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Notes on the process of evolution.
Keywords: evolution, variation, selection, natural selection, speciation, macroevolution
Living things are observed to change in important and sometimes fundamental ways over the course of many generations. If all we are seeking is a definition for a word, then this is what evolution means.
But a deeper understanding must at least attempt to account for the detailed patterns of change observed on all timescales, including the very long timescale of the fossil record, to provide a mechanism for such change, and explain how and why it works.
The following sections tackle these issues by first describing some of the phenomena that seem to require explanation, then discussing how “evolution” (the modern version of Charles Darwin’s theory) can explain what we observe.
Patterns in Evolution
A number of evolutionary “patterns” are revealed by both paleontological and neontological studies. A complete theory of evolution must adequately explain them all.
Strictly speaking, there are no facts in science; only observations to be explained and hypotheses or theories to do the explaining [→ sidebar]. The best kinds of scientific theories assume a little and explain a lot. The less and the more, respectively, the better. Darwin’s theory on the origin of species by means of natural selection is one of the best, because it assumes practically nothing and explains vastly more than even he imagined. Let’s first look at the sort of things which a useful theory of evolution should explain, or help to explain. I’ve got a list of some of them below. It’s neither exhaustive nor even deliberately representative – they’re things that interest me – but there are textbooks for whatever I’ve left out and also available are various forms of superstitious claptrap for those so inclined.
A really complete and well-written web page would now address all of these systematically. Well, I may get there some day, but don’t hold your breath. Meanwhile, in no particular order, here are some discussions.
Plesiomorphy is a concept directly derived from Darwin’s idea of “descent with modification”. If species 2 evolves from species 1, and in the process develops (or loses) some feature, the features which the two organisms still share are called plesiomorphies: things that have been inherited from their shared ancestry. The thing that is different is called an apomorphy. (Read more.)
The natural world is full of plesiomorphies. Indeed, they are still the primary basis by which life is classified. My cat and I share numerous plesiomorphies – backbones, four limbs, homeostasis (“warm blood”), hair.... We are variations on a theme. Less similar is the spider on the wall. He doesn’t have a backbone, or any bones. He wears his skeleton on the outside. But, his skeleton is made of chitin, the same as my fingernails and hair. His nerves and muscles work much like mine do. And even the tree outside my window uses DNA to carry its genetic code. Adenine, cytosine, guanine and thymine molecules arranged in a double helix.
Patterns Observed in the Field and Laboratory
From Kryazhimskiy et al. 2011, p. 1160: “Microbial evolution experiments in a simple, constant environment reveal a characteristic pattern: At first, a population rapidly acquires beneficial mutations, but then adaptation progressively slows so that thousands of generations pass between subsequent beneficial substitutions [Elena & Lenski 2003].”
Ibid.: “Epistasis describes how the fitness consequence of a mutation depends on the status of the rest of the genome. In one extreme example, called sign epistasis, a mutation may be beneficial if it arises on one genetic background, but detrimental on another.”
Patterns Observed in the Fossil Record
From Thompson 1998, p. 331: “Because of the nature of the fossil record, most of the comparitive estimates across different timescales have used rates of change based on morphological characters. These show an inverse relationship between the measured rate and the timescale on which the rate is based – fast evolution over short timescales and slow evolution over long timescales.”
Ibid.: “... rapid evolution over thousands of years is invisible in the fossil record. Organisms that evolved this rapidly would probably not be recognized as the same species in different geologic strata.”
Ibid.: “Values for long term rates are for sustained directional selection. Estimates of short-term rates also evaluate directional selection, but the observed changes might often be part of a longer term pattern of fluctuating natural selection.”
Maybe better under ‘Pace’: Some evolutionary biologists believe that morphological breaks in the fossil record represent speciation events, and suggest that natural selection plays only a minor role in these rapid transitions. Others maintain that natural selection may cause rapid transitions as well as slow and gradual change and that no new mechanisms need be invoked to explain punctuated morphological evolution (adapted from Seeley 1986, p. 6897).
“These data support the view that morphological transitions that appear abrupt in the fossil record may be a product of classical Darwinian selection and should not be assumed to represent speciation” (Seeley 1986, p. 6897).
