Posted tagged ‘Evolutionary constraints’

Appreciating what intelligence can do that evolution can’t

December 11, 2008

One problem for pro-science forces today is that we’re bored with progress and the “miracles” of technology.  Or at least, mentioning the many ways in which intelligent design far outstrips what “nature” has produced has been done to death, and we have instead turned our minds to contemplating what evolution has done and which design still cannot match.

This is not all bad, of course, since the celebrations of industry, technology, as well as the scientific hubris, of progressives and futurists  tended to ignore the mysteries and exquisite dexterity and control of biological organisms, like the hummingbird.  Computers blow us away at any number of tasks, yet simply driving along the road safely is at best at the limits of today’s computer technology.  And it is nearly certain that no computer enjoys the consciousness that a human knows.

So this post is in no way meant to suggest that we can equal or better evolution in general, let alone can we create the kind of intelligence and creativity that produces our wonderful machines.   As I noted previously, it appears that intelligence evolved to handle what evolution could not directly address, matters of space, time, and rationality. Even then, evolution does not so much give us a rational brain, as to supply the material and organization that allows development, sensory experience, and learning to shape our minds to do what evolution (or God, if you’re an IDist) cannot do directly.

So, while we must appreciate the manner in which evolution deals with tremendous complexity of the sort that our intelligence combined with computation still cannot properly organize, it would do us some good to contemplate once more how much our intelligence has outstripped “nature” in handling materials, in controlling fire, and in producing extremely fast machines and computers that have given us capabilities that “God” either could not or would not give to us.

Even something as simple as fire seemed to be a god-like “element” to the Greeks, as the Prometheus myth tells us.  The cheetah is fast, but topping out at around 60 mph, it runs at less than 1/10th the land speed record.  No bird powers itself to over 100 mph, while experimental hypersonic craft have reached 7500 mph.  New Horizons managed to hit 42,000 mph on its mission to Pluto.  And the internets connect the whole world in what is to humans a virtual instant.

That is what happens when minds make connections between concepts, empirical knowledge, and the recognition of what is needed and/or “cool.”  The simple reason why these phenomena never appeared prior to the evolution of human intelligence, plus a (humanly, not evolutionarily) long learning period, is that there is no intelligence behind biology.  One does not disparage the hummingbird, the ape, or the human by noting that the abilities supplied to these organisms in many areas pale in comparison with the abilities possible through scientific and technological progress.  Indeed, the fact that we now can harness genetic algorithms to partially mimic the capabilities of evolution only enhances what intelligence alone can do, and it does so by recognizing both the possibilities and limitations of the process(es) that gave rise to life, including ourselves.

Surely our understanding of evolution itself speaks well of our intelligence and of our ability to make creative leaps, something that is absent from the various records of evolution.  We have proven ourselves able to extrapolate evolutionary principles into a set of predictions that fit taxonomy, the fossil record, and genetic information (which speak to evolution beyond mere taxonomy), and to recognize how life does not fit with design principles and characteristics.  The proper use of intelligence seems to be what IDists desire to diminish, at least far enough so that we can no longer do proper life science.

Evolutionary theory is the product of intelligence.  ID is the product of anthropomorphization, anthropocentrism, and of superstition.  We have intelligence, no question, but evolution also bequeathed to us the propensities to avoid the use of our evolved intelligence.  Sadly, this is also what we would tend to expect of evolution (precise scientific predictions to this end do not seem likely, however) and not, say, of Alvin Plantinga’s god. 

The evolution of intelligence provided us a kind of “transcendent” capability, which may be seen in our technology, but by no means could it ensure that evolved organisms would make proper use of this capability.  That is the dilemma of evolution, for we only evolved to deal adequately, and often quite falsely, with the world, and not to delve carefully and honestly into what really happened to give us our world.  We have to watch to see if the best that evolution gave to us will win out over the worst that it produced, to see if the lure of intelligence will largely supplant the laziness and lack of thought found in ID and in the other pseudoscience.

This is part of a series of posts that I am combining into one long post, which may be found at Darwin’s Black Box.

Why is there substantial overlap between design results and evolutionary results?

December 2, 2008

There are a number of reasons why ID exists, from an unreasonable desire to hold onto religious myths, to the amazing lack of any sort of scientific rigor in the vast majority of either their criticisms or in their “models” (this statement is not to be confused with their frequent unreasonable demands that we supply rigor where unknowns remain, while they hold themselves to be exempt from any scientific rigor).  This is not the place to delve into the many evolutionary faults in the brain which keep pseudosciences like ID going, however. 

