You made several comments in your criticisms of my paper that reveal you to have a less-than-adequate grasp of evolutionary theory (and also didn't bother to read the first half of my paper). Most troubling were when I pointed out what modern scientists have to say on the matter, and your reply was, "then what are you arguing about?" as if it were my intent to prove modern science wrong. You seem to have come to the impression that my disagreements with you have been based in some sort of fundamental disagreement with modern evolutionary theory. Nothing could be further from the truth! I fully embrace modern evolutionary theory; you've demonstrated that your understanding of evolutionary theory is decades behind, however, and rather vague and hyperbolic even by the standards of past decades, which seems to be the source of your confusion.
I have _not_ been arguing with "modern science" or "contemporary evolutionary theory". Since you do not realize how out-of-date your concept of evolutionary theory is, you've taken my objections to what you've been teaching as objections to contemporary evolutionary theory. I need to make this very clear to you: I am _not_ disagreeing with contemporary evolutionary theory! (Which you knew all along, I think, in spite of how you tried to make yourself look, and how you tried to make me look in your e-mails to me, saying things like "you're free to reject whatever you want, but contemporary evolutionary theory is a big part of this class" -- possibly being intentionally obtuse as a pretense for failing me later?) I was pointing out where your knowledge of the subject needs updating. You were saying things in your class that are no longer considered appropriate (Coyne is being somewhat of an apologetic for archaic terms like "higher organisms" and "lower organisms", giving a geological justification but, I think, mainly for reasons of nostalgia -- that kind of terminology is generally avoided nowadays, and you don't seem to be aware that there's a reason for that). I am not the one who's out-of-step with contemporary evolutionary thinking, Karen. You are. You are closer to being an evolution-denier than I am.
Here are my responses to your comments on my final paper:
In response to the first sentence of my abstract, which reads: "Formerly in the field of biology there seemed to be consensus that the morphological complexity of organisms tends overwhelmingly to increase in evolution (McShea, 1991)," you wrote:
"It's clearly documented in the fossil record that diversity and complexity, absent major catastrophies [sic], has tended in macroscopic organisms overall to increase over time."
No, it isn't clearly documented in the fossil record. Diversity might increase in the absence of major catastrophes (or possibly it increases most right after major catastrophes, in which case it depends upon them, so not exactly "in absence of"), but increases in diversity don't necessarily mean increases in complexity, unless you're talking specifically about ecological complexity. (This is why, in the peer-reviewed literature (not fluff pop-science books written by Coyne and his ilk), scientists are nowadays very careful to qualify their statements by mentioning exactly what type of complexity they're referring to: morphological complexity, genomic complexity, genetic complexity, metabolic complexity, organismal complexity, &c.; they do this to avoid inappropriately hyperbolic over-generalizations which, such as in this case, might not even be true in the majority of cases.) While it's possible there's some correlation between ecological and organismal complexity, there's absolutely no reason to assume, a priori, such would be the case, nor is that obvious from the fossil record (as discussed in McShea's paper, many relevant sections of which I've quoted in my paper, and as discussed by many of the authors, even during the 20th century when this was still the prevailing opinion, who were quoted in McShea's paper).
While it's possible to cherry-pick specific examples of certain lineages increasing in one sort of complexity or another, there's also no shortage of counter-examples. Compare for example the skulls of Devonian fishes, including lobe-finned fish like the tetrapodomorpha, and those of modern tetrapods such as humans. The skull of almost any given Devonian fish will have more parts and more different kinds of parts than the comparatively simple human skull, which has only two major parts: mandible and cranium, the former of which is the only moving part. Would you call that an increase in complexity?
And please don't try again to claim, "simplicity can be a kind of complexity, too!" as you at first did when I brought it to your attention in class that prokaryotes (and numerous eukaryotic lineages) show signs of having been streamlined and simplified (i.e., reduced) over their evolutionary history. If you define the word "complexity" such that even simplicity (the literal antonym of "complexity") qualifies as a type of complexity, then you've essentially admitted that you have no clue what you're talking about here; you were mindlessly repeating a meme that prevailed during the late 19th to mid-to-late 20th century (evolution = increasing complexity) that you'd never really critically examined.
This was actually quite common in the 20th century. Scientists were often expected to memorize over-arching principles, "rules of thumb", or "obvious truths" that have since been revealed to be overly simplistic hyperbole (e.g., "speciation requires isolation") or outright falsehoods resulting from selection bias (e.g., "complexity tends to increase over time"). I realize that these were very deeply ingrained, to the extent that for many researchers these "facts" were internalized and made up the original mental context into which all future facts would have to fit, so that even when confronted with evidence to the contrary, your knee-jerk reaction is to hand-wave them away as mere "exceptions", or to doubt the evidence altogether.
I'm trying to be understanding of this, I really am, but what you need to understand is what the field of evolutionary biology has historically been most sneered-at for: seizing upon such "rules of thumb" or "obvious truths" after very little data has been compiled, generalizing inappropriately from that data, and then resisting challenges to aforesaid "rules of thumb" or "obvious truths".
In the speciation example, Darwin assumed that speciation required isolation, and speciation was artificially induced in many _Drosophila_ experiments in the mid 20th century by isolating individuals and artificially separating populations, which was seen as "confirming" the idea that isolation was required for speciation, in spite of the fact that spontaneous, sympatric speciation events resulting from polyploidy and/or hybridization had already been observed in domestic plant populations in the early 1900s, and parapatric speciation events (in which isolation is incomplete, and genetic isolation occurs slowly over time as geneflow is merely somewhat restricted) is now well-known in animals as well (baboons are a good example of this, and I'd be glad to point you to studies on this). Just because externally-imposed isolation had been observed inducing speciation events, scientists wrongly jumped to the conclusion that isolation was the _only_ way to get speciation to occur. So either the soundbyte, "speciation requires isolation" is wrong, or it becomes a useless tautology (because it's only referring to the genetic isolation that we use to define the speciation event itself).