The Pace of Evolution
There is an interesting and revealing passage in Stephen Gould’s (1980) book, The Panda’s Thumb, where he remarks upon “The conflict between adherents of rapid and gradual [evolutionary] change...” (chapter 17, p. 180). I am perplexed as to why Gould, a man of no small intellect or learning, should use the word ‘gradual’ as an antithesis to ‘rapid’. Surely the opposite of rapid is ‘slow’? The word gradual means, or can mean, in small increments, and a writer as adept as Gould would surely have been aware of the subtle trick he was pulling.
We shall employ no such sleight of hand, and will explicitly recognise that we have two quite separate and independent things to consider: the speed of evolutionary change per se, and also whether this change occurs in discrete steps or is smoothly continuous.
The Speed or Tempo of Evolutionary Change
Nobody doubts, now, that in some circumstances evolution can proceed very rapidly indeed. Many studies have been published describing significant phenotypic change in a wide range of organisms, including bacteria, gastropods (Seeley 1986), guppies, birds, and introduced plants (Buswell et al. 2010), in timescales as litte as 100 years. Moreover, rapid evolutionary changes can have important ecological consequences as well (Thompson 1998).
Continuous or Quantised?
Again, today there remains little doubt about the basic facts: genes are made of molecules and DNA can’t incorporate half a molecule. Substitions involve whole molecules so, by definition, they are quantised. But what does this really mean? After all, data on the familiar CD or DVD is also quantised (we call it ‘digital’) and yet the effect we perceive is one of smooth continuity.
Virtually every birth of sexually reproducing organisms represents at least a unique combination of alleles. No organism has such a simple genome – one so lacking in possible combinations – that any significant duplication comes about through chance alone.
A major mutation, producing an offspring which is significantly different from its parents, is called a saltation. It is not known what contribution, if any, saltations have made to evolution, overall. Certainly they are unlikely to play any significant role in the evolution of sexually reproducing organisms, because any major genomic departure from the parent population is likely to result in reproductive isolation: the individual cannot reproduce alone, and, being unique, there is no partner with which it will be fertile.
So far we have talked about genetic change. What about morphological change? At this point it is probably worth recalling to mind the oft-cited relationship between genetic and morphological differences in chimpanzees and humans: We differ by only about 1% in the nucleotide bases that can be aligned between our two species [??and the average protein differs by fewer than two amino acids??]. But a large amount of non-coding material is either inserted of deleted in the chimpanzee genome, as compared to the human, bringing the total difference in DNA between the two species to about 4%. (AAAS ‘Decade’ magazine, p. 42, and maybe hunt down the primary sources from 2005 as well) Even so, 4% is rather little to effect what we would consider to be substantial change: to appears that a little genetic mutation can go a long way.
It must be emphasised that stasis in the fossil record means morphological stasis. Nobody knows what is happening to the genes, although it is expected that genetic mutations are continually accumulating, at a more or less steady rate (the neutral theory). This accumulated genetic change remains invisible at a phenotypic (morphological) level for the most part. If it does manifest itself, the phenotypic consequences, more often than not, are non-adaptive (or even fatal) and the mutation does not establish itself or spread. It has long been conventional theory that the overwhelming majority of such mutations are quickly extinguished by natural selection, and that only once in a very great while does a phenotypic variation arise which is successful enough to become “visible” in the fossil record. This version of events, which is entirely consistent with both the neutral theory of mutation, and the observation of stasis in the fossil record, has been around for decades – certainly long preceding 1972.
However, we mustn’t become so fixated with stasis as to believe it is the only game in town. Stephen Gould’s (1980, p. 181) observation that the “extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology” simply isn’t true in all cases – and maybe not even in most cases. Again, part of the problem lies in the lack of rigour in which the debate has traditionally been framed. There is no objective benchmark upon which to base our definitions; this time of what is an “insensible gradation”. Two forms which an expert might immediately recognise as two different species may appear virtually indistinguishable to a non-specialist. [A couple of Beu’s molluscs in a sidebar?] And, in a good many cases, two such species might equally be challenged (e.g. as regional variants) by a different expert, as well. It simply isn’t cut and dried: interpretation and personal preference (e.g. for splitting or lumping) play significant roles. The very existence of the colloquial terms ‘splitter’ and ‘lumper’ tells us that.