One issue in the constant struggle against ID and other forms of creationism is that the inference to design in life is both an anthrocentric mistake (in that “purpose” is inferred where only evolutionary function can be demonstrated), and sometimes an honest mistaking of exquisite structures and processes as being exactly what a great intelligence would design.

Indeed, if we look at the wings of swallows and of hummingbirds, without any kind of detailed morphological and ontogenetic analysis, one might simply resort to “form follows function,” wholly within the design context in which that statement has typically been made.  Or, if we were to consider the cliche more closely, we might conclude that in our experience function is first considered and analyzed, and form is then designed and specifically articulated in order to fit that function. 

Yes, that is our experience, thus it is not altogether unreasonable for people who know only design processes to think that wing articulations must then have been designed.  But as biologists know all too well, that is not what we see in life.  More than once I’ve brought up the question of why all vertebrate wings are modifications of their ancestors’ legs, while human-designed wings are modifications of bird wings as well as having been partly designed from first principles.  The answer is all too clear, which is that vertebrate wings simply evolved, and were not designed in any manner as we would expect of an intelligence operating to produce them.

Yet the overlap between design and evolution is good enough for us to use bird wings as the basis for design, as the Chinese did with their kites (which is the origin of humanity’s airfoils–or so I have been led to believe), and as the Wright brothers did after adopting previous airfoils, and by studying birds and their flight abilities on their own.  So surely one must address such an overlap, partly to understand evolution, partly to understand design.

The short answer is that intelligence and design expand on what evolution (otherwise) provides.  But this answer itself requires expansion.  Probably a large part of the evolution of logic and rationality comes from the fact that intelligence adapted to an environment which in important ways is not the result of evolution at all.  This goes back to what many people understand, the fact that mathematics–especially geometry–and cognitive abilities such as following straight lines and succession, are to a large extent ways of dealing with space and also with time.  Straight lines happen to be efficient ways to get from one point to another one, hence animals tend to travel in straight lines, and predators learn that this is the case–until avoidance maneuvers kick in, that is.

Primates are believed to have evolved intelligence partly for the sake of spatial (and temporal) understanding, particularly as arboreal organisms operating within 3-D space and dealing with 3-D objects (of course all space and objects are 3-D, but lions do not need to be nearly as aware of the three-dimensionality of their plains and prey).  Social living extended this intelligence to models of complex organisms and their behaviors, so that we became able to understand what another primate (or prey) is likely to do next.  And at some point, primates began to use various spatial items in their surroundings to manipulate their surroundings, and a (usually fairly straight) stick extended the reach of the (usually fairly straight) forearms of the primate.  It should be noted in passing that the fact that we use intelligence to understand other animals and their “purposes” is likely a big reason why many people simply assume that the forms and functions of organisms ought to be understood according to purpose–if not the purpose of an observable being, then the purpose of an unobservable being.

Yet intelligence operates quite differently than evolution, which is why using a stick can effect a quantum leap over what the little primate can do with its arms alone.  Or, more importantly, from understanding evolution and its overlap with design, a stick which evolved simply to uphold leaves above other plants for a competitive advantage eventually becomes an extension of the animal’s spatial capabilities, so that increasing the extension of one’s reach is no longer tied to ancestry and the tedious and slow evolutionary growth of a primate’s arm. 

Oddly (and seemingly cluelessly in the case of Behe), this gets back to what Behe stated in Darwin’s Black Box, that Darwinian evolution requires physical precursors, while design can make do with conceptual precursors.  And indeed, that is exactly why we understand life to be the result of “Darwinian evolution,” for it is incapable of conceptualizing a line, or of taking up a stick to bridge the chasm between two organisms.  Evolution is quite limited while dealing with the geometries of space and of designed machinery (aside from the evolution of intelligence), and it can only respond with logical brains to do what evolution could never do directly.

One could look at evolution as incrementally (if not always incrementally, overwhelmingly so) providing the forms which most animals use, while intelligence evolved to use these forms and abilities well in unevolved time and space.  Thus, intelligence has evolved to understand organisms’ forms and functions (their own, and, in many cases, those of other species) in a spatial and temporal manner that is completely foreign to how evolution processes information, and it can even adopt and extend the spatio-temporal capabilities artificially.  Indeed, intelligence in humans can do what evolution could never do.

