Pigliucci wrote:Now there are a couple of important things that evolution is not, misleading claims by creationists [and mechanistic materialists] notwithstanding. For example, evolution is not a theory of the origin of life, for the simple reason that evolution deals with changes in living organisms induced by a combination of random (mutation) and nonrandom (natural selection) forces. By definition before life originated there were no mutations, and therefore there was no variation; hence, natural selection could not possibly have acted. This means that the origin of life is a (rather tough) problem for physics and chemistry to deal with, but not a proper area of inquiry for evolutionary biology.... It could be that life originated because of self-organization ... under the proper environmental conditions, soemthing that one of these days will require demonstration by a bright young scientists. (Pigliucci 2002: 76)
(....) Evolution is also most definitely not a theory of the origin of the universe. An interesting as this question is, it is rather the realm of physics and cosmology. Mutation and natural selection, the mechanism of evolution, do not have anything to do with the stars and galaxies. It is true that some people, even astronomers, refer to the "evolution" of the universe, but his is meant in the general sense of change through time, not the technical sense of the Darwinian theory.... The origin of the universe, like the origin of life, is of course a perfectly valid scientific question, even though it is outside the realm of evolutionary biology. (Pigliucci 2002: 77)
-- Pigliucci, Massimo (2002) Denying Evolution: Creationism, Scientism, and the Nature of Science. Sinauer Publishers.
Pigliucci wrote:Chapter 7: Scientific Fallacies
Of Whales, Bacterial Flagella, and the Big Bang
A good way to start is to appreciate that often evolutionary biologists dismiss creationist arguments out of hand because they are "obviously" wrong, without realizing that even a wrong argument can point the way to a legitimate question underlying the fabric of evolutionary theory. Let us consider a few examples to clarify. One of the creationists' persistent questions concerns the distinction between micro- and macroevolution. Scientists use these terms in a very different way from what creationists seem to imply, which is part of the problem. For a biologist, microevolution refers to changes in a species over short periods of time that can be explored with the conceptual and mathematical tools of population genetics and ecology. Macroevolution, on the other hand, refers to changes that occur over much longer periods of time; this is usually the research field of the paleontologist. (Pigliucci 2002: 236)
The relationship between micro- and macroevolution is a legitimate field of research within evolutionary biology, and one that has generated a large amount of controversy over at least the past 60 years. Indeed, the beginning of the debate is often traced to correspondence between Darwin and Huxley, in which the latter pointed out to the author of The Origin of Species that there was no need to postulate very slow and gradual changes as the only pattern of descent with modification, and that sometimes things could move along significantly faster, thereby speeding up the appearance of novel structures or groups of organisms, such appearance being a typical macroevolutionary event. (Pigliucci 2002: 236-237)
The debate resumed during the first part of the twentieth century, during the so-called neo-Darwinian synthesis that has shaped much evolutionary thought until very recently. One of the major contributors to the synthesis was paleontologist George Ledyard Stebbins, who proposed the concept of "quantum evolution" to explain the sudden (in geological terms) appearance of certain groups of animals in the fossil record. According to Stebbins, evolution can proceed at different rates, depending on the environmental conditions and presumably on the amount of available genetic variation in the population that are evolving (the larger the amount of variation, the faster evolution can proceed, other things being equal). But Stebbins, partly under pressure from his more "orthodox" (i.e., mor gradualistically Darwinian) colleagues, such as systematists Ernst Mayr, eventually dropped the idea of quantum evolution from later editions of his book, a process that Carl Schlichting and I have referred to as the "hardening" of the synthesis.[1] (Pigliucci 2002: 237)
Still, during the 1940s a challenge to the recently established neo-Darwinian consensus came from a prominent geneticist Richard Goldschmidt. … Goldschmidt questioned the assumption that simply extrapolating from microevolutionary phenomena would yield a satisfactory explanation of macroevolution, and he explored some of the possible alternatives. With little knowledge of molecular genetics and developmental biology, Goldschmidt couldn’t offer more than bold speculations, the most famous of which is his idea of "hopeful monsters." We need to discuss this concept in a bit of detail because it is still used today by creationists to alternately ridicule evolutionary theory for proposing different hypotheses and accuse evolutionary biologists of ignoring important alternatives that some of their own colleagues have proposed. (Pigliucci 2002: 237)