Another example of 20th century conclusion-jumping includes the idea that differences is chromosome number prevent interbreeding; we now know from numerous observations (_Leptidea sinapis_ provides a beautifully extreme example, however there are many instances known from mammals of the genus _Mus_ as well) that chromosome numbers can fluctuate in a single breeding population over time, and that interbreeding tends to occur most successfully between individuals who're less karyotically differentiated from one another, which presumably can lead to sympatric (or somewhere between sympatric and parapatric) speciation events, as this would explain why we often see large differences in chromosome numbers between closely related species.
Like physicists trying to find an equation that could best explain a phenomenon, biologists and other scientists (mostly physicists) dabbling in biology during the 20th century were constantly looking for quick-and-easy soundbytes, convenient principles and "rules of thumb" that could explain the phenomena they were seeing, and like physicists, they expected each effect to have a single cause, or for one "cause", "principle", or other easy-to-memorize soundbyte to be able to explain many different phenomena. These memes and soundbytes functioned as the biology student's equivalent of equations for many years
(I'm trying to be understanding of this, but it does not excuse how you treated me in class. One day, early on in the quarter, after you'd wrongly said before the entire class during the previous class session that "speciation requires isolation", I even showed up with a stack of peer-reviewed research for you, told you I had examples of speciation without isolation, and you just turned and walked away! You obviously care far more about appearing to be correct than you do about actually _being_ correct! You absolutely _do not_ know enough about contemporary evolutionary theory to justify your inappropriately dismissive attitude!)
Next you accused me of setting up a false dichotomy. By this, I assume you're referring to one of two things; either:
A.) The "straw man" (as you later call it) or "extreme viewpoint" (also as you later call it) that "nobody holds" (as you later claim), which is what most researchers in the late 19th and early 20th century actually believed, and what you yourself actually believed at the beginning of the quarter.
B.) The dichotomy you're possibly wrongly inferring that I think exists between what was once called "progressive" evolution (i.e., "complexification", or increases in complexity over time) and what was once called "regressive" evolution (i.e., reduction, such as neoteny, phenotypic loss, parasitism, &c.).
First, I'll briefly address (B):
A fair amount of both has obviously been going on in the history of life on Earth. There is no dichotomy there, and if you think that's what I was implying, then I would urge you to re-familiarize yourself with this subject and then read my paper again. If you wanted my paper to be readable to someone who's been living under a rock for the past 50 years, in a cave, on Mars, with her ears plugged, you should've said so. The question here is whether the "progressive" kind of change (where anatomical/morphological complexity increases in a lineage) can be appropriately generalized to "life on Earth" and is primarily responsible for Earth's current biodiversity, or whether it's something we merely see happening occasionally in particular lineages, for brief periods of time and in regard to specific features. It is a question of how broadly and to which situations we can justifiably apply this "increasing complexity" or "progressive" concept of evolution.
And this leads us to (A):
The words spoken by Allen in class, to which you, the supposed biologist of the duo, assertively agreed, were that, “if evolution were true, we’d expect to see [or the theory of evolution would predict] a smooth progression in complexity over the course of the fossil record, with no dips, spikes, or sudden bursts as might be predicted by an intelligent design or theistic evolution model, and when we look at the fossil record, that’s exactly what we see: a smooth progression in complexity over time.” (paraphrased from memory; although I have witnesses that can back me up on that being what you said, at least one of which has already offered to come forward). The only exception you allowed for this was mass extinctions, which you've chosen to refer to occasionally as "catastrophes"; the implication being that these mass extinctions have causes external to the "natural course" of evolution, such as meteor strikes or other externally-imposed catastrophes.
Neither of you qualified these statements by saying, "in multicellular eukaryotes", or "among already 'complex' multicellular lifeforms"; you didn't say, "we might possibly expect some already 'complex' multicellular lifeforms to become more exaggerated in their multicellularity over time", or anything remotely like that. You stated it as a prediction of evolutionary theory, unambiguously implying it's something that should seem to apply to all life everywhere unless, perhaps, looking very closely at certain isolated exceptions. I even pressed the matter, and asked you what your criteria for complexity were, and you went into a "Gish gallop" about the number and diversity of species, the number and diversity of cell types, the number and diversity of body parts &c., all very different things which cannot honestly be lumped in together and should all be taken as separate points, but, then, you don't do the "Gish gallop" if you plan on having an honest discussion about those points. Your priority was clearly to move the discussion along, which would've been acceptable had you not said something that completely flies in the face of modern biological thinking. You made a generalization about all life on Earth from a trend seen in a decided minority of lineages.
And I understand why. Our conversation early in the quarter about sexual reproduction, when I mentioned how surprising it was to learn that almost all eukaryotes are capable of it, and your response was, "pretty much everything has sex," but then only remembered to mention prokaryotes as an afterthought, was extremely telling and raised red flags. That your first impulse was to regard eukaryotes as "pretty much everything" showed me that you hadn't allowed yourself to experience a sufficient amount of cognitive strain over the changes, not only in evolutionary thinking but in biological thinking as a whole, that have taken place, either since earning your degree or settling down into teaching, but, in any event, far, far too long. You're clearly at least vaguely aware of some of the changes in thinking that have taken place but it's clear you haven't been in the sort of situation where they directly affect you, and/or you're having temporary anachronistic lapses into old thought patterns.
