to confer resistance to the drug chloroquine on malaria parasites:

A minimum of two mutations sufficed for (low) CQ transport activity, and as few as four conferred full activity. ... The findings presented here reveal that the minimum requirement for (low) CQ transport activity in both the ET and TD lineages of CQR PfCRT is two mutations.

(Summers et al., "Diverse mutational pathways converge on saturable chloroquine transport via the malaria parasite's chloroquine resistance transporter," Proceedings of the National Academy of Sciences USA, Vol. 111: E1759-E1767 (April 29, 2014) (emphasis added).)

Why does it matter? As Dr. Behe explained, this was a major point of contention among critics of his book. They claimed that Behe mistakenly thought chloroquine resistance required multiple simultaneous mutations, when in actuality it could arise through sequential mutations, each conferring a successively greater resistance-advantage. It can no longer be denied that the critics were dead wrong: chloroquine resistance does not arise at all until two mutations or more are present.

(To be precise, the paper found that the two minimum mutations break down as follows: one specific mutation is needed, plus a second mutation that's also needed which can occur in one of two locations. As the paper puts it, "Given that all known PfCRT haplotypes contain either N75E/D or N326D, these results indicate that PfCRT acquires the ability to transport CQ via one of two main mutational routes, both of which entail the introduction of K76T plus the replacement of an asparagine (N75 or N326) with an acidic residue.")

From the Beginning, the Critics Mischaracterized Behe

The critics were wrong from the outset. Behe's argument in The Edge of Evolution didn't depend on whether chloroquine resistance arose in a stepwise manner, or only after multiple mutations accumulated. His argument was based upon an empirically observed data point from public health studies which found that chloroquine resistance arose in about 1 in every 10²⁰ organisms. He had a strong citation for this empirical observation: Nicholas White, "Antimalarial Drug Resistance," Journal of Clinical Investigation, Vol. 113: 1084-1092 (2004). He called the mutations (whatever they were) that caused chloroquine resistance a "chloroquine complexity cluster" or CCC. Whatever molecular mechanisms may be behind a CCC, empirical data showed that 10²⁰ cells are required in order to produce one. Behe pointed out that if a trait required the molecular equivalent of two CCC's before providing any advantage, then that would pose major problems for Darwinian evolution.

It's a simple calculation. Behe observed that if 10²⁰ organisms were required to obtain one CCC, then the square of that amount -- 10⁴⁰ organisms -- would be required to evolve a trait that required two CCC's before providing any advantage. However, as Behe observed, a total of only 10⁴⁰ organisms have lived on Earth over the entire history of the planet. As Behe put it:

Recall that the odds against getting two necessary, independent mutations are the multiplied odds for getting each mutation individually. What if a problem arose that required a cluster of mutations that was twice as complicated as a CCC? (Let's call it a double CCC.) For example, what if instead of the several amino acid changes needed for chloroquine resistance in malaria, twice that number were needed? In that case the odds would be that for a CCC times itself. Instead of 10²⁰ cells to solve the evolutionary problem, we would need 10⁴⁰ cells. Workers at the University of Georgia have estimated that about a billion billion trillion (10³⁰) bacterial cells are formed on the earth each and every year. ... If that number has been the same over the entire several-billion-year history of the world, then throughout the course of history there would have been slightly fewer than 10⁴⁰ cells, a bit less than we'd expect to need to get a double CCC. The conclusion, then, is that the odds are slightly against even one double CCC showing up by Darwinian processes in the entire course of life on earth.

(Michael Behe, The Edge of Evolution: The Search for the Limits of Darwinism, p. 135 (Free Press, 2007).)

Behe inferred, based upon the great rarity of a CCC evolving, that it was a trait that probably required multiple mutations. Behe's argument didn't turn on that inference, but it was a reasonable one. Richard Dawkins himself used exactly the same sort of reasoning in other contexts to infer that a trait required multiple mutations to evolve.

Will Ken Miller, Jerry Coyne, Paul Gross, Nick Matzke, Sean Carroll, Richard Dawkins, and PZ Myers Now Apologize to Michael Behe?

Behe's critics misread him as saying that a single CCC necessarily required multiple simultaneous mutations, and castigated Behe for allegedly ignoring the possibility of a single CCC arising via sequential mutations. For example:

• Kenneth Miller: "It would be difficult to imagine a more breathtaking abuse of statistical genetics. Behe obtains his probabilities by considering each mutation as an independent event, ruling out any role for cumulative selection, and requiring evolution to achieve an exact, predetermined result." (Nature, 2007)
• Paul Gross: "Behe assumes simultaneous mutations at two sites in the relevant gene, but there is no such necessity and plenty of evidence that cumulativeness, rather than simultaneity, is the rule. As Nature's reviewer (Kenneth R. Miller) notes, 'It would be difficult to imagine a more breathtaking abuse of statistical genetics.'" (The New Criterion, 2007)


• Jerry Coyne: "Behe requires all of the three or four mutations needed to create such an interaction to arise simultaneously. ... If it looks impossible, this is only because of Behe's bizarre and unrealistic assumption that for a protein-protein interaction to evolve, all mutations must occur simultaneously, because the step-by-step path is not adaptive." (The New Republic, 2007)


• Nick Matzke: "Here is the flabbergasting line of argument. First, Behe admits that CQR evolves naturally, but contends that it requires a highly improbable simultaneous double mutation, occurring in only 1 in 10²⁰ parasites. ... The argument collapses at every step." (Trends In Ecology and Evolution, 2007)