Goldschmidt reckoned that one way macroevolutionary processes, such as the origin of a new body plan (say, the transition from reptiles to birds), could happen is by what he referred to as "systemic mutations." A systemic mutation, or genetic revolution, is a reorganization of an entire genome in which genes are duplicated and/or shuffled around on the chromosomes. Goldschmidt was aware that when much smaller genomic rearrangements take place (such as the change of physical position of one gene in the fruit fly), major phenotypic changes can occur. Indeed, he had done part of the fundamental work in this field and was therefore on solid empirical ground. Goldschmidt thought that if a genetic revolution were to occur in the offspring of an organism, the result would be, literally, a "monster" -- that is, an animal that would look (and possibly behave) very differently from its relatives and conspecifics. Goldschmidt realized that most such monsters would simply die, or at least would not be able to find mates and reproduce. However, occasionally some might survive to adulthood and even find mates among conspecifics that would not find them too repulsive. These "hopeful monsters" would then fuel the evolutionary change within a species and, if successful, in the long run serve as the origin of a different group of animals altogether. (Pigliucci 2002: 237-338)
Goldschmidt’s ideas, although ridiculed by creationists as an example of how absurd evolutionary biologists can become to defend their "irrational" faith in naturalistic explanations, have actually been abandoned by professional biologists for more than 50 years (roughly since our increased understanding of molecular biology from the 1950s on). Interestingly however, we do know of the existence of some very successful hopeful monsters: A large number of plant species (and almost all ferns) actually do originate through genomic revolutions caused by a spontaneous duplication of their entire set of genes -- a phenomenon called polyploidy. Polyploidy can occur either because of the failure of meiosis (the cellular process that reduces the number of chromosomes to half before each generation begins and that allows sexual reproduction to restore no more than the original full complement) or because of the mating of gametes from two different species, which occasionally can yield a fertile hybrid offspring. Polyploidy does not occur frequently in animals for reasons that are still not well understood and that probably have to do with key differences in the developmental processes of animals and plants. Ironically, however, Goldschmidt did identify a major process leading to macroevolutionary change in many species, just not in the animals he had in mind. (Pigliucci 2002: 338)
Thirty-two years after the publication of Goldschmidt’s book, two paleontologists -- Niles Eldredge and Stephan J. Gould -- reopened the macroevolutionary question with their theory of punctuated equilibria… This is another topic that is very much misunderstood and used out of context by creationists … Eldredge and Gould attempted to link a standard theory of the origin of new species proposed by biologist Ernst Mayr[4] with the observable fossil record -- that is, to link, to link micro- and macroevolution by means of an established theory and the available empirical evidence. They succeeded to a large extent... (Pigliucci 2002: 338)
The publication of Eldredge and Gould's original paper in 1972 spurred a healthy series of research papers aimed at either poking holes in their theory or at supporting it. The current consensus seems to be that there is enough empirical evidence to grant punctuated equilibria real existence, although we do not know how often this mode of macroevolution occurs when compared with more traditional, gradual, evolutionary change. Even so, however, the theory of punctuated equilibria does not solve the problem of micro- versus macroevolution because it provides only part of the answer. Specifically, we now have a model of how biological phenomena at the level of population demography can explain patterns observed in the fossil record, but we still don't know how these changes occur at the genetic and developmental levels... (Pigliucci 2002: 338-239)
Given all this, what, then, causes macroevolution in animals? By and large we still do not know.... Plenty of research has been done over the last few decades to study the developmental and genetic differences between different types of organisms, and this research is likely to lead eventually to a satisfactory anwer to the question of micro- versus macroevolution.... (Pigliucci 2002: 339)
Where, then, is the scientists' fallacy in explaining macroevolution within the context of creationism-evolution discussions? [Or any other discussions for that matter.] It lies in the pretense that we have a full answer when at most we have a few (tantalizing) clues. (Pigliucci 2002: 339)
(....) Perhaps the mother of all macroevolutionary mysteries is the Cambrian explosion... As we saw ..., there is nothing to indicate that the relatively rapid origin of many new body plans in animals is a mystery requiring anything more than our current understanding of evolutionary and ecological problems. [He ignores Evo Devo then] Yet the clues currently available are so few [Not any longer, if one looks at the evidence from Evo Devo] that it is not intellectually honest to say that we "understand" the Cambrian explosion. We are studying it, and we are making progress. One cannot ask more from science. (Pigliucci 2002: 240)
[1] See C. Schlichting and M. Pigliucci, Phenotypic Evolution: A Reaction Norm Perspective (Sunderland, MA: Sinauer, 1988).