The anthropocentric-eukaryocentric, "from-humans-outward", "fish-eye lense" perspective of biological life, where chimpanzees are regarded as the second most complex form of life, mammals more complex than reptiles, &c.,&c., obligate multicellular forms being regarded as more "complex" than protists, eukaryotes more complex (in an absolute sense, not just morphologically & genomically) than bacteria: It's not right, anymore, Karen. That's not considered appropriate in this day and age. It was odd to still occasionally see it in the peer-reviewed literature in the 1990s, and it's (almost) unheard of now. Terms like "lower animals" have almost entirely nowadays lost favor to more "P.C." phrasings like "evolutionarily successful forms" (no extant organisms, on an individual level, have existed for very long; just because some extant forms happen to look a lot like their very distant ancestors shouldn't be taken to mean they're "less evolved", nor should we regard any extant organisms as having existed for any longer than any other extant organisms, except in terms of individual lifespans). I'm not just being an iconoclast, Karen, you're the one who's out-of-step with modern evolutionary thinking. Please try to understand that.
People like Coyne and Dawkins might have at one time been perfectly passable scientists, but for decades they've made names for themselves, not in the laboratory or by going out and making observations of the natural world, but from arguing against creationism, or theism more generally, which is probably the most intellectually lazy and masturbatory thing a scientist could ever do. They're now cringey to listen to. They say things that would make anyone who's actually been keeping up on the subject of evolutionary biology wince. And they're very sloppy. Logical fallacies everywhere. They're barely even scientists anymore. They're mainly entertainers. They're great to quote when you want to drive-home a point, but you can't trust every "zinger" you hear from them as fact (because a lot of it is now laughably out-of-date, they get attached to particular arguments that they find most compellingly make their point, and tend not to modify those, because, let's face it, you don't spend the majority of your time arguing against something that basically debunks itself, like creationism, if your goal is to learn new things!), and you certainly shouldn't use their popular material as a substitute for legitimate continuing education for yourself or as a required text for a science / scientific philosophy class, except possibly for the purposes of debating whether fluff pop-science helps or hinders legitimate science (in this case, it seems to be hindering!).
Take Neil DeGrasse Tyson for example. On paper, he's a legitimate scientist. Numerous degrees, both earned and honorary. Yet he's on many occasions argued that since many bacteria can tolerate space-like conditions, we might all be descendants from Martians, neglecting to realize that the first lifeforms on Earth weren't bacteria, they were archaea, who more often show tolerance or affinity for decidedly planetary extremes like high pressure, high heat, et cetera., and that, since the number of microbes calculated to be contained in impact ejecta from meteor strikes is sufficient for the Earth to have by now seeded the entire galaxy with life, making it very unlikely the Earth Herself was not a benefactor of such a process, it is very unlikely that life on Earth would've have gotten its start either on Earth or on Mars, but is statistically very likely to have originated somewhere much, much further away. Neil holds a prestigious position and has a lot of clout, yet speaks in sloppy "hyperbolese" that would never, ever be appropriate for a college-level science class! And Coyne is even worse than Tyson in this regard.
As for the idea of a smooth, gradual progression in the complexity of living things, with the exceptions of mass extinctions and "living fossils":
(1) If Smith and Morrowitz (&al.) are correct about about what Smith calls the "inevitable life" scenario, and biological life (or the proto-biogeochemistry immediately preceding it) is an organic-chemical "discharge" resulting from a build-up of energy between the hydrosphere and the lithosphere, then we might actually expect to see the most complex biogeochemistry at or near the origin of life, and for complexity to have generally declined since the beginning.
(2) If the ancestral living things on Earth were essentially prokaryotic, then the leap in anatomical/morphological (and corresponding genomic) complexity was facilitated by the acquisition of the mitochondrion. It's not just the powerhouse of the eukaryotic cell, it's also an important staging platform for the cell cycle. Our cells have an AMPK (adenosine monophosphate kinase) pathway that responds to rising AMP and ADP levels and maintains an ATP:ADP ratio of about 10:1 by triggering our cells to shut down ATP-consuming processes and switching to ATP-producing processes. It's probably why our cells reproduce so much more slowly than prokaryotic cells, because when the gene that codes for the kinase is removed (as demonstrated in studies with _Drosophila_), there are severe phenotypic deformities, as the cells continue trying to divide even when they have insufficient energy to do so. This could be why bacterial multicellularity is so rare, and takes a much less exaggerated form than in multicellular eukaryotes; there may well have been a "complexity ceiling" making complex multicellularity impractical prior to mitochondrigeny. (Alternately, if the NuCom and Primal Eukaryogenesis models should turn out to be correct, mitochondrigeny might've been what constrained the evolution of the eukaryotes, and may explain why their lineage resisted enucleation (which would be a form of phenotypic loss / reduction) when all of the other archaeal and bacterial lineages, excepting, for some reason, the PVC bacterial phyla, have reduced and enucleated in their evolutionary histories. In either event, eukaryogenesis doesn't quite fit with a gradual-increase-in-complexity model; it immediately followed the Great Oxygenation Event, and so appears to have actually been triggered by a catastrophe, and represents either a rapid leap forward in morphological complexity -- in which case you're wrong about an overall gradual increase in complexity as well as about catastrophes reducing complexity -- or else the moment when the amitochondrial lineages began to reduce -- in which case you're right about at least one catastrophe being responsible for a reduction in complexity, but wrong about complexity overall generally going up over time.)