• Sean Carroll: "Behe's main argument rests on the assertion that two or more simultaneous mutations are required for increases in biochemical complexity and that such changes are, except in rare circumstances, beyond the limit of evolution. .. Examples of cumulative selection changing multiple sites in evolving proteins include ... pyrimethamine resistance in malarial parasites (6) -- a notable omission given Behe's extensive discussion of malarial drug resistance. (Science, 2007)


• Richard Dawkins: "If correct, Behe's calculations would at a stroke confound generations of mathematical geneticists, who have repeatedly shown that evolutionary rates are not limited by mutation." (New York Times, 2007)


• And then of course there's PZ Myers. He made much the same criticisms, and also wrote:

  Behe isn't just a crackpot who thinks he has a novel explanation for an evolutionary mechanism -- he's a radical anti-evolutionist extremist who rejects the entire notion of the transformation of species by natural processes. ... Most of the arguments are gussied up versions of the kind of handwaving, ignorant rationalizations you'd get from some pomaded fundagelical Baptist minister who got all his biology from the Bible, not at all what you'd expect from a tenured professor of biochemistry at a good university -- throwing in an occasional technical gloss or mangled anecdote from the literature is only a gloss to fool the rubes.

All these critics were wrong. You get no resistance to chloroquine whatsoever unless at least two mutations are present to begin with. You might be able to get some cumulative selection after that, where successive mutations improve resistance up to a certain point. It is, however, by definition a multimutation feature.

Behe reasonably inferred that chloroquine resistance requires multiple mutations. He was right. His critics misunderstood his argument and thought this inference was a crucial plank in his reasoning. It wasn't. But it now turns out that the position Behe's critics attributed to him, and then railed against, was itself correct. Even a single CCC apparently requires multiple mutations before conferring any advantage. In fact, it's probably very close to the "edge" of evolution that Behe identified in his book.

Is an apology from Behe's critics then forthcoming? In a world where debates were conducted with the goal of discovering truth rather scoring points, it sure ought to be. Unfortunately, I'm not sure we live in that world.

What we'll probably get is nothing more than PZ Myers's concession, offered in the context of the rant quoted above:

Fair enough; if you demand a very specific pair of amino acid changes in specific places in a specific protein, I agree, the odds are going to be very long on theoretical considerations alone, and the empirical evidence supports the claim of improbability for that specific combination.

Well, that's more or less what's required to generate chloroquine resistance. We'll gladly take this -- i.e., simply being proven right -- in lieu of an apology.

Urged to keep faith in the new gods.

Darwin Defenders Love Donald Prothero's Ranting Review of Darwin's Doubt

Casey Luskin July 23, 2013 5:29 PM

 

 

 

Since Nick Matzke at Panda's Thumb published a review of Darwin's Doubt that badly failed to preemptively knock down Stephen Meyer's thesis (see here, here, here, and here), the Internet's Darwin brigade has been hoping for something better. So the folks at Panda's Thumb along with Larry Moran and Jerry Coyne are all excited that geologist Donald Prothero has now posted an Amazon review of Darwin's Doubt. Their readers have eagerly voted up Prothero's post, artfully titled "Stephen Meyer's Fumbling Bumbling Cambrian Amateur Follies," as the "most helpful critical review."

According to Dr. Prothero, Darwin's Doubt is a mess of "fumbling," "bumbling," "distortions," and "blunders." The book is an "amateur" exercise, evidence of Meyer's "folly." It "butchers" the subject matter; was written by a "fool" who is "incompetent," guilty of "ignorance," is in "way over his head" and has a "completely false understanding of the subject." In case that's all a little too subtle for you, Prothero says Meyer argues "dishonestly" and promotes a "flat out lie," a "fundamental lie," and other "lies" to promote a "fairy tale."

Well, what justifies all the ad hominem invectives? Prothero's first complaint is that Meyer's Ph.D. is in the history and philosophy of science which, according to Prothero "give[s] him absolutely no background to talk about molecular evolution." Yes that's a lame objection (it's called the genetic fallacy). Indeed, Meyer's undergraduate degree is in geology and physics, and he worked as a geophysicist for four years, giving him formal training on geology-related issues -- the primary issues Prothero raises in his review. Prothero, however, has already undercut his own complaint, as he admitted:

[Y]ou don't need a Ph.D. to do good science, and not all people who have Ph.D.s are good scientists either. As those of us who have gone through the ordeal know, a Ph.D. only proves that you can survive a grueling test of endurance in doing research and writing a dissertation on a very narrow topic. It doesn't prove that you are smarter than anyone else or more qualified to render an opinion than anyone else. (Evolution: What the Fossils Say and Why It Matters, p. 16)

Prothero's review later complains that creationists "love to flaunt their Ph.D.'s on their book covers." I guess that means Meyer isn't a "creationist," since Prothero failed to notice that Meyer doesn't mention his Ph.D. on the cover of Darwin's Doubt. (And isn't it a bit ironic that Prothero touts his own Ph.D. in his bio over at Skepticblog?)