The fact is that bird wings have their forms because even legs are plastic over millions of years.  But bird, bat, and pterosaur, could never have come up with wings by rearranging, say, ribs into the proper form to make wings.  We can.  Or, like the Wright brothers, we can take trees (separated from us by hundreds of millions of years of evolution) and saw out exactly the parts needed to make an airfoil, and even to articulate this airfoil so that it can change shape somewhat like a bird wing can.  Rationality can leap past inheritance, in other words, while evolution could never come up with an aluminum engine, or any such thing, yet which the Wright brothers used to power their airplance.

It should be noted also that the aluminum–and the steel–in the engine used to power the Wright brothers’ airplane, along with the design of the engine, come almost entirely from the intellect, with not even an evolutionary conceptual precursor like the wings.  Intelligence evolved to analyze, and even to synthesize, articulations and ideas, so that wholly new things, like aluminum engines, could be thought up in the primate brain.  This is nothing like what evolution does, which is why we distinguish designed objects from living objects both by the formers’ conceptual leaps (which may not be altogether rational), and by the almost inevitable rational aspects which exist within intelligently-designed objects.

Notably, all intelligence of which we know is inextricably tied to evolution.  While evolution itself could never directly supply the leaps of logic and articulation used to analyze a bird carcase, or to create a spear with a pointy stone on the end of it, both evolution and development can shape the rational and communications abilities within animals (primarily humans, on this planet) to actually deal with knowledge of space and of bird articulations, and thus to enhance survival in this world through intelligence.  Intelligence overlaps with evolution both because it is selected to understand animals of one’s own and also of other species, and because it extends and enhances the behaviors of organisms.  This seems to be true to the degree that humans have actually lost many earlier behaviors and even innate capabilities, instead relying more upon intelligence itself to supply behaviors that once evolved to exist and then evolved not to exist.

Another reason for the overlap of the products of design and of evolution is simply that many of the same forms and articulations are needed simply to provide function, or at least to provide function at minimal cost.  While we may have copied airfoils from birds initially, the airfoil on a supersonic airplane owes little to any organism (except for the original idea), rather it is developed from empirical and theoretical studies.  Intelligence did there what evolution could never do, since the latter cannot provide the power needed for supersonic flight.  That said, subsonic planes have airfoils not unlike those of bird wings, not because we’re unable to think beyond copying bird wings for subsonic flight, but because millions of years of evolution, and 100 years of intelligent design, come to basically the same solution–because there really is only one good solution (and varieties of that solution to fit different criteria for flight–which are seen in both planes and in birds).

So one of the main reasons for the overlap between design results and evolutionary results is rather prosaic and probably obvious to most who think about it–good solutions are typically few, and both evolution and design can reach many of these solutions.

Nevertheless, the differences between evolutionary processes and intelligent processes are considerable, and the limitations of evolution are severe.  We can turn a tree into the body (if not the engine) of an airplane.  But only animals with articulated limbs of roughly the right position and tolerably within striking distance of a wing will ever evolve wings.  Even more apparent, evolution will not cause organic life-forms to evolve aluminum wings and piston engines to produce flight, while evolved intelligence has done so.  Likewise, one should remember that evolution has a kind of “parallel processing” power that, albeit only over very long periods, produces wing control that human designers continue to envy.  This seems to be in part because “evolvability evolves,” so that organisms can slowly change to exquisitely fit niches, like those that birds inhabit.

Finally, then, the question in biology comes down not to why evolutionary and intelligent solutions overlap meaningfully, since they would have to in order to produce functional “machinery.”  The real question is why biological solutions are at once so limited when compared to intelligent design, and, very often, so much more exquisite, despite their limitations.  Of course the answer is that the gradual change which predominates over the course of biological evolution can make no spatial, temporal, or rational leaps, while it refines the modifications that it does effect with a profligacy (of offspring), and via excruciatingly fine changes that is not at all easy for our rather blunt rational abilities to effect.

The limitations of evolution and the strengths of evolution are explained only in one way, through the natural selection of variations in organisms, for small modifications of the immediately preceding inheritance of organisms are the mill that grinds bird, bat, and pterosaur wings into such superb and beautiful shapes, while simultaneously preventing the adoption of unrelated forms or with any consideration of first principles.

