It's design all the way down II

Developments from the Study of Cells and Molecular Machines

Evolution News & Views April 28, 2015 3:57 AM |

 

Intelligent design becomes increasingly apparent at the smallest scales of life as imaging improves and scientists get a closer look at the cell's inner workings.

Dynein

Scripps Institute seeks to reveal the "structural secrets of nature's little locomotive." (Emphasis added.) The dynein-dynactin complex has defied analysis because "the complex's large size, myriad subunits and high flexibility have until now restricted structural studies to small pieces of the whole." Finer details have shown "how dynein and dynactin fit together on a microtubule, how they recruit cargoes and how they manage to move those cargoes consistently in a single direction."

Myosin

Another locomotive protein, myosin-5, is like a tightrope walker on thin actin filaments. A news item from the University of Oxford says, "Remarkably, these proteins not only function like nano-scale lorries, they also look like a two-legged creature that takes very small steps."

Yet the stiff-legged motion seemed awkward at first -- something like a Monty Python "silly walk" sketch. But by filming the machines at 1000 frames per second, the Oxford scientists could see that the molecular machines' motion is anything but random or silly (see the animation above). "The movement resembles the twirling of a dividing compass used to measure distances on a map," chemist Philipp Kukura says. It's a bigger feat than first appears. "Think of it being rather like trying to walk a tightrope in a hurricane whilst being pelted with tennis balls."

'We've uncovered a very efficient way that a protein has found to do what it needs to do, that is move around and ferry cargos from A to B,' explains Philipp.... This study shows that if we want to build machines as efficient as those seen in naturethen we may need to consider a different approach.'

It seems that if you're designing tiny machines 'silly' walks may not be so silly after all.

DNA Repair Helicase

Scientists at the University of Illinois School of Engineering have, for the first time, "observed thestructure and correlated function of specific proteins critical in the repair of DNA," finding that one of the key proteins, UvrD, swivels between an open and closed state and back again. "As it turns out, the closed state unwinds the strands, using a torque wrench action. The open state allows the strands to zip together." When in the closed position, it acts as "a 'superhelicase'capable of unwinding double-stranded DNA over a great distance."

Chromatin

Intelligent design is evident in this headline from Princeton Journal Watch: "Decoding the Cell's Genetic Filing System." Codes? Filing systems? Indeed: five feet of DNA is packed into a tiny nucleus on tightly-wound spools of chromatin. "Access to these meticulously packed genes isregulated by post-translational modifications, chemical changes to the structure of histones that act as on-off signals for gene transcription," the article says. Experiments to try to modify chromatin helps the Princeton team get closer to "understanding nature's remarkable information indexing system."

RNA Polymerase

This machine is responsible for transcribing DNA. Again, it's a lot more sophisticated than it first appeared. Research at Harvard shows that a fairy tale about it was in the scientists' imagination, not the cell:

Once upon a time, scientists thought RNA polymerase -- the molecule that kicks off protein synthesis by transcribing DNA into RNA -- worked like a wind-up toy: Set it down at a start site in our DNA and it would whir steadily along, reeling off an RNA copy, until it reached the stop site.

Lately, they've realized they didn't give RNA polymerase enough credit.

"It's more like a high-performance sports car," said Stirling Churchman, assistant professor of genetics at Harvard Medical School. "It has to speed up, slow down and deal with obstacles in its path."

In a one-minute video clip, Churchman explains why she is excited about the research, bringing at least a little clarity to a situation that often leaves her "overwhelmed by how complex it is," yet still manages to do its job. Her team found "a lot going on" as the machine proceeds down the DNA strand. The "sports cars" even know how to slow down for "speed bumps" and avoid head-on collisions. "Ultimately, it emphasizes the simplicity of our current views of how transcription occurs," Churchman says.