[4] Mayr's theory was the so-called allopatric theory of speciation. Allopatry means simply "in different places," and the theory says that if a small population becomes geographically isolated from a larger population from which it originated the small population may evolve independently from the mother group for some time. Population genetics theory (and empirical evidence) tells us that small populations often evolve faster than large ones (they have, literally, less "inertia") because their rare genes can spread relatively rapidly within small populations. If the geographical isolation between the new, small population and the original large one persists long enough, the new population might become different enough to be a new species. Once this happens, the new species, if successful, may expand its area of distribution and population size, and these demographic phenomena can occur very rapidly (during a few thousand of generations). Eldredge and Gould simply realized that allopatric speciation, seen in a geological time frame, would lead to long periods of no change (times of equilibrium, which they called stasis), "punctuated" by relatively rapid (geologically speaking) periods of change -- hence their theory of punctuated equilibria.
-- Pigliucci, Massimo. Denying Evolution: Creationism, Scientism, and the Nature of Science. Massachusetts: Sinauer Associates; 2002; p. 236.
Scott wrote:The classic microevolutionary porcesses are natural selection, mutation, migration, and genetic drift, though some scientists would also include isolating mechanisms and other factors involved in speciation. These are genetically based mechanisms that affect gene pools of species, and that result in change (adaptation) or stasis. Microevolutionary processes operate at the level of the species or population. (Scott 2004: 183)
(....) Evolutionary biologists use the term "macroevolution" to refer to the topics relevant to understanding the distribution of patterns that emerge as species and lineages branche through time. Some of these are the rate of evolutionary change (rapid or slow), the pace of evolutionary change (gradual or jerky), adaptive rediation, morphological trends in lineages (e.g., whether body size gets smaller or larger), extinction or branching of a lineage, concepts ... such as species sorting, and the emergence of major new morphological features (such as segmentation, or shells, or the fusion or loss of bones). Scientists sometimes colloquially refer to macroevolution as "evolution above the species level," but this term does not do justice to the complexity of topics included within the concept. (Scott 2004: 183)
Micro- and macroevolution are thus different levels of analysis of the same phenomenon: evolution. Macroevolution cannot solely be reduced to microevolution because it encompasses so many other phenomena: adaptive radiation, for example, cannot reduce only to natural selection, though natural selection helps bring it about. (Scott 2004: 183)
(....) There is a robust argument among evolutionary biologists over how new body plans or major new morphological features arose. No one disputes the importance of natural selection: it affects the genetic variation in populations, which may be the basis for a new species (in conjunction with isolating mechanisms). All parties likewise recognize the possibility or even likelihood of other biological mechanisms affecting morphological features that distinguish major groups of organisms. The issue in evolutionary biology is how and how much natural selection and other microevolutionary processes are supplemented by other mechanisms (such as regulatory genes operating early in embryological development). (Scott 2004: 184)
-- Scott, Eugenie C. Evolution vs. Creationism: And Introdution. California: University of California Press; 2004; p. 183; 184.
Scott wrote:Within the scientific community, of course, there are lively controversies, including over how much of evolution is explained by natural selection and how much by additional mechanisms such as those being discovered in evolutionary developmental biology ("evo-devo"). No one says natural selection is unimportant; no one says that additional mechanisms are categorically ruled out. (Scott 2004: 127)
-- Scott, Eugenie C. (2004) Evolution vs. Creationism: An Introduction. Univsersity of California Press.