In any case, Prothero's second complaint is that "Almost every page of this book is riddled by errors of fact or interpretation that could only result from someone writing in a subject way over his head, abetted by the creationist tendency to pluck facts out of context and get their meaning completely backwards." Of course Prothero doesn't list examples from "almost every page," but at least this time he tries to give one. He claims "we now know that the 'explosion' now takes place over an 80 m.y. time framework." Perhaps Prothero didn't notice that Meyer specifically discusses Prothero's own view on this in Darwin's Doubt, and refutes it (see Chapter 3). I refuted the same argument in my recent response to Nick Matzke, which cited numerous articles from the mainstream technical literature stating that the Cambrian explosion took no more than 10 million years.

Prothero's review goes on.

• He states that Meyer "dismisses the Ediacara fauna as not clearly related to living phyla," even though that's in fact the consensus view (see pp. 81-86, and accompanying endnotes).
• He charges that Meyer "confuses crown-groups with stem-groups" (giving no examples), when in fact Meyer explains this distinction (see pp. 419-420).
• He wrongly charges that ID is a "god of the gaps" argument, one that invokes the "supernatural," when of course ID does no such thing, and Meyer rebuts this charge decisively in chapters 17 and 19 of Signature in the Cell.
• He bizarrely misrepresents Meyer as saying Niles Eldredge and Stephen Jay Gould "are arguing that evolution doesn't occur" when Meyer said absolutely nothing of the kind.

Thus, a pattern in Prothero's review is that he puts words in Meyer's mouth, while failing to engage Meyer's actual arguments. As another example, Prothero writes:

Meyer deliberately and dishonestly distorts the story by implying that these soft-bodied animals appeared all at once, when he knows that this is an artifact of preservation. It's just an accident that there are no extraordinary soft-bodied faunas preserved before Chengjiang, so we simply have no fossils demonstrating their true first appearance, which occurred much earlier based on molecular evidence.

Of course Meyer never says the Cambrian animals appeared "all at once." And did Prothero miss Chapter 5 of Darwin's Doubt, where Meyer discusses in great detail the "molecular evidence" mentioned by Prothero, meticulously critiques the molecular clock hypothesis, and clarifies why it doesn't account for the absence of evolutionary precursors in the Precambrian? Or what about Chapters 2 and 3, where Meyer explores the artifact hypothesis in much detail, and makes clear why many Cambrian experts feel it doesn't explain away the Cambrian explosion? As Meyer observes, the Cambrian fossil record is full of soft-bodied organisms, making it difficult to argue that the lack of fossils from a particular group simply means they were too "soft-bodied" to have been preserved (see pp. 62-64). So it's not as if Meyer doesn't engage and discuss these objections in great detail; indeed Meyer cites many authorities to show why these objections don't resolve the Cambrian explosion. Prothero complains a lot, but neither engages with nor mentions any of these discussions.

Prothero asserts that the "rates of evolution during the 'Cambrian explosion' are typical of any adaptive radiation in life's history." Again, did he not read Section II of Darwin's Doubt where Meyer argues that even if there were tens of millions of years available to evolve the Cambrian animals (as Prothero asserts), unguided evolutionary mechanisms still don't work fast enough to produce many of their complex features?

Prothero gives no indication that he has appreciated this section. Indeed his only specific objection is that Meyer supposedly "repeats many of the other classic creationist myths, all long debunked, including the post hoc argument from probability (you can't make the argument that something is unlikely after the fact)." This is a bizarre claim. Does Prothero not realize that many arguments for common ancestry are after-the-fact and probability-based -- e.g., two similar gene sequences are unlikely to have arisen independently, and are thus said to have derived from a common ancestor?

My favorite part of Prothero's review comes when he says, "For a good account by real paleontologists who know what they're doing, see the excellent recent book by Valentine and Erwin, 2013, which gives an accurate view of the 'Cambrian diversification'." Excellent indeed! Prothero is referring to Douglas Erwin and James Valentine's 2013 book, The Cambrian Explosion. Let's look once again at what Erwin and Valentine have to say.

Regarding the length of the Cambrian explosion, they write:

[A] great variety and abundance of animal fossils appear in deposits dating from a geologically brief interval between about 530 to 520 Ma, early in the Cambrian period. During this time, nearly all the major living animal groups (phyla) that have skeletons first appeared as fossils (at least one appeared earlier). Surprisingly, a number of those localities have yielded fossils that preserve details of complex organs at the tissue level, such as eyes, guts, and appendages. In addition, several groups that were entirely soft-bodied and thus could be preserved only under unusual circumstances also first appear in those faunas. Because many of those fossils represent complex groups such as vertebrates (the subgroup of the phylum Chordata to which humans belong) and arthropods, it seems likely that all or nearly all the major phylum-level groups of living animals, including many small soft-bodied groups that we do not actually find as fossils, had appeared by the end of the early Cambrian. This geologically abrupt and spectacular record of early animal life is called the Cambrian explosion. (The Cambrian Explosion, p. 5, emphases added)

So it seems that unlike Prothero, Erwin and Valentine don't believe "the Cambrian explosion" took 80 million years, but rather that it took place during "a geologically brief interval between about 530 to 520 Ma."

Regarding the reality of the Cambrian explosion, Erwin and Valentine write:

Taken at face value, the geologically abrupt appearance of Cambrian faunas with exceptional preservation suggested the possibility that they represented a singular burst of evolution, but the processes and mechanisms were elusive. Although there is truth to some of the objections, they have not diminished the magnitude or importance of the explosion. ... Several lines of evidence are consistent with the reality of the Cambrian explosion. (The Cambrian Explosion, p. 6, emphases added)

So it seems, contra Prothero, that Valentine and Erwin don't believe the Cambrian explosion is merely an "artifact of preservation."