The only way that evolution could ever produce an aluminum engine, or a wooden skeleton of an airfoil, is by evolving the spatial, temporal, and rational capacities of intelligence.  That is why no vertebrate wing has been anything but the modified forelimbs of its ancestors (unless, again, we count the flying fish, which evolved gliding wings from the precursors to tetrapods’ forelimbs, the pectoral fins), while intelligence–once it evolved and developed culturally and technologically–made a huge number of leaps in capability never before seen in life.  

In addition, this is why most of the ancients differentiated considerably between life and technology, not only because technology is inferior in many ways to life, but because even then technology was startlingly superior in other ways.

Unfortunately for evolution-deniers, exquisite and complex adaptations of a very limited range of forms is exactly what is expected of evolution, and not at all what is expected of design.  Or, to put it into their terms, of course designers adopt and adapt solutions from life, for human intelligence both analyzes and synthesizes.  The insurmountable problem for them is that life never adapts anything from an unrelated and separate (with no, or very limited, lateral transfer of genes) lineages or from first principles, abilities that an actual intelligent designer is expected to have.

This is part of a series of posts that I am combining into one long post, which may be found at Darwin’s Black Box.

David Klinghoffer thoroughly misunderstands science

November 25, 2008

One problem with theistic evolution is that natural laws are predictable whereas Darwinian evolution, according to its own theorists, is entirely unpredictable. Think of those laws that govern weather patterns or the formation of geological features. Not so with Darwinian evolution, which can take any of countless very different directions. How could such a purposeless process reflect divine purpose?  Jerusalem Post

The excerpt above is also at the DI’s blog, which is why I am commenting on it.  I had seen the article previous to their post.

The man clearly knows nothing about logic, or he is deliberately conflating two different issues.  For, all of the laws behind evolution are the same laws behind all of science, including geology and meteorology.  Like any other complex system, evolution cannot be predicted very far out, which is certainly true of meteorology, and even many geological events (predict the timing of the next large California earthquake).  That’s what is wonderful about evolution as science, it brought life into the same scientific sphere as meteorology, geology, and ballistics.

Klinghoffer is clearly equivocating regarding the laws behind weather, which are quite stable, and the fact that the complex process of evolution itself is unpredictable in many of its aspects.  Of course he is just plain wrong when he claims that evolution “is entirely unpredictable,” since it would be in the same meaningless pit of baseless assertion that ID is in if that were the case.  The cladistic branchings in evolution are a firm prediction for any evolution involving primarily vertical transmission of genetic information, and any deviation from that must have a good explanation compatible with nature’s laws (as is the case with retroelements in eukaryotic genomes which came from viruses).

Related to the above prediction, but getting into some of the specifics, there can be no “common authorship” of modifications between lineages which have split from each other in “Darwinian evolution,” and indeed that is the case.  Also, complex working “machinery” of the cells is not going to arise de novo, but must have precursors.  This is almost certainly the case even with biochemical pathways which may conceivably (according to some) have arisen through processes other than “Darwinian processes,” for even “self-organization,” or some such thing, can hardly begin without complex precursors.  And again, these are the sorts of things we see in life, notably in the evolution of the two types of adaptive immunity, for once the two lines of immune evolution had split off from each other, no “common authorship” is visible, and both lines have crucial precursors existing in related related organisms which are without adaptive immunity.

Klinghoffer has long been a critic of evolution, but apparently has not even learned the solid predictions of “Darwinian evolution.”  He instead favors a “design process” which is truly without any constraints of “natural law” or of probabilistic processes.  So he criticizes evolution for being like his own mindless and undetectable “process,” which isn’t at all what evolution is about, while preferring exactly such meaningless tripe over the evolutionary theory which in fact brought life under the same causal understanding as Newton’s physics.

This all reminds me of when Paul Nelson was at Panda’s Thumb, complaining that evolution wasn’t predictable while other scientifically-understood processes were. So I asked him to join me in a thunderstorm and to tell me then (not days beforehand) where the next lightning strike would take place. Well, of course Nelson didn’t answer me, nor does he ever engage honestly and forthrightly with the difficulties raised by any of us. 

And to be really equal, I probably should have asked him to predict where the next lightning strike would occur well before the thunderstorm took place, since they’re asking for completely ridiculous predictions and impossible (due to lack of full information) explanations regarding evolution.  But I didn’t need to do so, because it is well beyond our present powers to predict where the next lightning strike will take place even a minute ahead during a thunderstorm.