Ribosome

Ribosomes process messenger RNA and translate it into protein. An article from CNRS (Institut de Génétique et de Biologie Moléculaire et Cellulaire) at the University of Strasbourg tells how French scientists mapped the complete human ribosome (all 220,000 atoms), including both subunits, at 3-angstrom resolution. The new model, much more detailed now than the simple animation in Illustra's 2002 documentary Unlocking the Mystery of Life, is bound to increase admiration of this "molecular nanomachine" so important to genetics. One finding so far: "after delivering the amino acids they are carrying, transfer RNA continue to interact with the ribosome at a specific site (the tRNA exit site)."

Incidentally, the April 24 issue of Science has a special section on "The delicate dance of translation and folding," with research papers about how the cell gets from messenger RNA to folded protein.

Lysosomes

Even the cleanup crew deserves our admiration. Current Biology produced a "Quick Guide" to lysosomes in the April 20 issue. Making up 5 percent of the cell's volume, lysosomes can break down a "wide variety of macromolecules" delivered to them by various pathways. Much more than "cell stomachs," though, these machines participate in the cell's signaling networks, membrane repair and defense against parasites. To maintain their acid requirement of pH < 5, they employ rotary machines similar to ATP synthase that pump protons into the interior. Lysosomes may also prove to be a fountain of youth: "Increased life span is the result of lysosomal production of the bioactive lipid oleoylethanolamide, which is translocated into the nucleus by a chaperoneprotein and affects the transcription of genes that regulate longevity."

Centrioles

Centrioles are involved in winching apart the chromosomes into the daughter cells. New findings announced by the Ecole Polytechnique Federale de Lausanne are of interest from an ID perspective: these molecular structures appear to be carriers of information outside of the genome. In the zygote, centrioles (which resemble the machines in cilia) are inherited from the father only. By tagging these paternal centrioles, the scientists found that they persist through at least ten cell divisions: "Even more intriguing are the implications the study has for biology at large, as it raises the possibility that centrioles, persisting across several cell cycles, could effectively be a non-genetic information carrier," the article says. "If this were confirmed, it could represent a paradigm shift in the way we think and understand the biology of an organellethat has been present across eukaryotic evolution."

Well, maybe not evolution. Since they have not evolved in all that time, we can think and understand them better as products of intelligence. That certainly makes sense of all these amazing molecular machines. If machines look better designed the closer you look, ID must be on the right track.

A line in the sand XI

May free speech R.I.P.:Pros and Cons

To be or not to be?Pros and Cons.

  

  

Building on quicksand?

PNAS Paper Admits Understanding the Origin of Cellular Features Is a "Glaring Gap" in Evolutionary Biology

Casey Luskin December 10, 2014 1:48 PM 

In 2001, biochemist Franklin Harold wrote in an Oxford University Press monograph that "there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations." Last month, a new paper in Proceedings of the National Academy of Sciences, "Evolutionary cell biology: Two origins, one objective," admitted much the same thing. The article states (emphasis added):

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. ... Because all evolutionary change ultimately requires modifications at the cellular level, questioning and understanding how cellular features arise and diversify should be a central research venue in evolutionary biology. However, if there is one glaring gap in this field, it is the absence of widespread cell-biological thinking. Despite the surge of interest at the molecular, genomic, and developmental levels, much of today's study of evolution is only moderately concerned with cellular features, perhaps due to lack of appreciation for their wide variation among taxa. However, a full mechanistic understanding of evolutionary processes will never be achieved without an elucidation of how cellular features become established and modified.