Evolution is a two-phase process, comprising variation and (natural) selection. The finest brief explanation of how this works that I have ever read, comes from the Prologue of Stephen Jay Gould’s 1977 book, Ever Since Darwin. Gould asks the rhetorical question, why has Darwin been so hard to grasp? In my opinion, his own attention-seeking and muddled theoretical offerings have been largely to blame! Nevertheless, they do not detract from the elegance of the following passage, which shows Gould at his best:
Why has Darwin been so hard to grasp? … The difficulty cannot lie in the complexity of logical structure, for the basis of natural selection is simplicity itself – two undeniable facts and an inescapable conclusion:
Evolution by natural selection leads to improved adaptation: not to perfection. There is an old joke about two explorers suddenly confronted by a lion. One says, resignedly, that there is no point in running, because the lion can easily outrun both of them. But the other, who has already taken to his heels, shouts back over his shoulder, “I don’t need to outrun the lion. I only need to outrun you.”
And that is how that works. To obtain an advantage, one does not need to be perfect; only better than the ‘competition’.
Life will be easier if we forget about meiosis for the moment; we’ll return to it all in good time.
MORE TO COME!
“One of the most important, and entirely unanticipated, insights of the past 15 years was the recognition of an ancient similarity of patterning mechanisms in diverse organisms, often among structures not thought to be homologous on morphological or phylogenetic grounds” (Shubin et al. 2009, p. 818).
“Homology, as classically defined, refers to a historical continuity in which morphological features in related species are similar in pattern or form because they evolved from a corresponding structure in a common ancestor. Deep homology also implies a historical continuity, but in this case the continuity may not be so evident in particular morphologies; it lies in the complex regulatory circuitry inherited from a common ancestor. In some instances, recognition of deep homologies can help in the identification of cryptic classical homologies, when morphological data alone are inadequate to make the case for homology. For example, the photoreceptors present in various extant clades would not be recognized as homologous without the observation of common underlying genetic cassettes” (Shubin et al. 2009, p. 818).
The unexpected finding that the homologous transcription factors Eyeless and PAX6 have crucial roles in the formation of the eyes of [Drosophila] melanogaster and vertebrates was the first indication that the markedly different eyes of long-diverged phyla had more in common than was previously thought (Shubin et al. 2009, p. 819).
Darwin didn’t know anything about genetics, but his theory requires that selected variations are inherited. Selection acts upon variations no matter how they arise – developmental, nutritional, environmental – whatever. But only if the variable characteristic is passed on can it give rise to a systemic drift in response to the selecting pressure.
The unit of selection is typically the individual: this is the “thing” which lives, dies, and possibly reproduces. However, various traits are “bundled” in the individual. Traits are not selected separately: the whole organism lives or dies, reproduces or not. My genes for outrunning lions (or at least other explorers) will not be passed on to my offspring if my heart is defective and I die at birth.
Although the unit of selection is the individual, it is not the individual that is passed on to subsequent generations. It is their genes which are passed on (or their sister’s genes, in the case of social insects such as ants and bees). This point seems very obvious, but many of the implications are subtle and were rather poorly appreciated prior to the publication of Richard Dawkins’s The Selfish Gene in 1976. Not all of the contentions in this book are universally accepted, but there can be no doubt that this aspect of inheritance is no longer passed over so readily.
|Paleontology generally concerns itself with morphospecies: groups of individuals which are morphologically indistinguishable. (Nobody pretends we know the genetic basis for these units, except in a very few, special cases.) Perhaps because of this, evolutionary studies have tended to revolve around the concept of a species also. This approach is mistaken, in my view, because the very concept of what is a species is an artificial, human construct. Certainly, most of the time it is easy and unambiguous to say a person is a person is a person, but what about a duck? Lots of animals look like ducks, waddle like ducks, and quack like ducks, but does that mean they are one species? Well, that all depends upon how we define “species” and that is not nearly so obvious.||
Allopatric and Sympatric Evolution
include some very simple definitions
include the bit from the AAAS ‘Decade’ magazine, p. 43
The Fossil Record
We do not need fossils to ‘prove’ evolution. The biochemical and structural commonality of life is obvious in every organism, and at every scale, and at every level of complexity. Darwin knew a fair bit about geology, but he deduced his famous theory from living things.