So as usual, they completely fail to understand science, evolution, to engage honestly with us the few times when they’ll even meet us on an uncensored (at least not much censored) forum, or to meet any of the demands that they try to impose upon our science.  Unfortunately, almost to a person, the proponents of this pseudoscience fail as much through a lack of morality as they do through their large lacunae in knowledge of science and of philosophy.

Causation without “naturalism” or “materialism”

November 14, 2008

Paley, of course, is to blame for not framing his arguments more tightly.  DBB, 213

Uh, yeah, Behe, then why have you backed away from all of the positive evidence that Paley adduced as being the effect of a mind similar to our own? That Paley lacked tightness of argumentation and exactness of fit between cause and effect I do not doubt, but it is the fact that Paley posited meaningful causation (that is, a mind similar to our own), which Behe completely fails to do, just as the “theories of origin” that Paley rightly criticized failed to do.  The reason glares out at us, of course, which is that evolution explains what we see in life, and design has nothing to explain the slavish copying evident in life, except that, wherever lineages break from each other, there is no commonality of “authorship” in any of the subsequent modifications.  The patterns are evolutionary, and unlike any design causation that we have ever observed.

The childishness, as well as the vacuousness, of ID is transparent whenever they whine about science’s devotion to “naturalism” or to “materialism”.  For, the fact of the matter is that mental causation was understood well before any “naturalistic” or “material” causes were known, and yet we still understand mental causes more commonly according to “non-natural” and “non-material” models than we do according to physics.  Most of the science-oriented types do not doubt that the brain operates according to physics, of course–and for very good reasons, especially the conservation laws, and small-scale cause and effect observations.  Yet we do not hesitate to understand causation outside of precise scientific understandings of the processes underlying our “theories of mind.”

This is all that we demand, all that we have ever demanded.  Let’s let Paley say so once again:

When we speak of an artificer or an architect, we talk of what is comprehensible to our understanding, and familiar to our experience.  We use no other terms, than what refer us for their meaning to our consciousness and observation; what express the constant objects of both; whereas names, like that we have mentioned, refer us to nothing; excite no idea; convey a sound to the ear, but I think do no more.  Natural Theology

How “design” means anything in the passage below I cannot say:

Features that strike us as odd in a design might have been placed there by the designer for a reason–for artistic reasons, for variety, to show off, for some as-yet-undetected practical purpose, or for some unguessable reason–or they might not.  DBB, 223

Yes, that’s why it’s called “design,” not “art.”  Paley was serious about design, which is why he discussed artificers and architects.  Darwin was also serious about design, which is why he noted that life does not look like anything we get from artificers and architects, but rather more like something that reproduced, faithfully for the most part, but with variations which were selected.

Partly I have been recapitulating the earlier, linked post.  But now it is for the additional reason that neither Darwin, nor most other competent scientists, ever hung the arguments regarding design vs. evolution on “naturalism” or “materialism”.  What is more, Darwin himself didn’t have a “natural” or “material” cause of the variations which “nature” selected, instead he was concerned about empirically-known causes matching up with empirically-discovered facts.  The gene fairy might have been responsible for inheritance and variation, for all he knew (by his time such fanciful “causes” were no longer taken seriously, however), but “survival of the fittest” explains (many of) the cumulative effects that we see.

And although he did not use this term, Paley hypothesized “rational choice” as being responsible for the “design” of organisms, exactly what we would expect of an artificer or architect.  His point was certainly not that the “designer” had to be “natural” or “material,” rather that it would be rational, and purposeful. And ultimately, Behe denies everything that we would expect of a designing mind, both purpose and rationality.

We just need causation of any hypothesized design, or in other words, we need to know the limits and peculiarities of a designer if we are ever to be able to identify such a cause.  That is all that Paley demanded of competing origination theories, and he rightly determined that they fell flat when they failed to explain anything by matching up cause and effect.  It hardly needs pointing out that Paley failed to explain much that he claimed to explain, let alone all that ignored.  Yet he at least claimed identifiable causation (or at least he analogized to identifiable causes–depending on what makes of God as a Cause) producing identifiable effects.  As loose as his argumentation was, it was indeed tight enough to be subjected to falsification tests, and thus it failed when organic articulations were shown to be explainable via natural selection, along with a host of data that design never could touch (although Paley tried get his readers to accept morphological similarities as produced by the “designer”).