Co-authored by some leading evolutionary biologists who are also critics of the standard neo-Darwinian paradigm, the article suggests that evolutionary and cellular biologists need to focus on "bridging the gap" between their two fields. However, though the authors aren't necessarily neo-Darwinians, they retain the evolutionary materialist view that biological processes produce clumsy features, evidence of an absence of design. They want to understand how "historical contingency" and the "opportunistic process of 'descent with modification'" have produced living systems. Thus, they take an efficient molecular machine like the ATP synthase and consider the possibility that it's a poor solution to the problem of generating ATP:

One remarkable example of how history continues to influence today's cell biology is the near universal use of ATP synthase as a mechanism for energy generation. Embedded in the surface membranes of bacteria and organellar membranes of eukaryotes, this complex molecular machine uses the potential energy of a proton gradient to generate a rotational force that converts ADP to ATP, much like a turbine converts the potential energy of a water gradient into electricity. However, the proton gradient does not come for free: cells first use energy derived from metabolism to pump protons out of membrane-bound compartments, creating the gradient necessary for reentry through ATP synthase. Even assuming that ATP production is an essential requirement for the origin of life, it is by no means clear that the path chosen for ADP-to-ATP conversion is the only possibility.

However, they acknowledge that selection can't explain everything:

A commonly held but incorrect stance is that essentially all of evolution is a simple consequence of natural selection. Leaving no room for doubt on the process, this narrow view leaves the impression that the only unknowns in evolutionary biology are the identities of the selective agents operating on specific traits. However, population-genetic models make clear that the power of natural selection to promote beneficial mutations and to remove deleterious mutations is strongly influenced by other factors. Most notable among these factors is random genetic drift, which imposes noise in the evolutionary process owing to the finite numbers of individuals and chromosome architecture.

Where selection fails, they propose forces like neutral drift. Yet as I explained here, under random genetic drift, features arise entirely due to random factors. At least natural selection offers some explanation as to how beneficial features are preserved. If selection has trouble building complex features, random drift would seem even more inadequate. Thus, incredibly, the paper argues that complex molecular machines evolved despite the fact that they may not have yielded a benefit:

Certainly, today's cells cannot survive without such molecular machines. However, the existence of complex cellular features need not imply that each of the myriad of changes that sculpted such structures over evolutionary time was adaptive at the time of establishment.

It seems doubtful that we can explain the origin of some of life's most complex, fundamental, and efficient machine-like features by appealing to random factors like random genetic drift, random recombination, and random mutation. This is hardly different from saying that molecular machines arose for no reason at all.

Be that as it may, their admission that explaining the origin of cellular features is a "glaring gap" shows that this remains a major problem for evolutionary thinking, whether under an adaptationist or a neutralist model. Though they don't put it quite as bluntly as Franklin Harold, this paper's message is no less potent: modern evolutionary biology lacks explanations for the origin of molecular machines.

More hand waving from materialists.

A Critic Asks: Doesn't Our C. elegans Video Commit the Post Hoc Ergo Propter Hoc Fallacy?

Paul Nelson April 20, 2015 11:39 AM | 

1. Does the video about C. elegans employ illicit "backwards" reasoning?

"How wise of the Creator," a lady is said to have remarked to a philosopher in an apocryphal exchange, "to have designed all the major rivers of Europe to run through its main cities." "And our noses were perfectly placed," a friend of hers added, "to support our spectacles."

Struck speechless by this double-barreled blast of blissful illogic, the philosopher could only manage a wan smile and shake his head.

A YouTube commenter, Vimal Ramachandran, argues that the video we just posted suffers from the samepost hoc ergo propter hoc ("after this, therefore because of this") fallacy. This merits a response. He wrote:

This is nonsense. Paul Nelson, you're making the mistake of looking at the end result -- a worm with muscle, nerves, germ cells, and intestine -- and concluding that this was the only possible outcome. Therefore, everything should have been programmed upfront to produce this particular creature with this particular characteristic. You then liken this to human architects who plan ahead to work towards a pre-decided end result.

But this is wrong and you won't understand evolution unless you free yourself from such teleological thinking. We know of even simpler animals that don't have such well-differentiated tissues or developmental patterns -- sponges, cnidarians, ctenophores, placozoans, all of which are evolutionarily even more ancient than C. elegans.