Fossils are essential to evolutionary studies, however. Without them, we could not be aware of the true diversity of life; of extinct forms. No amount of gene sequencing will ever reveal there were once such things as dinosaurs, or trilobites, or giant lycopod trees, or even the strange, umbrella-shaped protists we call Kakabekia which lived more than two billion years ago.
|Without accurately dated fossils, nor could we know when today’s lineages diverged. (Much nonsense is spouted, today, about molecular dating. The substitution rates from which these dates are initially calibrated are derived from fossil evidence, and fossils provide reality checks to test whether calculated divergence times are credible. Doubtless these molecular techniques will improve greatly in time to come, but the track record so far has been spotty, to say the least.)||
In the words of Richard Fortey, “Fossils provide evidence of when, how, and why history happened” (Fortey 2011, p. 280).
The principal misunderstanding to deal with, here, is that no living thing is “more evolved” than any other. Whether bacterium or human being, both share a common ancestor at least 3.4 billion years ago, and both have been evolving ever since.
Truly, there is a fascination about certain organisms – a brachiopod called Lingula, horseshoe crabs, coelacanths, the New Zealand tuatara, ... – which seem little changed from their fossilised ancestors, but this is really just a conceit. To quote from Richard Fortey’s book, Survivors “... I have been rather cautious about using the tag ‘living fossil’ too readily. Just as it is untrue that evolution erases the past, it is also the case that no organism remains completely unchanged through long periods of geological time. The horseshoe crab may carry an ancient carapace on its back [he’s speaking figuratively here, people], but it has still moved with the ages. Even the tuatara has evolved at the genomic level for all that its obscurely smiling visage seems to speak directly of the Triassic” (Fortey 2011, p. 280-281).
Speciation, and Extinction
We have already met one – perhaps the only – form of speciation: anagenesis.
It is popular nowadays to emphasise the role of blind luck (’contingency’) in extinction. To an extent, this is both undeniable and trivial, especially in the context of mass extinctions. If a meterorite falls out of the sky and wipes out a localised taxon, that surely is bad luck: no amount of adaptation is going to cope with that.
But it should not be forgotten that most organisms have gone extinct in other circumstances. Yes, a meteorite may have been instrumental (though just how much is still debated) in wiping out the last of the dinosaurs. However, it should not be forgotten that the great majority of “the dinosaurs” evolved and went extinct long before the end of the Cretaceous. Jurassic forms – Allosaurus, Apatosaurus (=”Brontosaurus”), Brachiosaurus, Stegosaurus, and all the rest – were 80 million years dead before the end-Cretaceous event, whatever it was.
Most organisms appear to go extinct because they are out-competed or fail to adapt to climate change. Consider the panda, for example. Certainly, human beings may well be responsible for hurrying the creature along to an eventual demise, but any analysis of the creature’s ecology shows an organism with little capability to cope with any perturbation in its environment.
However, punctuated equilibrium does not advocate any important role to saltation: “In describing the speciation of peripheral isolates as very rapid, I speak as a geologist. The process may take hundreds, even thousands of years; you might see nothing if you stared at speciating bees on a tree for your entire lifetime. But a thousand years is a tiny fraction of one percent of the average duration for most fossil invertebrate species – 5 to 10 million years. Geologists can rarely resolve so short an interval at all; we tend to treat it as a moment” (Gould 1980, p. 184).
Some evolutionists imagine that the recognition of stasis is a relatively new development, many crediting the concept to Eldredge & Gould 1972. Nothing could be further from the truth. Biostratigraphers have been utilising the concept of stasis since before the publication of Origin. Indeed, almost all of the finer divisions of the geological time scale (ages) are based upon zones defined by the persistent presence of one or another taxon over an extended time range. For example, the age/stage division of the Cambrian through Silurian Periods was completed by Sedgwick and Murchison in the 1830s. Indeed, one of the preferred characteristics for a good index fossil is that its stratigraphic range should not be too long. Even the great period divisions themselves may implicitly recognise the persistence of higher taxa; who does not know that the Cretaceous-Paleogene boundary brought an end to the “age of dinosaurs?”
Stasis is an old idea.
The Role of Determinism in Evolution
It is common to describe evolution as completely ‘random’. Authorities as diverse (in every sense of the word) as Matt Ridley and Stephen Jay Gould make statements such as “Evolution has no pinnacle and there is no such thing as evolutionary progress” (Ridley 1999, p. 24). But, of course, that is nonsense.