(3) It's not clear that complexity has increased in any absolute sense at the organismal level since the Cambrian explosion (another extremely rapid increase in morphological complexity that presumably took place in response to the oceans losing their opacity, slightly over half a billion years ago), and even less clear (to put it mildly) that we should expect any increases in complexity since that time to take the form of a gradual incline in the absence of catastrophe. Hagfishes have turned out to be reduced agnathan vertebrates related to lampreys, for examples, rather than as a "living fossil" of "primitive" craniates, while the vertebrates themselves are looking to be neotenous (reduced) forms of tunicate-like creatures. The skull of modern birds seems to be neotenous (reduced) when compared to juvenile crocodilians, and although the evolution of feathers from scales would seem to be an increase in the morphological complexity of their dermal tissue, we have as a counter-example crocodilian scales probably having fused from filamentous proto-feather-like structures (in other words, since their common ancestor, both have experienced a great deal of reduction). Humans are neotenous apes, who in-turn show pronounced allometric cranial ontogeny compared to other monkeys, and they in-turn to other primates, as well as they in-turn to other mammals. In fact, encephalization (brain size compared to body size) seems to have generally and steadily increased among land-vertebrates since the tetrapods first came onto land, and this is mainly related to neoteny (a form of reduction, or "regressive evolution" -- this is most resoundingly _not_ an increase in complexity!).
(4) The only reason we might possibly expect to see the average complexity level of life on Earth increasing gradually over time, rather than varying over time in response to the varying conditions of the environment (except for mass extinctions / catastrophes), would in fact be if there were an orthogenesis-like "internal drive" propelling the complexity level upward. You're more likely to hear such a description of the evolutionary history of life on Earth in a re-run of Star Trek than in the peer-reviewed literature today. There's nothing about allele frequencies changing in a population over time that would predict this. You're mischaracterizing evolution. Even _if_ the average complexity level for life on Earth has been creeping upward over time, the model that would best predict that would far more likely come from thermodynamic theory or information theory than from evolutionary theory. Whether life on Earth has become more complex over time, less complex over time, or has stayed roughly the same with regard to the average complexity level, evolution is still necessary to explain change over time. There's nothing in evolutionary theory that predicts an increase in complexity, and demonstrating that there's not been an increase in complexity would in no way damage standard evolutionary theory (it wouldn't "undo" the observation that allele frequencies can fluctuate in populations over time). You're completely and utterly mischaracterizing evolution and what it's meant to explain. There's no such thing as a "forward direction" in evolution, Karen! You even stated this much in class. Why, then, this statement that we would "expect" complexity to have increased over the course of the fossil record, with the simplest organisms appearing earliest and the most complex being the most recent, and the "observation" (insistence) that it seems to have done this confirms evolution? A pre-Cambrian rabbit, would not, as Coyne states, disprove evolution; it would be highly inconvenient (since it would mean mammals must've evolved long before the transitional forms, who must've continued to exist relatively unchanged for half a billion years, began to reach large enough populations that some of them were likely to fossilize), but it would not disprove the observation that allele frequencies change in populations over time. A creature as complex as a rabbit being found in pre-Cambrian strata would likewise pose no problem for evolution. Whether complexity increases or decreases over time is irrelevant to the question of whether evolution is true, and no matter what kinds of change we see occurring over time, so long a those changes involve heritable traits succeeding over alternate versions of those traits, it's still evolution. Evolutionary theory does not in any way depend on what we see in the fossil record, but the fossil record does require evolution as an explanation for change over time.
(5) Archaic 20th century soundbytes from outdated highschool biology textbooks, misconceptions and mischaracterizations of evolutionary theory so appalling they seem to have come from the pages of pulp science fiction, and hyperbolic fluff from pop-science entertainers like Coyne should not be used as substitutes for legitimate scientific facts in a college-level class! even if it is a 12 credit nights-and-weekends class. This is abhorrent. There's no excuse for it.
(6) If you absolutely _insist_ on listening _only_ to famous people, see Stephen J. Gould.
Anyway, on with your criticisms:
On page 12 (which seems to be the first page you actually, read, after page 1), you made several comments on the following passage:
"Often times, if not most of the time, it seems natural selection tends to simplify and streamline rather than to 'complexify'. It tends to be the simpler systems, not the more complex ones, which are more efficient, as our bacterial brethren prove with their rapid reproductive rates and enviable adaptability..."
You circled the first sentence, "often times, if not most of the time, it seems natural selection tends to simplify and streamline rather than to 'complexify'," and asked me for evidence. In the instructions to the assignment, Karen, you directed us to spend the first half of our paper talking about the change(s) that had taken place in scientific thinking, something we used to think was true but no longer do, and then to provide the evidence (observations / experiments) in the second half of our paper. Funny how you completely forget your own instructions when you need an excuse to make it look as though I'd made a statement based on insufficient evidence. Especially when I mentioned a good piece of evidence in the very next portion of the sentence (and included several more in the appropriate portion of my paper, per your directions that you seem to forget about when you need an excuse to criticize me).
Then you circled the word "efficient" and asked the question, "defined how?" Defined in terms of cost-benefits, Karen. The more successfully an organism can reproduce for the amount of energy it has to expend. This is why sedentary lifeforms like plants have been more evolutionarily successful than animals. Why parasitic organisms are so prolific. Why bacterial morphology and bacterial genomes appear so perfectly ordered and elegantly simple compared to eukaryotic morphology and eukaryotic genomes even though the bacteria have experienced far, far more generations since our last common ancestor (and hence should be the most "evolved"). Why larger creatures with more elaborate morphologies (i.e., "more complex") tend to be the first to go during mass extinctions yet less-derived or more-reduced forms tend to survive (which is why birds, being neotenous dinosaurs, were the only dinosaurian survivors of the KT extinction event, and why the amphibians, many of whom still have a body plan and lifestyle comparable to the basal tetrapods that the amniotes evolved from, have endured many mass-extinctions that have taken out huge waves of "more-derived" synapsids and sauropsids). Also why immediately _after_ mass extinctions, when selective pressure is low, we see explosions in morphological complexity among already-complex multicellular organisms (and if prokaryotes have the ancestral morphology for life on Earth, it may be that complex multicellular life never would've evolved to begin with were it not for mass extinctions) due to mass extinctions relieving selective pressure and allowing otherwise costly new traits to pass as neutral mutations possibly long enough to be modified, such as in redundancy-and-differentiation scenarios for increasing morphological complexity. Why many of the evolutionary transitions we've traditionally viewed as increases in complexity, such as the appearance of vertebrates or the gradual increase in encephalization among tetrapods, have been looking more and more to be instead and/or simultaneously cases of reduction. Why reduction seems to be such an successful evolutionary strategy in general. This is basic stuff, Karen! There's no excuse for you not knowing this!