Thus, we can see that animals don't have to have nerves and muscles to survive, they started out as mere colonies of daughter cells, gradually acquiring specializations through evolutionary time. Different mutations produced different animal lineages which went different ways. One lineage led to the ancestor of C. elegans and its cousins including us. Random chance events and adaptation can explain this because the way C. elegans ended up was just one among countless possible outcomes, out of which only one outcome stuck. This outcome stayed on because it was good enough to produce a creature that can survive enough to reproduce in its given environment.

Likewise, another outcome stayed on for placozoans and yet another outcome stuck for sponges. It is wrong to look at the end result and see teleology. Rather, you must appreciate the role of how chance and contingency can produce diverse patterns from a simple beginning. I'm worried about young students who will be misled by such wrong propaganda.

To which I can only add: of course.

Of course animals don't need to have the anatomical features or the developmental pathways ofC. elegans. Sponges don't, nor do placozoans, nor do cnidarians, or ctenophores -- and so on.

But that's not the problem. C. elegans does need its specific features. And that IS the problem to be solved.

Let's assume that all animal species, including C. elegans, share a common ancestor, which is what evolutionary theory claims. This geometry entails -- necessarily requires -- a sequence of intermediate forms leading to C. elegans from its unicellular eukaryotic ancestors. Now, whatever those intermediates happened to be, the lineage they constitute must arrive at C. elegans, with all of its developmental details and features, somehow. The target for explanation is thus provided by nature herself.

Saying this doesn't invoke teleology or post hoc reasoning in the least. Rather it's a straightforward deduction from the existence of C. elegans, given the theory of common descent. If C. elegansindeed evolved by an undirected historical process, the lineage leading to the species through space and time, from other different species, must have existed. And the target of interest, namely, C. elegans itself, is here today and requires explaining, whether we assume teleology or not.

So what evolutionary lineage constructed C. elegans?

2. Focusing on what's relevant

Suppose your doorbell rings, and you open the front door to find me standing there. You live on the 37th floor of an apartment building, at the end of a long brick hallway with no other doors or windows. The building has one elevator reaching the 37th floor, a single stairwell, one public entrance with a security desk staffed at all hours, and is located in Manhattan.

These facts constrain the possible explanations that we can reasonably consider about how I came to be standing at your front door. To say, "But Paul could have gone to hundreds of other apartments in that building, or to another building altogether, or to Boston, or London," is true, but strictly irrelevant. Those possibilities concern other outcomes -- but not the explanatory target of interest. If we wish to explain why I am standing in your hallway, that's the universe of relevant information. Likewise, if we wish to explain the origin of C. elegans, focusing on unrelated species only defers the task, or misdirects our attention to irrelevancies.

Vimal Ramachandran writes:

...animals don't have to have nerves and muscles to survive, they started out as mere colonies of daughter cells, gradually acquiring specializations through evolutionary time. Different mutations produced different animal lineages which went different ways. One lineage led to the ancestor of C. elegans and its cousins including us.

Okay, let's go with this hypothesis. Here are some questions that must be answered:

• What colonial (or other) species were the ancestors of C. elegans?
• How did cells in those species gradually acquire the specializations seen in C. elegans?
• What mutations in those species produced the anatomical features or developmental pathways of C. elegans?

Nobody knows, including Vimal Ramachandran -- which is why his explanation is so hopelessly vague and hand waving. Once one begins actually to grapple with the precise details of C. elegansdevelopment, for instance, "gradually acquiring specializations" immediately turns into a just-so story of zero value.

3. This problem won't go away, and calling it teleology won't make it go away

The point of the videos is to highlight what needs to be explained when we come to a well-understood system such as C. elegans. In particular, the origin of the developmental stages between fertilized egg and reproductively capable adult are hard (or impossible) to explain via natural selection. This problem was the topic of my poster at the 2014 annual meeting of the Society for Developmental Biology.

Vimal Ramachandran's objections would be weightier if they had any genuine substance. I'll stic k with the evidence.