Holmes wrote:The fossil record is not the only source of insight into the Cambrian Explosion. Scientists also have evidence from developmental biology the study of how a fertilized egg turns into an organism. Some early-acting genes can have profound effects on a developing embryo, and changes in these genes are inferred to have initiated the body plan changes of the Cambrian. Working together, molecular biologists and paleontologists are starting to untangle a fascinating scientific puzzle. (Scott 2004: 174)
When We Were Worms
... The paleontologists struggling to explain the Cambrian explosion face a tough task--500 million years separate them from their subject. Until recently their only option was to study the animal fossil record. But now, more and more researchers are taking a different path to enlightenment: scrutinizing the genetic record that has been handed down through the ages to today’s creatures. Comparing the genes of living animals has enabled biologists to crawl back down the evolutionary tree to deduce which genes were present back then and what roles they might have played. (Scott 2004: 176)
The exploration has led some researchers to make the heretical claim that the Cambrian explosion never happened, and others to say it certainly did, and that they have found a likely mechanism: the genes that help the cells of a developing embryo know front from back, top from bottom, and near from far. They believe that these genes were a necessary prerequisite for the exploration--though they may not have been what set it off. (Scott 2004: 176)
The most famous of these genes belongs to a set known as the hox cluster. Hox genes are the mapmakers that tell the embryo’s cells where they are on the body’s front-to-back axis and thus what they should become. In fruit flies, in which they were first discovered, eight hox genes line up on their chromosome like a train of boxcars. The gene at the front of the train tells cells there to make a head and other paraphernalia characteristic of that part of the body, number two takes over a bit further back, and so on back to the guard’s van (Americans call it the caboose), which holds sway over the hindsight end of the animal. By mucking up this orderly sequence, researchers create startling freaks such as flies sprouting legs from their heads. Other sets of genes lay out the body’s up-down axis or distinguish the base of a leg or a wing from its tip. (Scott 2004: 176)
… And about two years ago, three paleontologists began to suspect that these genes could be the answer to another great enigma, the Cambrian explosion. The modular way in which the genes map body regions would have provided evolution with a mechanism to modify one part of the body without changing the rest, to duplicate segments, or add new appendages where none existed before. This is the line taken by James Valentine, of the University of California at Berkeley, David Jablonski of the University of Chicago, and Douglas Erwin of the National Museum of National History in Washington, D.C. (Scott 2004: 176)
… Valentine, Jablonski, and Erwin needed to show that these mapmaking genes actually existed in the Cambrian. That posed a problem--Jurassic Park notwithstanding, genes don’t fossilize, least of all for half a billion years and more. (Scott 2004: 176)
… Fortunately, living organisms hold much of the secret. "The present is the key to the past," says Rudolf Raff, an evolutionary developmental biologist at Indiana University in Bloomington. Raff’s reasoning is simple. Living organisms are the tips of branches in the evolutionary tree. If the same gene occurs in two of these animals, that gene must also have been present in their common ancestor, back where their lineages first split apart. By comparing ever more distantly related organisms, biologists can move down toward the earliest branches near the tree’s root. (Scott 2004: 176)
Fruit flies and frogs--two veterans of the biology labs--have very different body designs. And they occupy twigs on two of the most fundamental branches of the animal tree, the groups known to biologists as protostomes and deuterostomes, respectively (named after the way in which the embryonic mouth forms). Paleontologists know from the fossil record that these two lineages diverged no later than the early Cambrian, 535 million years ago. They could scarcely be more distant cousins. (Scott 2004: 176-177)
… Yet over the past few years, developmental biologists have accumulated more and more evidence of astounding similarities between the DNA sequences in the mapmaking genes of these two groups. Flies and frogs, and by inference their common ancestor in the Cambrian or before, share six hox genes.… [T]he two have diverged so little in more than half a billion years that scientists can snip the gene out of a fly, plug it into a frog, and it will work perfectly, triggering the development of the bottom half of a frog wherever you insert it in the embryo.... Even genes that dictate the development of such modern-seeming accoutrements as hearts, [eyes,] nervous systems, and body segments appear to have been present in the frog-fruit fly common ancestor, way back in the Cambrian or earlier. (Scott 2004: 177)