No more of that from Behe, certainly.  He’s flailing away so badly that he’s bringing up art that is deliberately obscure, in order to avoid the fact that all of his “design” is lacking any of the expected marks of design–particularly rationality and purpose.  He knows that some of Paley’s arguments were poor, indeed, but he will not admit that his principal problem with Paley is that the latter invoked empirically-known causation which was falsifiable and falsified.  Worse, evolution is falsifiable, and has not been falsified, and it explains what his “design” deliberately avoids addressing–such as the aforementioned slavish copying along lines of vertical transmission, and no “common authorship” of modifications in lines which permanently broke away from each other.

We have only demanded that causes should actually produce their expected effects, from Paley, through Darwin, and down to the present day.  The utter lack of rationality and purpose behind organisms is enough to invalidate any “designing mind” worthy of the name (actual reference, as Paley demanded), quite apart from the evolutionary evidence. 

What is more, evolutionary theory has no dependence on the dearth of evidence for “design,” rather it is the match of cause and effect in the patterns of life (“slavish copying along lines of vertical transmission, and no “common authorship” of modifications in lines which permanently broke away from each other”), wherein causes with deep “memory” and no “knowledge of what is happening in unrelated lines” produce just the effects expected (predicted) by those causes.

This is part of a series of posts that I am combining into one long post, which may be found at Darwin’s Black Box.

How could the molecular clock work with design happening?

October 30, 2008

The molecular clock has been vigorously debated since it was proposed, and many issues surrounding it are still contended.  Overall, however, it remains a viable possibility.  Michael Behe, DBB, 174

He is right both about questions remaining, and that it is a viable possibility.

But how could it be, if ID were correct?  From Aristotle, down to Paley and the creationists, τεχνη or design has always been marked off from “nature” (nature in the exclusive sense) or “physis”.  Indeed, Behe and most of the other prominent IDists like to suggest that the “Cambrian Explosion” is an obvious time when “design” was effected (DBB 27-28).  And yet the molecular clocks (mostly DNA, now) tick through the “Cambrian Explosion” without marking any break from the usual processes, even though it is possible that more refined methods could yet capture an uptick in change (not the break that most would expect from a designer intervening, however).

For so long the various sorts of creationists have tried to argue that intervention by God would be obvious.  Since it never has been, however, Behe increasingly writes as though no intervention can ever be observed, from any sort of mark of design, to any break in the molecular clocks.

This criticism has nothing to do with the accuracy of molecular clocks, which may in fact not be as reliable as some have claimed.  It is that Behe never expects any of the effects of intervention to be visible in life (if these were found, you can be sure that most IDists, probably including Behe, would quickly adopt them, though).  This, perhaps, is the most important change that ID has produced, since the older IDist Paley, and traditional creationists, always expected design to be observable–and generally not by christening complexity as “evidence for design,” like Behe illegitimately does.

As it happens, we could easily apply Paley’s criticisms of the evolutionary concepts of his day (before Darwin came up with a scientific theory) to Behe’s evidence-free designer/evolution-tweaking God, because a major argument of Paley’s book was precisely that design has positive evidence in its favor (arguable then, but not now), while evolutionary ideas were lacking in evidence (not entirely true, since common ancestry did comport well with evolution).  Really, anyone who wanted to show conclusively how ID avoids all legitimate tests (falsification being the best rule-of-thumb) would do so by comparing Paley’s attempts to show that design is falsifiable, with Behe’s never-ending attempts to avoid all reasonable tests of ID.

This is part of a series of posts that I am combining into one long post, which may be found at Darwin’s Black Box.

Shorter generation times speed molecular evolution

October 9, 2008

It’s not an especially surprising result, but it’s good to confirm what seems intuitively to be true.  Here’s the abstract from the Science research paper:

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

Stephen A. Smith* and Michael J. Donoghue

Variable rates of molecular evolution have been documented across the tree of life, but the cause of this observed variation within and among clades remains uncertain. In plants, it has been suggested that life history traits are correlated with the rate of molecular evolution, but previous studies have yielded conflicting results. Exceptionally large phylogenies of five major angiosperm clades demonstrate that rates of molecular evolution are consistently low in trees and shrubs, with relatively long generation times, as compared with related herbaceous plants, which generally have shorter generation times. Herbs show much higher rates of molecular change but also much higher variance in rates. Correlates of life history attributes have long been of interest to biologists, and our results demonstrate how changes in the rate of molecular evolution that are linked to life history traits can affect measurements of the tempo of evolution as well as our ability to identify and conserve biodiversity.  Science

Here’s some more of the history, specifics, and commentary on the results.