Why the tool will never be equal to the tool maker/tool user

Machines Will Always Be Things, Never "Persons"

Wesley J. Smith April 14, 2015 11:19 AM

In light of transhumanist advocacy for "machine rights," should artificial intelligence (AI) ever be realized, I decided to weigh in at First Things on the craziness of it all. Machines will always be things, not "persons." From "AI Machines: Things Not Persons":

Machines have no dignity and no rights, which properly belong exclusively to the human realm.

Moreover, AI contraptions would only mimic sentience. As inanimate objects, AI contrivances could no more be "harmed" (as distinguished from damaged) than a toaster. Even if the machines were built with human cells or DNA, they would never be integrated biological beings.

Machine rights advocacy is subversively reductionist. It forthrightly diminishes the meaning and unique value of human life.

Peter Singer claims that the brain is just a computer, and so if an AI machine were ever developed, it could be considered a person too. But that's ridiculous:

The approach here rests in a leveling maneuver. If the brain is a really machine, then any thinking machine deserves the same rights that a working brain possesses. But the human brain -- and, more importantly, the mind -- is much more than a complex organic computer.

As the Stanford physician and bioethicist William Hurlbut told me, "Human consciousness is not mere computation. It is grounded in our full embodiment and intimately engaged with the neural apparatus associated with feeling and action." In other words, human thought arises from a complex interaction of reason, emotion, abstract analysis, experience, memories, education, unconscious motivation, body chemistry, and so on.

That can never be true of AI robots. Even if an AI machine were to attain unlimited processing capacities, it wouldn't be sentient, just hyper-calculating.

Here's the bottom line:

If we ever accept that machines (or chimpanzees or Old Faithful) "are people too," our own value would cease to be seen as intrinsic or unique. Human entities would be just like other entities that possess a touch of processing capacity. This is not an act of respect and ennobling lesser beings. It is disrespect of human beings.

There is so much anti-humanism out there. And now the idea is being applied in the context of inanimate objects. I believe this madness must be resisted at every opportunity.

Some more on Dawinists' condescension toward Darwin sceptics

Suspicious? Darwin Defenders Have Two Modes of Communication -- One for the Uninitiated, One for the Guild

David Klinghoffer April 8, 2015 5:43 PM 

This is the last thing I'm going to write about Kevin D. Williamson's responses to Stephen Meyer's post here, "What Should Politicians Say When Asked About Evolution?" I've expended time on this only because Kevin is a reporter for National Review, of which I'm an alumnus and of which I cherish many fond memories, and so I take an avuncular interest in his work. Kevin tweeted, among other thoughts, that the theory of intelligent design is "basically a fraud":

Well, what about that? Actually, ID advocates address the scientific community and the general public -- and in much the same language. That's probably a bit of a self-imposed handicap for us. ID theorists like Meyer, Behe, or Dembski don't dumb it down. It likely would be strategic if they did, though less honest.

That's in contrast to the approach taken by what Steve Meyer calls "Darwin's Public Defenders." Is it unfair to characterize what they do as "defending," with all that implies of bias, of fixed and preconceived ideas? Not at all. They themselves call what they do "defending Darwin." Our colleague Casey Luskin writes at The Blaze about University of Kentucky biologist James Krupa's cri de coeur over at Slate, "Defending Darwin." Luskin contrasts it with the way professional evolutionary biologists write when they think only their own fraternity is listening.

Krupa says he gets some pushback from religious students on his campus who take issue with his presentation, his defense, of human evolution. But listen to the way he speaks of his mission as a teacher:

Some colleagues ask why I bother, as if I'm the one who's the provocateur. I remind them that evolution is the foundation of our science, and we simply can't shy away from explaining it. We don't avoid using the "g-word" when talking about gravitational theory, nor do we avoid the "c-word" when talking about cell theory. So why avoid talking about evolution, let alone defending it? After all, as a biologist, the mission of advancing evolution education is the most important aspect of my job.