This was just the evidence the three paleontologists needed--and its implications are still sinking in. For a start, it questions the old assumption that the common ancestor of horses and horseflies, lobsters and Londoners--the giga-great-grandmother of the early Cambrian or before--was a "roundish flatworm," little more than an oozing blob of cells. After all, if the genetic evidence is to be believed, that ancestor could equally well have been a sophisticated, segmented worm with eyes, a heart, a nervous system, possibly even antennae or legs, says, Eddy De Robertis, an embryologist at the University of California at Los Angeles. (Scott 2004: 177)
Another explanation, and the one that fits in best with Valentine and Co’s hypothesis, is that those key developmental genes existed in that roundish flatworm, but didn’t trigger the growth of eyes, limbs, hearts, and segments as they do in post-Cambrian animals…. The Precambrian "eye" that pax6 helped form may have been nothing more than a crude photosensor with a pigment cell to back it up, for instance. Indeed, the fossil record shows no trace of anything as sophisticated as the insect and vertebrate eyes in the earliest protostomes and deuterostomes. (Scott 2004: 177)
… John Finnerty and Mark Martindale of the University of Chicago report that sea anemones have a rich set of hox genes, even though these most primitive of animals have no head nor tail--they face the world equally well in all directions. … Finnerty suspects that [hox genes] may map out the anemones’ far simpler up-and-down axis instead. The best guess is that Precambrian flatworm then commandeered these crude mapmaking genes for use in the crucial front-to-back axis of its more complex body plan--possibly their first big role as the "language of evolution." (Scott 2004: 177)
"Creationists have often said that the one thing we can’t explain is the extremely rapid appearance of body plans in the Cambrian," says Valentine. "And this is the answer. We haven’t understood it until these development guys." (Scott 2004: 177)
... [W]hatever happened to kick-start the Precambrian worm into an evolutionary frenzy, it probably found it much easier to spin off new body plans than a creature would today. "You can do a lot to that animal in terms of its basic body arrangement for two reasons," says Raff. "One is that the world is empty ecologically, so there can be a lot of experiments. Whatever you're making doesn't have to be very good, because there isn't much competition. The second thing is that because the body's relatively simple, changes that would now be horrendous--like changing dorsal and ventral--would have been nothing at all. (Scott 2004: 177-178)
"In the post-Cambrian world, competition is severe, so if you're not good at making a living, you're dead meat. And body plans have become more elaborate, so changes that you make have more consequences. You've connected the genetic machinery together in a certain way, and it may be hard to unconnect it. That's left us with a world in which evolution is largly within body plans." (Scott 2004: 178)
In short, animal life on Earth has grown up. The heady, experimental days of its carefree youth are past and now, saddled with a job, a mortgage, responsibilities, it has settled down into a steady, plodding respectability. Looking back now, we can shed a tear for those days so long ago when life was young and we were worms. (Scott 2004: 178)
Selection excerpted from:
Holmes, Bob. 1997. When We Were Worms. New Scientist 156 (2104): 30-35.
-- Scott, Eugenie C. Evolution vs. Creationism: And Introdution. California: University of California Press; 2004; pp. 174-177.
Jose wrote:There's the "regulatory genome," meaning that portion of the genome involved in regulating gene expression, and thereby regulating developmental form. One of the hallmarks for many animals is a repeating pattern of segments, or "meres." The guys above have repeating patterns of segments--even the little frisbee at the bottom, Tribrachidium, whose three "arms" are wrapped around in a little triskelion. Look at those obvious segmental units on each "arm." I'll guess that we're seeing the results of the Master Switch genes ..., and that we're seeing diversity of form because of the way the Regulatory Genome has produced different patterns of expression of those Master Switch genes.
(....) There are constraints. Once you've got a Hox gene family, and once you're using it in a particular way, you can't make big changes to how you use these genes without screwing up development so much that you're dead. Tiny changes can be tolerated, but not big ones.... So, the normal rules of ecology, and the normal constraints of genetics and development, conspire to place limits on what can be achieved evolutionarily.