For the whole afore-quoted passage of my paper, you commented, "then why are there so many species?" Because lineages become reproductively isolated from each other, Karen. Not to mention that the word "species" can only be defined non-arbitrarily with regard to sexually reproducing organisms, and most of the genetic diversity among cellular organisms exists in non-eukaryotic archaea, the second most in bacteria. The number of reproductively isolated lineages of sexually-reproducing eukaryotes isn't a good measure of the diversity of life on Earth, it's an even poorer measure of the complexity complexity of life on Earth. A speciation event isn't synonymous with an increase in complexity, and saying that reduction is a successful evolutionary strategy and seems to be the best strategy for enduring most selection pressures isn't the same as saying we should never see differences between lifeforms. Although it is interesting that the greatest genetic diversity on this planet exists among the creatures with the least morphological complexity and the fewest phenotypic variations in their overall anatomy/morphology. This is to be expected if reduction tends to be the more successful evolutionary strategy and if natural selections tends not to favor complexity.
I'm not being an iconoclast here, Karen. You are the one who's out of step with contemporary evolutionary thinking. Your concept of "contemporary" evolutionary theory is decades out-o-date!
In response to the statement, "Complexity tends to arise when selective pressure is low," you commented, "it's certainly true that strong unvarying selection pressures must reduce variation over time." It isn't just that, Karen. It's that mass extinctions are evolutionarily important not because they temporarily inhibit some over-arching general increase toward higher levels of complexity, but because they reduce selection pressure and open up niches, and often lead to evolutionary "revolutions" like, for example, eukaryogenesis. We wouldn't necessarily expect the organisms that exist long after a mass extinction event to be more morphologically complex than the organisms who existed a shorter period of time after said mass extinction. We might even expect to see complexity levels start to decline long after a mass extinction, as selective pressures rise (in fact rising selection pressures might be what spurs mass extinctions to begin with!). Mammals became more diverse and more morphologically complex after the extinction of the non-avian dinosaurs, but it is not clear that their diversity and morphological complexity has been climbing steadily since that time (or at least until the Pleistocene extinction event), nor is it clear that modern mammals are more diverse and morphologically complex than the non-avian dinosaurs were. Not to mention that the non-avian dinosaurs were on the decline and possibly even extinct millions of years before the K-T meteor strike. This idea of a constant gradual increase in complexity interrupted only by mass extinctions and excepted from only by "living fossils" who've somehow managed to evade the forces of natural selection isn't something the fossil record supports. It's a figment of the 19th century imagination, created by inappropriately force-fitting a trend-line onto the history of life on Earth back when we were also, just as inappropriately, using the 5 kingdom system of taxonomy that put multicellular eukaryotes center-stage. It's archaic 20th century pseudoscientific fluff and pretty much everyone knows it now. Entertainers like Coyne are behind the times. They aren't authorities on modern evolutionary thinking. The fact that you aren't capable of understanding this is startling.
Next, with regard to the passage:
"While we can say with a high degree of certainty that there now exist on the Earth organisms far more morphologically complex than any that lived a billion years ago, and while it seems probable, though it is far from certain in light of recent theories regarding primal eukaryogenesis, that there were on Earth a billion years ago creatures more complex than anything that existed two billion years thither, which were, in turn, presumably, at least according to traditional and now it seems very possibly incorrect views regarding eukaryogenesis and abiogenesis, more complex than the first living things, it is not clear that this has been the overall evolutionary trend or that the cases of increasing complexity we've seen aren't actually the exception rather than the rule for evolution."
You underlined "...high degree of certainty that there now exist on the Earth organisms far more morphologically..." and "it is not clear that this has been the overall evolutionary trend..." with an arrow, a question mark, and then the query, "non-sequitor?"
No, it absolutely is not a non-sequitor, Karen! In order for there to be an overall evolutionary trend for complexity, you'd have to see it in a statistically significant majority of lineages. You might be able to get away saying there's a trend toward complexity when it comes specifically to the multicellular eukaryotes (which is _not_ what you said in class; in class you generalized this to all life on Earth, and we had several arguments about that later!), but even that much isn't obvious anymore when many of what in the late 19th century were traditionally considered instances of increasing complexity might actually have been cases of reduction (such as neoteny leading to larger brain sizes), and there are numerous cases of reversions to unicellularity. Just because something happens some of the time doesn't make it an over-arching trend, Karen. That's not a non-sequitor, that's just reality. Do you not understand basic statistical thinking?
Next, with regard to, "it is now commonly believed that there has overall been no significant net-increase in the complexity of life on Earth," you underlined "commonly believed" and said, "by whom? cite source".
It doesn't work like that, Karen. You don't ask someone to cite a source for a commonly known fact. You obviously need to re-take English 101.
I cited sources for the scientific evidence that led us to that point in the relevant section of my paper (you know, the place where you told us to put it in your instructions). Your instructions for the assignment were to describe what we now believe and what we used to believe in the first part of the paper, and then go over the evidence and the experiments and observations in the second part of the paper. I followed your directions, Karen. It's not my problem that you've apparently been living under a rock for the last 50 years (although you appear to be making it my problem!). I'm not the one arguing against contemporary evolutionary theory, here. You are.