In Krupa's own telling, "advancing" education in biology means "defending" Darwinian evolution, including the idea of a smooth, uncontroversial transition from pre-human to human:

Humans and monkeys evolved from a common ancestor. One ancestral population evolved in one direction toward modern-day monkeys, while another evolved toward humans.

The transition may in historical fact have been as simple as that -- but as Casey goes on to detail in his own article, the evidence itself is far from simple, as evolutionary scientists themselves admit.

Recently the prestigious scientific publisher Springer released a 2015 book titled "Macroevolution: Explanation, Interpretation and Evidence." One chapter, "Macroevolution in and around the hominin clade," co-written by respected George Washington University paleoanthropologist Bernard Wood and post-doc Mark Grabowski, reviews the fossil evidence for human evolution.

...

While lamenting "[t]he dearth of unambiguous evidence for ancestor-descendant lineages," they admit that the evolutionary origin of most hominin species is unknown:

[T]he evolutionary sequence for the majority of hominin lineages is unknown. Most hominin taxa, particularly early hominins, have no obvious ancestors, and in most cases ancestor-descendant sequences (fossil time series) cannot be reliably constructed...

After reviewing many fossil species, they observe: "At one time, or another, every early hominin discussed above has been presented as 'the' ancestor of later hominins, but in our opinion, only two pairs ... are plausible examples of ancestor-descendant relationships." Both examples say little about human evolution.

One pair is Australopithecus anamensis and its supposed descendant Australopithecus afarensis -- even though Au. anamensis is only known from a few jaw scraps and an otherwise highly fragmented skeleton, and is an entirely unimpressive "transitional form." The other possible "ancestor-descendant" pair pertains to two members of the genus Paranthropus, a gorilla-like offshoot whose lineage is thought to have gone extinct and is far removed from human origins.

In other words, according to two leading experts in a recent authoritative technical review, evolutionary relationships between hominins are in great doubt, and it's impossible to construct a credible lineage of ancestors and descendants leading from ape-like creatures to our own species Homo sapiens.

Kevin Williamson? Let's, I would say, all ease back on using words like "fraud" to describe ideas we don't like. Instead, tell us why you don't like them, without resorting to fallacious appeals to authority.

ID advocates are the ones who speak the same language to anyone willing to listen. Darwin "defenders" are the ones with separate modes of communication, distinct channels. One, for the uninitiated, including students and the lay public, speaks of Darwinian accounts of evolution as straightforward, uncomplicated fact, to be stoutly "defended," as readily demonstrable as gravity or the contents of the cell.

The other, intended for specialists, is far more candid about the challenges and frustrations in giving an account of human origins, among other things.

Having two manners of discourse -- one for the public, one for behind the scenes -- may not be evidence of fraud but it surely justifies some skepticism on the part of thoughtful adults.

Ps.Richard Dawkins has  claimed that any intellectually honest individual of average intelligence would readily be persuaded by the "overwhelming evidence"for Darwinism.More recently we've had Darwinian spokesmen claiming that,like the emperors clothing,only those especially 'sapien' members of the species homo are qualified to properly evaluate these matters and that the benighted masses ought to uncritically receive their edicts on these issues.Perhaps it's time for the Darwinian clergy convene some sought of council and issue an authoritative edict on the issue.

Materialists' protests notwithstanding;There is something to see here.

Why one should never buy a watch from a blind watchmaker

Why St. Denis Should Be the Patron Saint of Evolutionary Theory

Paul Nelson April 7, 2015 11:39 AM | 

Pain is a great teacher, I tell audiences. Take it from me. If PZ Myers hadn't designated April 7 "Paul Nelson Day" a few years ago, to lampoon me for my failure to explain the concept of "ontogenetic depth," I would never have learned just how intractable the problem of animal macroevolution would turn out to be.

"Oh, come on, Paul -- you're exaggerating," says the skeptical reader.