Perhaps I should add that Behe operates on this assumption, particularly in his Edge of Evolution.  This does not, of course, change anything about how unfounded his assumptions are (like assuming that only two changes to one gene were needed, just because these are the only two changes in common within the sets of many changes found in one type of resistance to chloroquine), and the vast lacunae in his calculations which bypass fitness issues which are crucial to fixation by natural selection (that is, he totally ignores in his calculations the fact that chloroquine resistant P. falciparum are less fit in the absence of chloroquine). 

Which just goes to show that you can’t get everything wrong, no matter how pathetic your knowledge base and capacity for scientific judgment is.

Evolution of Adaptive Immunity II–Building on Innate Immunity

October 9, 2008

This is another installment in my response to chapter 6 of Darwin’s Black Box.

The first mouse Toll gene isolated turned out to be defective in two mouse strains that cannot respond to bacterial lipopolysaccharide (LPS), one of the pathogen-associated molecular patterns, or PAMPs, recognized by innate immune system pattern recognition receptors. These mice lack TLR-4 [Toll-like receptor-4] function; in one strain the defect is due to a point mutation in the so-called TIR domain (Toll/IL-1 receptor domain, since it is found in both Toll and IL-1 receptors), while in the other strain it is due to a null mutation that abolishes expression of the gene altogether. These mice are exceptionally susceptible to infection with gram-negative bacteria, which carry LPS on their surface, and cannot mount an adaptive immune response against them. This was, in a sense, the first proof that the loss of innate immunity had a discernible effect on the adaptive immune response, and served as a proof in principle that the adaptive immune response depended on an effective innate immune response, at least in some cases. The question remaining is: How general is this basic principle?  Evolution of the innate immune system

And the answer is, the dependency of the “adaptive immune system” upon the “innate immune system” is very general.  Just as the eukaryotic flagellum/cilium depends upon previously-existing transport structures which are shared by both the flagellum and cytoplasmic transfer machines, the adaptive immune system is, and apparently was from the beginning, part of and dependent upon the earlier-evolved innate immune system.  Of course the “innate immune system” has also evolved in vertebrates, yet it continues to function much as it did in the past, while also priming and signaling the adaptive system to begin defending the body days after the initial response by the innate system.

As typical, my point is not to belabor the details, it is to give a sense of how the “irreducibly complex” adaptive immune system arose from and depends upon the innate system, while details are made available through links.  The evolution of molecules is not the focus now, rather it is the fact that adaptive immunity reveals the characteristic and predicted evolutionary expectations of having been built into, and from the parts of, previously existing systems and structures.  Some of the specific links to the past will come later, as some parts of adaptive immunity do not seem to have much (if any) role in innate immunity at the present time.

In my last post in this category, I pointed out that Toll and “Toll-like receptors” (TLRs) have evolved in the patterns expected of microevolution, or any other kind. The fact that other molecules of the immune system (adaptive and innate) reveal essentially the same patterns was also pointed out. But the fact is that Toll and the other “innate immune system” proteins are not simply to be found in the “innate” systems of vertebrates as well as in, for instance, fruit flies, they continue to utilize basically the same pathways–and they regulate and inform the adaptive response.  All except the last part is borne out in the following quote:

In fruit flies, there is a very strict order of Toll pathway gene products starting with Toll and going on to dMyD88, Pelle, Cactus, and Dif/Relish, all of which are cytoplasmic proteins involved in the transmission of the signal from Toll, a cell-surface receptor, to the nucleus to induce the activation of specific sets of genes. The same order is found in the homologues of the Toll pathway found in the innate immune system in vertebrates(Fig. 1). The plant genes do not seem to be arranged in the same order. However, if one examines the plant genome carefully, there are signs of all these signaling elements.  Evolution of the innate immune system

I included both the link to the figure, which shows the striking similarities between fruit fly and human immune systems (not including adaptive immunity, of course, which the fly lacks) and the part about similar parts but different order in plants, because the accidents of heredity have left an indelible mark on even the plants.  Significant differences between animal and plant pathways do not seem surprising at all, because we split from plants very early.