Next, with respect to the passage:
"Much of this change in evolutionary thought has already filtered down into the popular culture. In the 2001 sci-fi comedy Evolution, for example, an ill-conceived attempt to use napalm to destroy an alien threat that reproduces and therefore evolves much faster in the presence of heat energy produces a gigantic amoeba-like organism, causing one character to remark, 'That's evolution?!' to which another replies, 'The 'simplest' organisms are often the most fit,' which was a refreshingly accurate scientific observation in a major Hollywood production. Similarly, the articles Making Life Simple (Morton, 1999) and Evolution myths: Natural selection leads to ever greater complexity (Le Page, 2008) at New Scientist, as well as the Wikipedia article on the Evolution of biological complexity (Wikipedia, 2018) all reflect that evolution is no-longer seen as a unidirectional process that leads intrinsically to evermore morphologically complicated forms. That evolution is opportunistic and has no inherent preference for complexity is now so well-understood that to call it "academic" would be an understatement; that natural selection often favors simplicity and that organisms can vary not only in degree of complexity but in type (i.e., genomic complexity, morphological complexity, metabolic complexity, &c.), is now largely regarded as simply a matter of common sense."
You circled the bit where I used Wikipedia as an example of how this shift in evolutionary thinking has already filtered down into the popular culture, and noted, "OK entry point but not generally an academic source unless your point is just so document what viewpoint is common." Was that not exactly what the paragraph was about, Karen? That was what I said in the topic sentence for the paragraph. Why would you even feel the need to put that comment in there? I'm not some 18-year-old freshman who's never taken English 101, Karen. You're the one asking people to cite sources for well-known facts. You're the one who needs to re-take English 101. Or maybe you just need to work on your reading comprehension. Or both.
Then you bracketed the portion, "That evolution is opportunistic and has no inherent preference for complexity is now so well-understood that to call it "academic" would be an understatement," circled, "no inherent preference for complexity," and left the comment, "then what are you arguing about?"
What am I arguing about? Really? Your instructions for this assignment were to pick something people used to believe, but which we no longer believe, and talk about one or more scientific discoveries that led to that change in belief. I followed your directions, Karen!
I'm not being an iconoclast, Karen. I've been sticking up for modern evolutionary theory. That you don't understand this is appalling! Every time I disagree with something you say, you accuse me of rejecting contemporary evolutionary theory. I'm not. I'm rejecting an out-of-date version of evolutionary theory that was little different form orthogenesis and little better than creationism. You don't understand that because your idea of "contemporary" evolutionary theory _is_ that! (Or at least was that, at the beginning of the quarter. You seem to have back-peddled significantly since then, as evidenced by what you say in your comments next).
Next, you say, "To say that generally the overall diversity trend to increase over time and this diversity includes species that are more complex than their ancestors is not to say that evolution, in all lineages, always leads to increasing complexity. Your argument is a bit of a straw man."
Excuse me?! Never once did I say that saying complexity sometimes increases in some lineages is the same as saying it must always increase in all lineages! Not one single time did I say that or anything like that! What you're attempting to do here is deceitful, Karen. I never made any such argument and you damned well know it, Karen!
It took several arguments for me to get you to finally admit that the "increase in complexity" you've been rambling about was something that could at best only be seen in a minority of lineages! I had to fight you to get you to admit that much! I argued with you that it wasn't appropriate to use an anthropocentric-eukaryocentric "fish-eye lense" when looking at the biological world and that it wasn't appropriate to make unqualified generalizations about "life on Earth" from trends that you think you see in multicellular eukaryotes! I had to fight you on that, Karen!
I'm not going to let you pretend that the point I've argued you to is the position you've held all along. Other people heard the things you said before, Karen! What you're trying to do here is extremely intellectually dishonest, Karen!
You set up the straw man that I knocked down, Karen. You created the straw man. Not I. You. Through your sloppy, hyperbolic, and ultimately untruthful portrayal of biological evolution as a process that inevitably pushes life in the direction of increasing complexity. This out-dated version of evolutionary theory you were teaching in class is essentially the same straw man of evolutionary theory that creationists argue against. That's why I had a problem with it. It was such an infantile version of evolutionary theory that even an exceptionally bright creationist could easily debunk it. And I'm not a creationist or an evolution-denier. Creationism debunks itself. You made inappropriate, incorrect, hyperbolic generalizations about how if evolution were true, we'd expect living things (you didn't qualify your statement by saying, "complex multicellular eukaryotes", you were clearly talking about living things in general), for the most part, to gradually become more complex over time throughout the fossil record. That's just wrong. It's an infantile understanding of evolutionary theory that doesn't even turn out to be true for the majority of lineages. You're the one who's unwittingly arguing against contemporary evolutionary theory simply by trying to argue for it without understanding it. You're claiming things for evolutionary theory that evolutionary theory doesn't claim, just because it seems to make a good anti-creationist argument. Evolutionary theory doesn't need you to do that for it. Evolutionary theory is in solid standing; lying for it is unnecessary and insulting. We don't need overly simplistic creationist misunderstandings of evolutionary theory to also be made to look correct. There's no reason to expect increasing complexity over time, only that it would be a possibility among some lineages for some traits if that happened to be selected for.
You may not have said that we should expect complexity to increase in each and every lineage, all the time (nor have I, as you claim, argued as if you were claiming this), but you did state, very vaguely and hyperbolicly, that if evolution were true, we should see "life" (you did not say "multicellular eukaryotic life", you just said "life", and we had several arguments about this later) increasing gradually in complexity over the course of the fossil record, with the exception of mass extinctions and "living fossils". You failed to understand that the cases of increasing complexity _are_ the exceptions, or else you wouldn't have argued with me the way you did in class without mentioning that. You also likely would've mentioned that cases of reduction are plentiful and that reduction is very often a successful evolutionary strategy, had you known about that at the time of giving that lecture, or else when I responded to with, "if you're saying that biological evolution is a process that inherently makes living things more complex over time, there are a lot of biologists who'd disagree with you," you wouldn't have agreed when Allen said, "I don't know of any biologist who'd disagree with that" (and you wouldn't have continued to argue with me about it in your comments in my paper). You clearly didn't know, Karen, and now you're trying to pretend that's what you were saying all along, and that I've been arguing against a strawman? That's unbelievably intellectually dishonest! There were witnesses, Karen!