Not really. Before PZ's critique, ontogenetic depth (OD) seemed pretty obvious to me. The metric could be calculated as a straightforward product in any animal species, by multiplying the number of adult cell types by the number of cell divisions, from fertilization and first cleavage onward, yielding a good estimate for comparing developmental complexity among the animals. Smaller animals with fewer cell types should exhibit a lesser degree of OD than larger animals with more cell types. Easy, right?

Easy, that is, until one actually tries to calculate the value. And that's where PZ's original critique sent me off on a long path that continues today. I see more clearly than ever why the origin of developmental pathways requires a cause with foresight.

In presentations and writings from the mid 1990s until PZ's original OD critique, I had tended to say that the origin of animal body plans was mainly a question of (1) increasing cell number, and (2) increasing cellular differentiation. While both of those points are still true, they don't come close to touching the main problem. Whatever caused animal body plans to arise had to know where it (namely, the cause) was going. And the first step on that road is the hardest to take.

Given that the origin of animal body plans and the origin of animal development are intimately connected, this means that the problem of animal macroevolution will not be solved using the current limited toolkit of evolutionary theory. Foresight is a teleological, or design-based concept, and thus verboten (for philosophical, not evidential, reasons) at the moment in evolutionary biology. Concepts that are off-limits need a change in philosophy before they can be reintroduced into a discipline.

But you know what? You can see this for yourself. Try the following exercise.

On the Origin of the First Cleavage Stages in the C. elegans Worm

Caenorhabditis elegans is a model system about which biology has learned a great deal over the past forty years. Compared to mammals, or even fruit flies, C. elegans is a relatively simple animal, with 1,031 cells in its adult male phenotype (959 in the hermaphrodite), apportioned into a variety of specialized cell types and tissues within the tapering nematode body plan. C. eleganswas the first animal to have its entire genome mapped, and remarkably, the developmental lineage of every cell in the adult worm has been painstakingly tracked (work that won the Nobel Prize for John Sulston). From the perspective of detailed biological knowledge, it's hard not to fall in love with these little worms.

If one looks up "origin and evolution of nematodes," however, one will find papers on the phylogeny of the clade -- but all such papers presuppose the existence of the nematode body plan. (Some people find "body plan" a bothersome and unhelpful concept, laden with typological baggage. But as you'll see, the problem we'll examine would exist whether we placed C. elegans in Phylum Nematoda or not.) What one won't find are any papers showing how the nematode body plan itself came to be, from eukaryotic unicellular or colonial ancestors. And, as you'll see from the exercise below, there's a good reason for that.

Since "body plan" may seem too abstract, let's stick with well-understood C. elegans. Following fertilization, the first event in C. elegans development is the establishment by cell cleavage of the major founder lineages (see Figure 1). This cellular branching pattern, characteristic of C. elegans, is remarkable in many respects, but we should focus on just a couple of aspects. As a shorthand, let's call this character CEICP (for "C. elegans initial cleavage pattern").

Fig. 1. The initial cell cleavages following fertilization in C. elegans. AB and P1 are the primary daughter founder cells, giving rise to the AB, MS, and C lineages (containing mixtures of ectodermal and mesodermal cells), D (muscles), E (intestine), and P4 (germ cells). AbbreviatedCEICP in text.

First, let's consider the evolutionary framework for the puzzle. Like all animals, C. elegans must have descended from unicellular eukaryotic ancestors, perhaps via -- well, there is the mystery.

Figure 2 shows the road on which the evolutionary processes at the origin of C. elegans must travel, where the distance marker is increasing cell number. On the left, the starting point, is the unicellular eukaryotic state. On the right, our destination, lie the approximately 1,000 cells of the adult C. elegans.

Fig 2. The distance, measured in terms of cell number, between an ancestral single-celled eukaryote and adult C. elegans. Along this evolutionary branch, cell number must increase.

Okay, the question for the exercise: Where on this interval did CEICP first evolve?