Regarding rates of evolution during the Cambrian explosion, Erwin and Valentine write:

As geologists, we view this tension as a debate over the extent to which uniformitarian explanations can be applied to understand the Cambrian explosion. Uniformitarianism is often described as the concept, most forcefully advocated by Charles Lyell in his Principles of Geology, that "the present is the key to the past" (Lyell 1830). Lyell argued that study of geological processes operating today provides the most scientific approach to understanding past geological events. Uniformitarianism has two components. Methodological uniformitarianism is simply the uncontroversial assumption that scientific laws are invariant through time and space. This concept is so fundamental to all sciences that it generally goes unremarked. Lyell, though, also made a further claim about substantive uniformitarianism: that the rates and processes of geological change have been invariant through time (Gould 1965). Few of Lyell's contemporaries agreed with him (Rudwick 2008). Today, geologists recognize that the rates of geological processes have varied considerably through the history of Earth and that many processes have operated in the past that may not be readily studied today.

...One important concern has been whether the microevolutionary patterns commonly studied in modern organisms by evolutionary biologists are sufficient to understand and explain the events of the Cambrian or whether evolutionary theory needs to be expanded to include a more diverse set of macroevolutionary processes. We strongly hold to the latter position. (The Cambrian Explosion, p. 10, emphases added)

In other words, Erwin and Valentine are skeptical that "uniformitarian explanations can be applied to understand the Cambrian explosion." Why? One reason could be because evolutionary mechanisms we observe in the present day operate at rates that are too slow to explain what took place in the Cambrian period. They are careful not to put it in such plain terms, but that is the essence of their argument. But they do acknowledge that there was an "unusual period of evolutionary activity during the early and middle Cambrian" (p. 6) and later expressly state:

Because the Cambrian explosion involved a significant number of separate lineages, achieving remarkable morphological breadth over millions of years, the Cambrian explosion can be considered an adaptive radiation only by stretching the term beyond all recognition. ... the scale of morphological divergence is wholly incommensurate with that seen in other adaptive radiations. (The Cambrian Explosion, p. 341, emphasis added)

In other words, unlike Prothero, Erwin and Valentine think the Cambrian explosion was a real event, took far less than 80 million years, and involved unique mechanisms that acted more rapidly and at a greater scale than other radiations. These directly contradict Prothero's core claims, but there's more.

Probably the most striking statement by Erwin and Valentine comes when they concede that we lack resolved evolutionary explanations for how the diversity of the Cambrian animals arose, and why these basic body plans haven't changed since that time:

The patterns of disparity observed during the Cambrian pose two unresolved questions. First, what evolutionary process produced the gaps between the morphologies of major clades? Second, why have the morphological boundaries of these body plans remained relatively stable over the past half a billion years? (The Cambrian Explosion, p. 330, emphasis added)

Thus, when recently reviewing Erwin and Valentine's book, the journal Science stated: "The grand puzzle of the Cambrian explosion surely must rank as one of the most important outstanding mysteries in evolutionary biology." Likewise, a 2009 paper in BioEssays stated, "elucidating the materialistic basis of the Cambrian explosion has become more elusive, not less, the more we know about the event itself."

That pretty much nixes Prothero's confident, unbacked assertion that "scientists have explained most of the events of the Early Cambrian and find nothing out of the ordinary that defies scientific explanation."

What more is there to say? I wonder who in the community of Darwin-defenders will have a go at Darwin's Doubt next. The best of luck to them.

How do you like me now?

1Corinthians14:33-38NRSVA"for God is a God not of disorder but of peace.
(As in all the churches of the saints, ³⁴ women should be silent in the churches. For they are not permitted to speak, but should be subordinate, as the law also says. ³⁵ If there is anything they desire to know, let them ask their husbands at home. For it is shameful for a woman to speak in church.^{[d] 36} Or did the word of God originate with you? Or are you the only ones it has reached?)

³⁷ Anyone who claims to be a prophet, or to have spiritual powers, must acknowledge that what I am writing to you is a command of the Lord. ³⁸ Anyone who does not recognize this is not to be recognized."


Church of England General Synod backs women bishops

The Church of England has voted to allow women to become bishops for first time in its history.

Its ruling General Synod gave approval to legislation introducing the change by the required two-thirds majority.

A previous vote in 2012 was backed by the Houses of Bishops and Clergy but blocked by traditionalist lay members.

The Archbishop of Canterbury Justin Welby said he was "delighted" but some opponents said they were unconvinced by the concessions offered to them.

The crucial vote in the House of Laity went 152 in favour, 45 against, and there were five abstentions. In November 2012 the change was derailed by just six votes cast by the lay members.

In the house of Bishops, 37 were in favour, two against, and there was one abstention. The House of Clergy voted 162 in favour, 25 against and there were four abstentions.

Analysis By Robert Pigott, religious affairs correspondent, BBC News

It is hard to exaggerate the significance of today's decision at the York Synod.

It breaks a hitherto unbroken tradition of exclusively male bishops inherited from the first Christians almost 2,000 years ago.

Some Anglicans see it as a "cosmic shift" - arguing that the Church's theology has been changed by its acceptance that men and women are equally eligible to lead and teach Christianity.

With the decision, the Church is acknowledging the importance secular society places on equality, signalling that it wants to end its isolation from the lives of the people it serves.