I really hope this is just some kind of dementia, that you're just covering for Alzheimer's-induced relapses into old thought patterns, because if this has been intentional then you've hoist yourself up by my intellectual shirttails, used my knowledge of the subject of evolutionary biology to bring your own knowledge up to an adequate level (which it obviously still isn't quite at yet), and then, rather than thanking me and giving me full credit for giving you a much-needed crash-course in modern evolutionary thinking, decided to be spiteful, accuse me of of "straw-manning" you ("I never said that! What I actually said is what you're saying right now! Your argument is a straw man!") and flunk me as thanks for proving your out-of-date notions wrong, which would not only be dishonest but inexcusably petty. You're obviously just trying to save face, either for not having the appropriate knowledge of evolutionary theory to begin with or for having had anachronistic mental lapses, and it's not going to work. I'm not going to let you throw me under the proverbial bus to cover for your ignorance/dementia.
This is not okay, Karen!
Next, with regard to the first sentence of the second part of my paper:
"While orthogenesis might seem relatively easy to debunk from a modern point of view, it was not so when the only alternative being offered as a version of evolutionary theory that, like orthogenesis, posited that complexity should increase over time."
You circled the word "should" and wrote, "not really that it should, but that, empirically, it does." No, Karen, there is no empirical evidence that it does, except in certain lineages for certain amounts of time. It's not something you can generalize to all life on Earth or something you can claim as a feature of evolution. Cases of reduction are also extremely common, possibly even more common, but probably roughly as common. And yes, Karen, "should". Scientists in the 19th century to the mid 20th century commonly believed that more complex lifeforms were inherently more fit, and that therefore complexity should increase over time. This is not empirical fact, it was an incorrect prediction that is unsupported by the fossil record. The kinds of evolutionary changes we've seen taking place over the history of the fossil record can only rarely, and even then only controversially, be characterized unambiguously as increases in complexity. Very often, as with the transition from basal chordates to vertebrates, or from basal African apes to humans, these changes turn out to be due to reductive processes like neoteny.
The fact that you felt the need to place that particular correction in that particular spot also shows that you think the late 19th to mid-to-late 20th century version of evolutionary theory I'm arguing against is the one that's still current, and that that's been the only real opposition to orthogenetic theory, which is disturbing, to say the least. I'll refer you to the comparison I made with the heliocentric model on page 8 of my paper (you know, in that stretch from page 2 to page 11 that you didn't actually bother to read).
On page 17, where I make the following point about reduction in sharks: "Phenotypic loss describes morphological simplification and streamlining over time (Maughan &al, 2007). Modern sharks have for the most part adopted a generic 'shark shape' that while now familiar is a much simplified version of the morphologically diverse and often intricately morphologically complex group from which they evolved. Consider for example ancient sharks like the 420 MYO Mongolepis, 390-320 MYO Stethacanthus, the 365 MYO Cladoselache, the 360 MYO Falcatus, the 350 MYO Edestus, the 270 MYO Helicoprion, the 259-66 MYO Hybodus, the 200 MYO Xenacanthus, or the 120-70 MYO Scapanorhuynchus. Modern cephalopods also show evidence of simplification and phenotypic loss compared to ancient cephalopods, many of whom had incredibly elaborate shell designs. Similarly, slugs evolved from snails, not the other way around. Modern jellies have likewise been much simplified compared to the ancestral group out of which they evolved."
You bracketed the statement, "modern sharks have for the most part adopted a generic 'shark shape' that while now familiar is a much simplified version of the morphologically diverse and often intricately morphologically complex group from which they evolved," and added the comment, "biophysical, hydrodynamic principles + natural selection".
Yes, Karen, it's good that you know those words. Would you like a gold star for that?
That is why we've seen the reduction and streamlining we have in those lineages. We see the same hydrodynamic, fusiform body plan in tuna, dolphins, and icthyosaurs. It's a beautiful illustration of how reduction is often the ideal evolutionary strategy. Reduction of body hair in aquatic mammals is also a great example of this. McShea even points out that the vertebrae of aquatic mammals seem to "un-differentiate" and become more uniform in their evolutionary histories (yet another example of reduction/simplification). Sharks and rays also now have a cartilaginous skeleton, reduced from their bony ancestors. This completely contradicts the version of evolutionary theory you were teaching in your class (which is distinct from the version of evolutionary theory you are now dishonestly -- and inconsistently -- claiming to have held all along! There were witnesses, Karen! Other people heard what you said in class!).
On page 18, your comment on my "calculations / armchair stuff" for "blind" orthogenesis (the idea that more complex lifeforms are inherently more fit). You circled the word "invariably" and asked, "does anyone say that?" Yes, people used to say that complex organisms were inherently more fit. That natural selection tended to "prefer" complexity. If that were true, natural selection would invariably favor complexity, and we'd need something else to explain reduction. It was a popular idea back in the 19th and 20th centuries. "Bacteria" (which at the time were considered to include the archaea) were seen as little more than germs, as "primitive" creatures not unlike our distant ancestors, "life on Earth" was seen as mainly being about animals, plants, and fungi, the fossil record was generally regarded as containing nothing of great interest before the Cambrian explosion, and reduction/simplification was sometimes termed "regression" or "de-evolution", and thought to be examples of something contrary to natural selection.