(....) [T]here are a great many well-documented examples of gradual change. Many of them were unknown at the time the old quotes were freshly spoken. So, while it may be true that at one time gradualism was not documented in the fossil record, that is no longer true.... In the case of the Cambrian Explosion, it is no longer justifiable to hang onto the old model, that all of the phyla just sort of suddenly appeared. We may not know the precise route that evolution followed, but we certainly know that there wasn't a *pop* and there everything was. There was a very long time beforehand during which lots and lots of gradual events could occur at their leisure. So life tootles along for a long time, without having the occurrence of an unplanned, and unplannable, fortuitous event. Then, for whatever reason, a fortuitous event occurs. Whether it's a type of mutation, or a cell-fusion, or what isn't critical right now. The point is, a fortuitous event occurred. After that event occurred, some new possibilities were made available.
Jose wrote:The fact remains, however, that it demonstrates beyond a shadow of a doubt how major morphological changes occur: by mutations in the regulation of developmental-control genes.
I think it is an obfuscation to equate this genetically- and molecularly-understood process with the vague term, "saltation." Saltation was invented to fill a knowledge gap, using the concept of sudden, major changes in form (mechanism unknown). Now that we know the mechanism for changes in form, and know the genes involved and how they work, we know that the reality doesn't match that old concept.
Of course, scientists can't "produce" major morphological changes on purpose, given that mutations occur at random. Even in searching explicitly for new Antp mutations, for example, one is at the mercy of probability distributions. I can expose flies to X-rays, but I can't tell the X-rays what to do. So, scientists can create collections of animals with different mutations, and perform crosses to move multiple mutations into the same strain--which is what Ed did to create the 4-winged fly--but they can't purposely set out to make a new form of animal with pre-planned characteristics.
(....) [T] there are now well-understood mechanisms for morphological change, involving the "regulatory genome" and "master switch genes" (i.e. changes in regulation of the genes that determine how development proceeds). These mechanisms solve the "problem" of morphological change, and simultaneously eliminate the need for terms like "macromutation" and "saltation." These terms are now seen to refer to mutations (and their effects) in regulatory genes.
I might note, by the way, that stating this fact is not falling into the false ideology of panselectionism. Panselectionism claims that selection is the primary, if not exclusive, means of sorting among mutations and converting genetic diversity into evolutionary change. Describing the mutations and their effects makes no claim of how they become fixed in populations. Often, selection has little to do with it--there are founder effects (e.g. one individual is the founder of an isolated population), or genetic drift (e.g. a few individuals survive a flood). It's actually rather amusing to listen to discussions among evolutionary biologists about the relative contributions of selection vs other mechanisms of fixing alleles in populations. Things can become quite heated, with people calling each other names (like "you rabid selectionist!"). I think the short answer is that we don't know the relative contributions. On the other hand, we hear a lot more about selection, because it's conceptually pleasing; it's hard to teach students about genetic drift and founder effects and keep them awake.
Jose wrote: I think it's an obfuscation to bring in Fisher's and even Goldschmidt's thoughts about things that were then unknown. The only difference between a "micromutation" and a "macromutation," as defined by evo devo, is which genes the mutations are in. So-called micromutations are in genes that don't control morphological characteristics (like hair color, or in the case of Peppered Moths, wing color). So-called macromutations are in genes that do control morphological characteristics....
The kind of "macromutation" that The Ancients imagined when they coined and used the term was for the imagined process of "saltation" in which a Whole Bunch of Things change at once, and presto-chango, there's a new form. This is, as you suggest, the way we'd have to think of the Cambrian "explosion," if we believed in such a thing any more, and if we had no knowledge of the metameric nature of the preceding animals (ie, they were segmented). Now that we do know some things about the preceding animals, why bother to postulate a magic solution when ordinary genetics will do the job nicely?
There is no data to support any other form of life, with unpredictable Lamarckian inheritance patterns. We're pretty much constrained to proposing mechanisms that involve normal genetics.
(....) Individuals cannot evolve. The only way to produce offspring that are different is by having one or more mutations occur in their sex cells, and of course, the reshuffling of existing alleles through meiosis. So, if a mutant offspring is born, he's either similar enough to the others that he can mate with them and pass on his mutations, or he's a dead end--he can't be a new species. He might have some morphological differences, due to mutations in regulatory genes, but if they make him look too different, potential mates won't recognize him. Of course, these "rules" might not apply to self-fertilizing hermaphrodites, like C. elegans.
What are you saying?