The legislation leaves traditionalists relying largely on the goodwill and generosity of future women bishops, a source of anxiety for many, but heralded by some as a sign of a new culture of trust and co-operation in the Church.

With the even more divisive issue of sexuality on the horizon, the Church will need that culture as never before.

Before he announced the vote, the Archbishop of York John Sentamu, asked for the result to be met "with restraint and sensitivity". But there was a flurry of cheers when it was announced.

The result overturned centuries of tradition in a Church that has been deeply divided over the issue.

It comes more than 20 years after women were first allowed to become priests. More than one-in-five of priests in the church are now female.

The motion will now go before Parliament's ecclesiastical committee, which examines measures from the Synod. The Synod would then meet again on 17 November to formally declare that women can be bishops.

'Big moment'

The first woman bishop could potentially be appointed by the end of the year.

 

 

The Rev Canon Nikki Arthy said she would welcome the appointment of a woman bishop in Gloucester

The vote followed after almost five hours of debate at the University of York.

The Dean of Salisbury, the Very Reverend June Osborne, said it was a "historic day".

She told the BBC: "I don't think you can overstate the fact that the Church of England allowing women to take up the role of bishop is going to change the Church.

"I think it's going to change our society as well because it's one more step in accepting that women are really and truly equal in spiritual authority, as well as in leadership in society."

The Reverend Lindsay Southern, from the parish of Catterick with Tunstall, North Yorkshire, said "it's been a really long journey but we were so pleased with the graciousness of the Synod debate".

But Lorna Ashworth, a lay member of the Synod who voted against women becoming bishops, suggested it was "not going to be a smooth road ahead".

She said she had no plans to "run away" from the Church but predicted there could be "difficulties" in a number of areas, such as those involving new priests opposed to the changes.

 

Archbishop Welby: "We'll require... a long period of culture change"

Another lay member, Susie Leafe, director of the conservative evangelical group Reform, said she was "very disappointed" by the vote.

"There is still at least a quarter of the Church for whom this package does not provide for their theological convictions," she said.

The motion had the backing of the Archbishop of Canterbury and Prime Minister David Cameron.

Speaking in the debate, Archbishop Welby said Church of England bishops were committed to meeting their needs should the legislation be passed.

It contained concessions for those parishes that continue to object to the appointment of a women bishop - giving them the right to ask for a male alternative and to take disputes to an independent arbitrator.

In a statement issued by Lambeth Palace later, Archbishop Welby said: "Today marks the start of a great adventure of seeking mutual flourishing while still, in some cases disagreeing. The challenge for us will be for the church to model good disagreement and to continue to demonstrate love for those who disagree on theological grounds."

The Archbishop of York said it was a "momentous day".

He said: "Generations of women have served the Lord faithfully in the Church of England for centuries. It is a moment of joy today: the office of Bishop is open to them."

There were celebrations outside the General Synod meeting at York University

Mr Cameron said it was a "great day for the Church and for equality".

And writing on Twitter, Deputy Prime Minister Nick Clegg praised Archbishop Welby's "leadership" on securing the Yes vote, adding that it was a "big moment" for the Church of England.

Labour leader Ed Miliband said it was "wonderful news".

But Prebendary David Houlding, a member of the Catholic Group on the General Synod, who voted against the legislation, expressed concerns at the potential impact the result could have on relations with the Catholic Church.

The Anglican Communion has the largest Christian denomination in Britain and a presence in more than 160 countries. Women bishops are already in office in a number of provinces including the US, Canada, South Africa, Australia and New Zealand.

On target?

On Paul Nelson Day 2014: The Target Problem

Paul Nelson April 7, 2014 11:04 AM

 

 

 

 

Thanks to P.Z. Myers's annual lampoon of me, I've thought more deeply about the relationship between development and evolution than I ever expected to do.

Moreover, "Paul Nelson Day" provides me with an annual teaching opportunity, because I can link from the comments thread at Pharyngula to the discussion here.

So -- today, kids, I want to introduce you to a great puzzle, one that is central to the unsolved problem of the macroevolution of the animals.

Here's the context you need to know to understand the significance of the puzzle, which we can dub "The Target Problem," for reasons that will become obvious.

Three key points:

(1) A hundred and fifty years after the Origin of Species, the evolutionary pathways from unicellular eukaryotes to any of the animal body plans remain entirely unknown. For details, see Steve Meyer's book Darwin's Doubt.

(2) These missing pathways are often blamed on the absence of "transitional" fossils. While having more fossils might help, the evolutionary mystery -- at its core -- would still not be solved. The Target Problem remains.

(3) The necessary evolutionary pathways will remain hidden as long as one seeks to explain their origin via undirected processes.

Now, (1) is simply the case. If you don't agree that (1) is a fact, choose any of the phyla -- or (Nick M., I'm thinking of you), if you don't like the taxonomic category "phylum," choose any animal species present in the Cambrian -- and send me the evolutionary pathway leading to that group from its unicellular eukaryotic ancestors. (Email me here.)

What's the easiest way to grasp the Target Problem? Start by watching a short YouTube clip, of course, to ground the discussion in a concrete and well-understand example -- namely, the development of the nematode Caenorhabditis elegans.