In the sense that it has a direction (actually several), as opposed to being guided by some supernatural agency, then evolution is indeed directed. It does, for example, proceed from simple to complex – from primordial slime to hormonally-fuelled teen angst – though this may not always seem like an “advance” in the usual sense. This is elementary reasoning: complex things do not spring into existence, fully formed, without antecedents. They are built from simple components.
But some kind of direction or polarity isn’t the only form of determinism we expect from evolution. We obviously expect the overall adaptation of any lineage to a given environment, to improve over time, until it reaches an equilibrium point where further accommodation to the environment is offset by the biological costs. Writ large, this means that some evolutionary innovations are not only predictable, but are likely to recur in diverse lineages. Mobility, multicellularity, heterotrophy, symbiosis, the acquisition of skeletal elements for support, and the cooption of hard parts for defence, vision, ... the list goes on. And not only is it possible to make such a list, the sequence in which such innovations must arise is also predictable.
In the foregoing, the word ‘predictable’ is intended in a probabilistic sense. I do not resile from it; I sincerely believe that it was inevitable that some form of vision, for example, should have evolved not just once, but many times, independently, among vagile organisms. Not only that, but the broad range of wavelengths that animal eyes respond to is readily explicable to any physicist. The exact when, where, and why, however, are beyond us, at least for the present: there are too many subtlties. For example, a study of the common bacterium Escherichia coli found that two clones having the beneficial mutation which eventually took over the experimental population, initially showed significantly lower competitive fitness than other clones having mutation which later went extinct. Repeated experiments, replaying evolution many times, led to the belief that the initially less competitive clones eventually prevailed because they had a greater potential for further adaptation (Woods et al. 2011).
My preferred analogy for evolutionary “progress” is the two-gases-in-a-divided-box demonstration of entropy: although each individual interaction is purely random, in aggregate the result is as inevitable as it is irreversible. Certainly there are examples of simplification – a flea has lost its wings, a tapeworm has lost its gut – but it is not accidentally that we call such characters ‘derived’ and claim that possession of wings or gut are ‘primitive’ for these organisms. Simplifications can represent progress, too. Moreover, in many such cases, it is uncertain that the organisms’ genomes are “simplified” in any meaningful sense, even if their bodies seem to be.
Re-read and reference Arthur’s Creatures of Accident.
However, this most emphatically does not mean that evolution somehow “knows” where it is headed. It is quite possible for evolution to “steer” an organism into a blind alley which ultimately proves to be non-adaptive.
Sometimes macroevolution is defined simply as evolution of taxa above the level of species. Aside from being worryingly imprecise (see the discussion of species concepts, above), this is not very edifying. In the words of Jeffrey Levinton, it omits the most interesting stuff.
The really good question, here, is whether macroevolution is simply the outcome of “ordinary” evolution (microevolution) carried on for a sufficiently long time, or whether, as some have suggested, there are actually some different processes at work.
In the interests of full disclosure, I’ll declare my hand immediately: I don’t think there are. Some examples of “higher selection” commonly advanced seem flawed to me:
It is sometimes suggested that species with a broad geographic range are less vulnerable to extinction; if they are wiped out in some part of their range, they are more likely to survive in some refuge or another if they are very widely distributed. I feel this argument is flawed because it assumes an essentially random (“field of bullets”) extinction scenario, rather than an event which attacks an ecological niche or food source required by the organism, and also because it is unclear to me how a “species” behaves any differently to a population or any other grouping of individuals in this context.
It is also sometimes suggested that organisms with “short haul” dispersal mechanisms are more likely to speciate frequently, thereby making the clade as a whole less vulnerable to extinction. This model assumes allopatric speciation which, for some reason, seems to have become the almost exclusive fixation of contemporary evolutionary theorists ever since the dubious contribution of Eldredge & Gould 1972. Annoying though that may be, it does not invalidate the example, because nobody doubts that allopatric speciation is important, at least for multicellular, sexually reproducing organisms (by no means the majority of life on Earth). I am more concerned about the arbitrary definition of “the” clade under consideration. Don’t misunderstand me: unlike “species” or any other taxon, clades are real; they are natural phenomena. I just don’t see the relevance of saying this or that particular clade survived an extinction because it is highly diverse. Most evolution theorists believe that all presently living things are descended from a single common ancestor: be we elephants or pond scum, we are all one clade. Some bits went extinct; the rest of us are still here.