However, so far in this post I have written little about adaptive immunity.  The figure linked just above shows how close some of the innate signaling is in humans and in fruit flies, this link (picture and caption) shows how the human innate signaling pathway interfaces with adaptive immunity. Notice the TLRs (1-11), which are homologs with fruit fly Toll receptors, and MyD88 which also appeared in the previously linked figure in both humans and in fruit flies. As one may see from the illustration, the TLRs of the innate system signal infection (often via interleukins, ILs, or MyD88) in order to produce T helper cells (Th’s) in the adaptive immune system.  The article from which this illustration comes goes into great detail about how the adaptive immune system relies upon the “irreducibly complex” (as Behe would have it) pathways of the innate immune system–which are little changed between humans and flies (which, one should recall, diverged before the “Cambrian explosion” that fills IDist chatter).

This puts the Toll-like receptors into perspective, as evolved molecules which retain something close to (but not identical with) the functions that Toll receptors perform in insects, and even in plants.  These proteins are crucial to the function of our adaptive immune system, which surely is not to be ascribed to anything other than accidents of heredity, mutation, and environment (especially to heredity).  No design function is served by the evolution of such a conservative complexity–and of course other aspects of our adaptive immune system are not at all conservative, when compared to the divergent and independent evolution of agnathan (lampreys and hagfish) adaptive immunity.  And even if we may have shared the agnathan adaptive immunity, or vice-versa, clearly an independent evolution occurred in one line or the other one.

In keeping with my desire not to bog down in details covered well by others (see here for a reasonably good discussion of the immune system, and the basics of its evolvability), I will allow the linked illustrations to carry the argument that adaptive immunity evolved just as evolutionary theory predicts, by co-opting existing pathways and (in Behe’s phrase) “physical precursors.” Yet before closing I would like to note another generally neglected aspect of the “irreducibly complex” adaptive immune system, which is that it did not simply become complex at once and then not evolve (as Behe implies), rather adaptive immunity has evolved greater complexity while conserving its core structure (another commonality of evolution):

While increasing complexity of the adaptive immune system is evident with vertebrate evolution, the same basic construction of the adaptive immune system is conserved throughout the gnathostome [jawed vertebrate] radiations. The Evolution of Adaptive Immune Systems

So it is not as if the adaptive immune system was created in peak complexity, which did not evolve, instead it evolved its basic structure early, and then it evolved further.  This should not be the case if such complexity could not evolve in the first place, for how would the irreducibly complex system evolve even more non-trivial complexity?  A degenerate complexity might evolve under an ID scenario, but not the adaptive complexity that has evolved in adaptive immunity.

Of course one may tweak one’s “design theory” endlessly to have the unconstrained “designer” do whatever has happened, including the manipulation of mutations and natural selection.  The trouble is that one needs constraints and entailed “predictions” if one is to do science at all, and evolution is what is constrained to produce the patterns we see (roughly the same in either microevolution and in macroevolution, at least in the aspects discussed here), while all known design constraints, like rationality and purpose, have the advantage of surpassing the limitations of evolution.  The effects of such a transcending intelligence is not seen in life, except where humans have genetically modified organisms.

For instance, there is nothing at all in design that suggests that adaptive immunity should use the same pathways as innate immunity does in both humans and in fruit flies, and the same “physical precursors,” while evolution requires both (or at least modifications of the mentioned pathways–given the developmental constraints imposed prior to our divergence from the ancestors of fruit flies, that is).  Evolution predicts the bridges that we see between the prior innate immunity and the later adaptive immunity, while one of the values of using intelligence to design a system is precisely so that one bypasses such constraints. 

It is absurd to claim that design was necessary to make all of the rather small (very small by design standards) steps predicted by evolution, when in fact leaps are to be expected of intelligence.  Future posts will discuss more of the evidence of small steps, which in fact produced two complex adaptive immune systems, simply because in vertebrate evolution no complex biochemical system can be transferred to a divergent line, while another complex evolution of a needed biochemical system is possible.  A quote from one of the above sources well summarizes the matter:

This consistency of function, structure, order, and purpose over such a wide evolutionary range is a most impressive example of the evolution of a biological function, save for essential processes such as DNA and RNA replication and cell division.  Evolution of the innate immune system

This is part of a series of posts that I am combining into one long post, which may be found at Darwin’s Black Box.