This clip shows, in four minutes, the twelve-hour developmental trajectory from fertilized egg to hatching worm. As you watch, keep in mind that all these cell divisions, with their asymmetric daughter cells (and their daughters, and theirs, and so forth, right down to the terminally differentiated cells in the hatching worm), must have been constructed by the undirected processes of evolution, if that's what happened at the origin of C. elegans, anyway. John Sulston won the 2002 Nobel Prize in Physiology or Medicine for working out the details of the cell lineages in this species, from fertilized egg to hatching. You can see the famous diagram of the lineage here.

All right -- so what's the Target Problem? It arises when we consider the relationship between "developmental time" and "evolutionary time" (see the figure below). Developmental time we can actually observe and track in C. elegans. That's what you just watched in the YouTube clip, and what Sulston's branching diagram depicts schematically.

Evolutionary time, by contrast, we can't observe or track, but we know what must have happened during evolutionary time, if an undirected process constructed what we can see unfolding in C. elegans. Several things must have occurred, among them:

• an increase in cell number, from one (i.e., in the unknown unicellular eukaryotic ancestors) to approximately one thousand cells in an adult C. elegans.

• the origins of cellular differentiation, namely, specialized cell types, such as cuticle, gut, nerve, etc., cells, with corresponding genetic controls

• the origin of the three-dimensional architecture (body plan) of C. elegans

• the origin of C. elegans sexual reproduction and gametes (eggs and sperm).

And, never to be neglected, the small difficulty of staying alive during the whole of evolutionary time, as required by the Principle of Continuity.

The Target Problem? How to describe functional (and reproductively capable) organisms, which must have existed during evolutionary time, as cell number count goes up, and cellular differentiation increases. We're using C. elegans as our example because we have a complete cell lineage, genome, and lots of other details to ground the discussion, but the Target Problem exists for any other animal species thought to have evolved from a non-animal ancestor.

The Target Problem has never been solved. That's why no one can tell you how the animals evolved from single-celled ancestors.

 

Junk science exposed.

Not So Simple: Fruit Fly ENCODE Arrives

Evolution News & Views March 20, 2014 10:53 AM

 

 

 

You know about ENCODE, the project that found 80 percent or more of the human genome is transcribed and appears functional. Now, along comes modENCODE: the ENCODE project for model organisms. Results from the fruit fly are in, and Indiana University shares the surprises (for evolutionary theory, that is): "Study of complete RNA collection of fruit fly uncovers unprecedented complexity."

The paper shows that the Drosophila genome is far more complex than previously suspected and suggests that the same will be true of the genomes of other higher organisms. The paper also reports a number of novel, particular results: that a small set of genes used in the nervous system are responsible for a disproportionate level of complexity; that long regulatory and so-called "antisense" RNAs are especially prominent during gonadal development; that "splicing factors" (proteins that control the maturation of RNAs by splicing) are themselves spliced in complex ways; and that the Drosophila transcriptome undergoes large and interesting changes in response to environmental stresses. (Emphasis added.)

Ten of the 41 researchers from 11 universities working on modENCODE came from IU. They found many genes transcribed only under stress, such as exposure to heat, cold, and toxins. "In total, 5,249 transcript models for 811 genes were revealed only under perturbed conditions," they said. As if the "junk DNA" myth needed any more pounding, the lead author testifies:

"As usual in science, we've answered a number of questions and raised even more. For example, we identified 1,468 new genes, of which 536 were found to reside in previously uncharacterized gene-free zones."

The news item notes that "biologists have developed increasing appreciation of how well genes and critical life processes are conserved over long evolutionary distances."
Cambrian Conservation
Meanwhile, the transcriptome of another model organism, the sea anemone, was studied by researchers at the University of Vienna. This creature, like the fruit fly, shows a similar unexpected complexity in its gene networks. The news release claims that this creature is "half animal, half plant," but what they mean is that gene regulation for both kingdoms of the tree of life is so similar, it must have already existed in the microbial common ancestor 600 million years ago:

The team led by evolutionary and developmental biologist Ulrich Technau at the University of Vienna discovered that sea anemones display a genomic landscape with a complexity of regulatory elements similar to that of fruit flies or other animal model systems. This suggests, that this principle of gene regulation is already 600 million years old and dates back to the common ancestor of human, fly and sea anemone. On the other hand, sea anemones are more similar to plants rather to vertebrates or insects in their regulation of gene expression by short regulatory RNAs called microRNAs. These surprising evolutionary findings are published in two articles in the journal "Genome Research".

So here is another apparently "simple organism" with "complex gene content." What they found contradicts another evolutionary expectation:

In the last decades the sequencing of the human and many animal genomes showed that anatomically simple organisms such as sea anemones depict a surprisingly complex gene repertoire like higher model organisms. This implies, that the difference in morphological complexity cannot be easily explained by the presence or absence of individual genes. Some researchers hypothesized that not the individual genes code for more complex body plans, but how they are wired and linked between each other. Accordingly, researchers expected that these gene networks are less complex in simple organisms than in human or "higher" animals.