Saint Denis Carrying His Head, and Evolving Initial Cleavage Patterns De Novo

"La distance n'y fait rien; il n'y a que la premiere pas qui coûte," observed Marie Anne de Vichy-Chamrond, marquise du Deffand: "The distance is nothing; it's only the first step that counts." She was a wise woman. Writing to d'Alembert in 1763 about the miracle of St. Denis -- who, according to legend, after his execution by decapitation at Montmarte carried his head for several miles through Paris, preaching a sermon as he went -- the Marquise observes that the entirety of the feat resides in the first step. The rest is routine.

So let's try to take the first step in the origin of CEICP, by placing the character at its correct location (i.e., the point of first appearance) on the phylogenetic road from single-celled eukaryote to adult worm.

Obviously CEICP cannot evolve very late (see Figure 3) -- anywhere in the neighborhood of 1,000 cells -- because CEICP is necessary to specify the terminal fates of those 1,000 cells. No CEICP, no worms.

Fig. 3. Origin of CEICP when total cell number is closer to 1,000 than 1.

So let's move CEICP to the other end of the interval, much closer to fewer cell numbers. (See Figure 4.) How about here?

Fig. 4. Origin of CEICP when total cell number is closer to 1 than 1,000.

But now we face two different, but related, problems:

• The exact features of CEICP, whose origin we want to explain -- namely, the precise decision-tree logic by which the zygote is subdivided into founder lineages with specific fates -- disappear entirely. Those features disappear because the normal functional role of CEICP is end-directed, aiming towards the adult worm, and the adult worm doesn't exist yet. Its evolution lies in the distant future. The processes of evolution, whether selection, drift, or some other mechanism, have no foresight.

• As cell numbers drop towards the single-celled state, it is unclear that functional cell types and tissues will continue to exist. Again the difficulty is descriptive. "Simpler" animals, such as Trichoplax, with only a handful of cell types, actually possess many more cells than C. elegans. The paucity of detailed anatomical or developmental descriptions of metazoan ancestors, for C. elegans or any other existing animal species -- beyond cartoon or nondescript "schmoo" drawings, at any rate -- testifies to the challenge of describing genuinely functional organisms where the total cell number of the adult has significantly decreased. Take away enough cells, and again, there's nothing left to explain, at least that we can actually describe.

In short: no worms, no functional need for CEICP.

So whatever CEICP was doing when it first came to be had nothing whatsoever to do with its current role.

This may not seem troublesome to evolutionary thinkers accustomed to explaining by using concepts such as "exaptation." Yet we still need to describe CEICP, because the character needs to evolve somehow in the phylogeny of C. elegans, at some point in the interval, and now description is impossible. The very features of greatest interest to us have been scrubbed away. There is nothing left to explain.

If Saint Denis carried his head through Paris, that would have been a bona fide miracle -- but really, only his first step mattered. If CEICP evolved via an undirected evolutionary process, that developmental character must have come into existence by violating what is thought to be the case for natural selection, or drift, or any other realistic evolutionary mechanism. It's the first step that counts in explaining the origin of any developmental pathway, because everything downstream relies on the starting point.

And the first step remains unexplained.

This Problem Lives Everywhere in Explaining the Macroevolution of Animals

Ontogenetic depth was my first attempt to grasp how and why animal developmental pathways showed varying degrees of complexity, and to measure those differences. The attempt failed (OD-ed, if you will) because the phenomena in question go well beyond the crude metrics of cell type and number of divisions from fertilization.

Thanks to PZ Myers's annual prodding, however, I have thought much more deeply about the problem of evolving animal development than I ever expected to do. And, in searching the literature (indeed, in conversations with PZ himself, at Society for Developmental Biology meetings), I've found that current attempts to solve the problem fall hopelessly short of the mark. I've focused here on C. elegans, because the species is (relatively) well understood, but the same general difficulty applies to the origin of any animal group. Go into the literature yourself, and you'll see what I mean.

Current evolutionary theory falls short because it excludes a priori notions such as foresight -- not for any evidential reason, but because foresight requires mind, and mind is philosophically unacceptable within the prevailing materialist outlook.