Another supposedly “species-level” property is the potential for further adaptation. The study in which initially less competitive clones of Escherichia coli eventually took over the experimental population (Woods et al. 2011) may seem like an example of this. Again, I am unconvinced. The potential for further adaptation lay in the mutations carried by individual members of the two eventually successful clones; not by the clones as a whole.
I cannot improve upon the argument presented by Wallace Arthur as long ago as 1997,
“Let us now return to the question of what constitutes a ‘macromutation’. This is a difficult issue, and in fact most users of the term have failed to define it.... My response to this problem, however, is not to attempt a definition but rather to argue that the view of a dichotomy between micro- and macromutation is an unenlightened one that provides a particularly poor basis from which to make progress in understanding how the genetic architecture of development is modified in the course of evolution.
However, Arthur further points out an argument arising from a consideration of germline development, which must be answered:
“This approach has important consequences for the neo-Darwinian view that major morphological differences between organisms from different higher taxa have been produced through the gradual accumulation of very small changes. Specifically, while in a non-developmental approach it seems plausible that many small changes can indeed accumulate to give a larger one, in a developmentally explicit approach it is clear that many late changes can not accumulate to give an early one. Thus if taxonomically distant organisms differ right back to their early embryogenesis, as is often the case, the mutations involved in their evolutionary divergence did not involve the same genes as those involved in the typical speciation event, where usually the early embryogeneses of the daughter species concerned are virtually identical.
I’ve quoted Arthur at length, so the reader can understand his point of view. That’s only fair, because I am about to disagree with it. For myself, I do not regard ontogenetically early versus late mutations to be necessarily different in kind – only in degree – and I do not make the same distinction that Arthur does between internal and external selection mechanisms [sidebar]. (That is to say, I appreciate the difference, but they are both forms of selection; the similarity of effect seems to me far more important than their difference in agency.) To me, the “mechanisms of genetic change” are not different in any definable sense, statistical or otherwise, based on Arthur’s criteria. (And the availability or otherwise of niche space, etc., is completely irrelevant to the mechanisms at play; only to the degree to which external selection may be effective.)
If one were to make a case for distinctive macro- versus microevolution, then it seems to me that the only objective criterion to offer any hope is the distinction between regulatory versus target genes. But even this is not a clear-cut dichotomy; Arthur again: “It is clear, then, that adult limb formation is no different from embryonic body axis formation in that both involve a complicated network of gene interactions, many of which … remain to be discovered” (Arthur 1997, p. 146).
In summary, mutations that take effect early in ontogeny have more fundamental effects, and lead to more pronounced differences, and tend to remain constant over very long periods of time because they have become developmentally “entrenched”, than mutations that take effect later. But there is no dichotomy; different genes (and therefore mutations to those genes) become active throughout ontogeny. It is a continuum. And, early or late, all mutations are subject to selection, both internal and external. Developmental entrenchment has a far greater effect upon changes early in ontogeny than those which occur later, but it does not “switch off”. Again, it is a continuum. The same mechanisms are evident in all “scales” of evolution; the micro- macro- dichotomy is a false one. Although we may have gotten there by different routes, I believe Arthur would probably agree with me there.
The general tenor of this discussion has been to support the sufficiency of orthodox evolutionary theory.
The phenomena which need to be explained by a credible theory of evolution include anagenesis and stasis in the fossil record, as well as the sometimes abrupt appearance of new taxa which are notably different from any antecedents. I contend that the foregoing discussion of the pace of evolution, which encompasses both stasis and change, sometimes at genuinely rapid rates, together with a clear understanding of how sediments form, and a sensible acknowledgement that no package of rocks represents every moment of its deposition, fully explains the fossil record. There is no need to appeal to mysterious (or at least abyssmally articulated) alternative theories (such as PE) or speculative selection mechanisms (such as species sorting). There may yet be something in these ideas, but I believe the burden remains on their proponents to demonstrate their usefulness; not upon conservative Darwinian theorists to “disprove” them.
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— 1980: The Panda’s Thumb. Norton: 1-352.
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