Well, surprise. When they examined the epigenetic mechanisms for gene expression and regulation (the "grammar" of the genetic code), they found that "Gene regulation [is] comparable to higher animal model systems." For instance, they estimate that 30 to 50 percent of genes are regulated by microRNAs, just one of the facets of regulatory processes.
Rescuing Evolution
The dominance of complex regulation in such a simple organism leads these evolutionary biologists to postulate that "this principle of complex gene regulation was already present in the common ancestor of human, fly and sea anemone some 600 million years ago." Yet the simple Precambrian animals lacked most of the developmental processes and organ functions of those that emerged fully formed in the Cambrian explosion.
To bolster their story, the researchers claim to have found microRNA activity in these animals that resembles that of plants. Since the discovery contradicts the hypothesis that the regulatory elements arose independently in the two kingdoms, they believe they have uncovered "the first evolutionary link between microRNAs of plants and animals." But then they try to have it both ways:

In summary, while the sea anemone's genome, gene repertoire and gene regulation on the DNA level is surprisingly similar to vertebrates, its post-transcriptional regulation is plant-like and probably dates back to the common ancestor of animals and plants. This is the first qualitative difference found between Cnidaria and "higher" animals and the findings provide insight on how important levels of gene regulation can evolve independently.

Of course, the identity of the common ancestor was left as an exercise.
In 2013, ENCODE turned the tables on Darwinian evolutionists with their assumptions about junk DNA, showing that the human genome is overwhelmingly transcribed and most likely functional. And it's not just functional, but regulated with mind-boggling layers of complexity -- switches, networks, and codes controlling other codes. Now, the modENCODE project is showing the same pattern for fruit flies. The Vienna study shows the same thing for sea anemones. Both expect that "unexpected complexity" will be the norm for all "higher" organisms.
Yet if all this inter-related complexity has to be pushed back to some mythical common ancestor, it is tantamount to believing multiple miracles happened to a simple organism that had no gut, eyes, sex, limbs, or nerves. The mythical "common ancestor" that possessed these abilities serves only as a placeholder for ignorance -- not a scientific explanation.
Intelligent design, which does not rely on such religious premises, knows how to explain the observations. Whenever we see a complex, functioning system (like a rollout of a software system), we know intelligence played a role in its origin. We also know that intelligence can explain multiple, independent instantiations of similar systems. We never see, however, complex, networked systems arising de novo by unguided natural processes.
In 1980, Carl Sagan knew nothing about ENCODE and modENCODE. With all the revelations of genetic complexity coming to light in the past 34 years, these must be hard times for Neil deGrasse Tyson to keep a straight face while sweeping his hand up the cartoon-drawn Tree of Life in Cosmos 2.0 and ascribing "all the beauty and diversity of life" to random mutations. As Casey Luskin noted, it only makes sense if you don't think about it.
 

Genius well beyond the new gods

Thou shalt not test the new gods.

Thou Shalt Not Put Evolutionary Theory to a Test

Douglas Axe July 18, 2012 6:41 PM

 

 

 

Paul McBride, a PhD student studying vertebrate evolution in New Zealand, is concerned that religion may be driving the research that Ann Gauger and I are doing, or perhaps that we've been driving under its influence. As you might guess, there's some irony in this. His criticisms of my chapter in Science and Human Origins suggest that he may actually be the one whose scientific reasoning is being impaired by his beliefs.

We all agree that evolutionists are crediting remarkable things to an unguided material process. McBride also agrees with us that this process has significant limitations. In his words: "Evolution is not a process that is capable of producing anything and everything, at all times in all species. It is, conversely, a greatly constrained process." This being so, surely McBride ought to agree with us that the claims of evolutionists need to be evaluated in light of these constraints. It seems to me that to disagree with this would be to adopt a decidedly unscientific stance.

In essence, the scientific approach here should follow two steps: 1) determine unequivocally what the evolutionary mechanism can do (present tense) by performing experiments with appropriate mathematical models used to interpret the results, and 2) determine whether the things that evolutionists claim it did do (past tense) marry up nicely with what we've found that it can do. Ann and I have invested heavily in this undertaking, and we have some work to show for it. I can't fault McBride for not investing in it, because the evolutionary community he finds himself in certainly doesn't cater to this. For him to adopt their aversion to critical analysis of Darwinism, though, is regrettable.

Like many of his peers, McBride seems to thinks it's illegitimate to suggest that laboratory tests showing what evolution can't do have anything to say about what it can do (or did do). Ann and I conducted experiments to find out how many changes would have to occur in a particular enzyme X in order for it to begin performing the function of another enzyme, Y. We found that they are too numerous for unguided evolution to have accomplished this transformation, even with the benefits of a massive bacterial population and billions of years. Having carefully made the case that our chosen X and Y are appropriate for the aims of our study, we think this result has catastrophic implications for Darwinism. McBride disagrees:

The real question is not "Can X be turned into Y?" because that sense of direction requires preordination, which is not theorized to be a part of evolution. If we remove this preordination, the question becomes "Can X turn into something else?"

In my book chapter I compared our X-to-Y conversion to the challenge of converting one golf club into another -- a putter into a pitching wedge. Now, if someone were to claim that there's a natural unguided process that refashioned not just golf clubs but thousands of other things as well, producing a great variety of extraordinarily sophisticated things from humble starting points, the scientist in me would want to see some evidence to back that claim up. Cruise missiles from roller skates? Really? Smart phones from flashlights? Are you sure about that? And my skeptical stance would naturally intensify if I were to find that this highly touted process can't actually produce a pitching wedge from a putter in the time it supposedly performed all these miracles.

Not everyone approaches the subject from a skeptical stance, though. McBride wants to say that because evolution operates in an unpredictable hit-and-miss way, one documented miss doesn't mean anything.