I'm troubled by your use of the present-tense while asking that question. You seem to be under the impression that I'm looking for a reason to "pick a fight" with modern evolutionary thinking. I am not. I'm following the directions you gave us for the assignment. Your instructions were to describe something _we no longer believe_, that _we used to believe_, and what happened in the world of science that led to that change. You don't seem to be able to tell that's what I'm doing because you think the archaic version of evolutionary theory that I'm criticizing is still current, and therefore think when I criticize it that I must be intending to criticize modern evolutionary theory. It is because you lack a solid grasp of contemporary evolutionary theory that you're making this mistake.
I'm also very troubled by the fact that you apparently forgot what the directions to your own assignment were, yet again. I'm not sure if this is dishonesty or dementia, but it's deeply troubling.
Then, under "predictions", where I write, "there should be no known cases of modern organisms appearing to be simplified..." you circle "no known", and ask, "who takes that extreme position?" No-one, Karen. That's the freaking point! Even the people who believed in orthogenesis couldn't account for everything, and had to modify their theory so that there could be at least some known cases of simplification. The same is true for the belief that more complex organisms are inherently more fit. If that were true, and if natural selection were the major force responsible for evolutionary change, there might be "living fossils" who've apparently evaded the pressures of natural selection, but there shouldn't be any known cases of organisms actually becoming simpler over time. Therefore, more complex organisms are not inherently more fit. That's the whole point, Karen. Do I need to spoon-feed you everything?
Next you circle the term "irreducible complexity" and wrote, "typical of the 'intelligent design' crowd". Right. Good. Gold star. Glad you know that. What was the purpose of the comment? I used the term to draw attention to the similarity between this latest "complexity floor" model of a "passive trend for complexity", due to its eerie similarity to the creationist belief of the same name. I made that clear in the first part of my paper. You'd know that if you'd bothered to read the first part of my paper, Karen. There's no excuse for this, Karen!
On page 19, under figure three, where my key says, "a comparison of what we would expect to see occurring over evolutionary time assuming either passive or active evolutionary trend toward increasing complexity," you circle the words "passive or active", and ask, "where do you explain how these _processes_ are different? You show graphs of expected outcomes..."
I show graphs of expect outcomes over time, Karen! They're not different processes, Karen! Why the hell are you assuming they're different processes? They're descriptions of trends! One is what we would expect to see if, for any reason whatsoever, complex organisms tend to be the ones who benefit from natural selection (or whatever the main force of evolutionary change is; it doesn't matter for the purposes of that comparison), the other is what we'd expect to see if complexity arose mostly by random chance, not because of a stronger likelihood of being selected for.
I explained the difference between active and passive trends in the first half of my paper, Karen! Why would you tell us to explain what was believed in one half of the paper and why it changed in the second half of the paper if you didn't actually want us writing the paper that way? Why do you keep forgetting your own instructions?
On the next page, page 20, under "predictions", I write, "complex multicellular organisms should by now vastly outnumber "simple" multicellular organisms, which should in turn vastly outnumber unicellular organisms." You question, "i.e, # of spp.?" Yes, Karen. It's the number of species.
On page 21 you circle the word "passive" out of the phrase, "a passive evolutionary trend", and ask, "meaning? random drift?" Sure, Karen. Close enough. "Constructive neutral evolution" is a term you might want to look up. Or, y'know, you could just read the first half of my paper, where you told us to include all that stuff! Yet again, you seem to have forgotten your own instructions for this assignment.
On page 25, your write, "That's not what I see described as "irreducible complexity". You would have if you'd bothered to read the first half of my paper, Karen! What the hell is wrong with you? You have the audacity to give me half-credit for this class, after reading only half my paper? Is this intentional hypocrisy or just severe dementia?
Finally, on page 29, you bracket my statement, "The relevant question now is why past generations of scientists wrongly inferred an overall, over-arching, largest-possible-scale..." and commented, "I think you're misrepresenting the position - I don't know anyone who holds this extreme view you describe."
You hold that view, Karen! You held that view at the beginning of the quarter! You said that if evolution were true, we would expect "living things" (without qualifying that statement to make it clear that you were talking about a specific branch of the Tree of Life) to become more complex over time. You made the generalization, Karen! You, the person who has a hard time remembering that prokaryotes exist! You said that should [or evolution predicts that that would] be the trend for "life". And no, that's not the same as saying complexity should increase in every lineage, all the time. An over-arching, largest-possible-scale trend absolutely _does not_ mean an all-pervasive, true-in-every-case, inviolable law. You're the one confusing those two things, Karen. You need to re-take English 101. I never accused you of saying increases in complexity were an all-pervasive, inviolable law. You did, however, claim that it was the over-arching trend at the largest-possible-scale (because you generalized the statement to "life", which would have been understandable -- albeit still incorrect -- back when complex multicellular eukaryotes made up 3 of the 5 kingdoms of living things, which is what you'd previously relapsed into in your conversations with me, and what we later had many, many arguments about!). You made that claim. Not I. You. I am _not_ "straw-manning" your position. I am describing a position that evolutionary scientists at one time held (as per your instructions for this assignment), but you keep thinking I'm attacking modern evolutionary thinking because your knowledge of the subject is so pathetically out-of-date that you can't even tell the difference!
There's no excuse for this, Karen!
Now that I've given you a much-needed crash-course in contemporary evolutionary thinking, I'd appreciate you giving me full credit for this class (I've more than earned it after everything I've put up with from you), and, while you're at it, the school should give me an honorary teaching degree for bringing one of their instructors up to speed on her own field of study.
I've certainly demonstrated, beyond even a shadow of a doubt, that I could've taught a class on contemporary evolutionary theory much better than you.
There's no excuse for this lack of professionalism.
- D. Jon Scott