Really? If we're going to be scientific about this, shouldn't we withhold judgment on that until we've put some effort into step 2 above? In particular, shouldn't we pay some attention to the fact that evolution has to explain invention on a much larger scale than we examined -- not just single new enzyme functions, but the suites of these needed for new metabolism, often requiring completely new protein architectures... and not just new architectures at that molecular level, but also at the level of cells, and tissues, and body plans? If evolution is hit-and-miss at the very bottom level of this hierarchy, how would it ever succeed at the top level, which depends so critically on the lower levels? That would be like struggling with simple words in Japanese but being fluent when it comes to high-level conversation. It's not just unlikely. It's incoherent.

The importance of step 2 -- reconciling what we know evolution can do with what we claim it did do -- was precisely my intended point near the end of the second chapter of Science and Human Origins. There I laid out the experimental evidence that would be needed to show that an evolutionary transition from apes to humans is indeed feasible. McBride misconstrues my challenge in his haste to dismiss it:

Axe is suggesting that until the day that each single mutation leading from a common ancestor with chimpanzees to man is predicted in order, with each mutation individually investigated for its fitness effects, there is still room to argue about holes in evolutionary theory and leave room for the calm, guiding hand of the Intelligent Designer.

Again, he's focusing exclusively on the past, whereas I'm asking evolutionists to do what other scientists do when they aim to say something credible about the distant past. They do the work of connecting it in a credible way to the present. They base their claims about what did happen on their understanding of what does happen. Before scientists claim that a natural process produced humans from apes, they ought to spend some time reflecting on what would have to be true in order for this really to happen within the constraints that McBride has acknowledged.

For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time. Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years).

My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they're in the position of insisting that something is a scientific fact without having the faintest idea how it even could be. That's just not what scientists should be doing.

The divine Law and blood VI

Was The Decree to "Abstain From Blood" Only a Temporary Requirement or Obligation to Christians?

The Book of Acts clearly shows that many years after the Jerusalem council issued that decree, Christians continued to comply with the "decision that they should keep themselves from what is sacrificed to idols as well as from blood and what is strangled and from fornication." (Acts 21:25) They demonstrated that the requirement to abstain from blood was not merely limited to one area or for just a brief period of time.

Historical evidence is clear and abundant concerning Christians abstaining from blood throughout the following centuries. Note what early Latin theologian Tertullian (c. 160-230 C.E.) stated:

"Let your unnatural ways blush before the Christians. We do not even have the blood of animals at our meals, for these consist of ordinary food. . . . At the trials of Christians you offer them sausages filled with blood. You are convinced, of course, that the very thing with which you try to make them deviate from the right way is unlawful for them. How is it that, when you are confident that they will shudder at the blood of an animal, you believe they will pant eagerly after human blood?" -Tertullian, Apologetical Works, and Minucius Felix, Octavius, translated by Rudolph Arbesmann (1950), p. 33.

And Minucius Felix, a Roman lawyer who lived until about 250 C.E. wrote:

"So much do we shrink from human blood, that we do not use the blood even of eatable animals in our food." - The Ante-Nicene Fathers, Vol. IV, p. 192.

"The Primitive Christians scrupulously complied with the decree pronounced by the Apostles at Jerusalem, in abstaining from things strangled and from blood." -The Ecclesiastical History of the Second and Third Centuries (1845), by John Kaye, Bishop of Lincoln, p. 146

File under "well,if you say so?"

NIH Announces New Software for Scientists Publishing Articles in Evolutionary Biology

Evolution News & Views April 1, 2014 12:01 AM

 

 

The National Institutes of Health (NIH) have created a computer program to assist scientists who are writing articles in evolutionary biology. According to NIH Director Francis Collins, authors can access the program for a nominal fee (subsidized by their federal research funding), choose from a variety of templates, and simply insert their latest research data. The sophisticated software then integrates the data into standard evolutionary algorithms and adds relevant technical terminology.

The program is based on computer code written by scientists at the Massachusetts Institute of Technology, and it is accessible on the NIH website. Here is the title and abstract of a computer-generated article recently accepted for publication in Nature:

Genetic evidence reveals a heretofore-unsuspected evolutionary relationship between roundworms and fruit flies

ABSTRACT

All species are descendants of common ancestors that have been modified by genetic mutations, natural selection, and random genetic drift. We studied two desert-dwelling organisms, the roundworm Caenorhabditis drosophilae and the fruit fly Drosophila nigrospiracula. The former spends part of its life inside the head of the latter, and the rest of its life on rotting cactus tissue. We sequenced a homopolymeric gene that is expressed proleptically in both organisms and found a surprisingly high degree of homology, indicating a heretofore-unsuspected evo-lutionary relationship between the two asymptotic species. Nonlinear phylogenet-ic regression using a binary dummy variable of 2 suggests that C. drosophilae and D. nigrospiracula diverged because of mutationally stable disequilibria due to frequency-independent apostatic natural selection and simultaneously converged because of ecologically constrained stochastic gene sorting. To the best of our knowledge this represents the first demonstrated case of allopatric speciation in the absence of geographical separation. We conclude that C. drosophilae and D. nigrospiracula are descendants of common ancestors that have been modified by genetic mutations, natural selection, and random genetic drift.

Kathleen Sebelius, Secretary of the U.S. Department of Health and Human Services (which oversees the NIH), has assured potential users of the new software that they will not encounter the same problems as people who recently tried to sign up online for health insurance under the Affordable Care Act, and that their work will not suffer the same fate as 120 articles in mathematics and computer science that were recently withdrawn from publication after being exposed as computer-generated gibberish.

Image: Francis S. Collins/NIH