Inside the Process of Speciation

Adaptive radiations are messy, so no wonder we have a hard time reconstructing them.

Darwin drew a legendary diagram in his great book, of lineage trees tracing speciation from ancestors to descendants. It was just a sketch, and naturally had clear fork points where one species turns into two. But in real life, speciation is messier, with range overlaps, inter-breeding, and difficulties telling species apart. Ornithologists are still lumping and splitting species to this day, as more data come in about ranges, genetics, sub-populations, breeding behavior, etc. And if defining existing species is difficult, defining exactly where they split in the distant past is even harder.

Darwin's notebook sketch of speciation, from ancestors ... to descendants.

The advent of molecular data from genomes gave a tremendous boost to the amount of information on which to base phylogenetic inferences. It gave us a whole new domain of life, for one thing. And it has helped sharpen countless phylogenies that not been fully specified by fossil and morphological data. But still, difficulties remain. The deepest and most momentous divergences, like the origin of life itself, and the origin of eukaryotes, remain shrouded in hazy and inconclusive trees, as do many other lineages, such as the origin of birds. It seems to be a rule that when a group of organisms undergoes rapid evolution / speciation, the tree they are on (as reconstructed by us from contemporary data) becomes correspondingly unclear and unresolved, difficult to trace through that tumultuous time. In part this is simply a matter of timing. If dramatic events happened within a few million years a billion years ago, our ability to resolve the sequence of those events is going to be weak in any case, compared to the same events spread out over a hundred million years.

A recent paper documented some of this about phylogeny in general, by correlating times of morphological change with times of phylogenetic haziness, which they term "gene-tree conflict". That is to say, if one samples genes across genomes to draw phylogenetic trees, different genes will give different trees. And this phenomenon increases right when there are other signs of rapid evolutionary change, i.e. changing morphology.

"One insight gleaned from phylogenomics is that gene-tree conflict, frequently caused by population-level processes, is often rampant during the origin of major lineages."

They identify three mechanisms behind this observation: incomplete lineage sorting (ILS), hybridization, and rapid evolution. Obviously, these need to be unpacked a bit. ILS is a natural consequence of the fact that species arise not from single organisms, but from populations. Gene mutations that differentiate the originating and future species happen all over the respective genomes, and enter the future lineage at different times. Some may happen well after the putative speciation event, and become fixed (that is, prevalent) later in that species. Others may have happened well before the speciation event, and die off in most of the descending lineages. The fact is that not every gene is going to march in lock step with the speciation event, in terms of its variants. So phylogenetic inference is best done using lots of genes plus statistical methods to arrive at the most likely explanation of the diverse individual gene trees.

Graphs drawn from different sources relating gene conflicts in lineage estimation, (top), versus rate of morphological change from the fossil record, (bottom), in birds, and over time on the X axis. There are dramatic upticks in all metrics going back towards the end-Cretaceous extinction event.

Similarly, hybridization means that proto-species are still occasionally interbreeding with their ancestors or other relatives, (think of Neanderthals), thereby mixing up the gene trees relative to the overall speciation tree. This can even happen by gene transfer mediated by viruses. "Rapid evolution" is not defined by these authors, and comes dangerously close to using the conclusion (of high morphological change during periods of "gene-tree conflict") to describe their premise. But generally, this would mean that some genes are evolving rapidly, due to novel selective pressures, thus deviating from the general march of neutral evolution that affects most loci more evenly. This rate change can mess up phylogenetic inferences, lengthening some (gene) tree branches versus others, and making a unitary tree (that is, for the species or lineage as a whole) hard to draw.

But these are all rather abstract ideas. How does this process look on the ground? A wonderful paper on the tomato gives us some insight. This group traced the evolutionary history of a genus of tomato (Solanum sect. Lycopersicon) in the South American Andes (plus Galapagos islands just off-shore, interestingly enough). These form a tight group of about thirteen species that evolved from a single ancestor over the last two million years, before jumping onto our lunch plates via intensive breeding by native South Americans. This has been a rapid process of evolution, and phylogenies have been difficult to draw, for all the reasons given above. The tomatoes are mostly reproductively isolated, but not fully, and have various specializations for their microhabitats. So are they real species? And how can they evolve and specialize if they do not fully isolate from each other?

Gene-based phylogenetic tree of Andean tomato species. The consensus tree is in black at the right, while alternate trees (cloud) are drawn from 2,745 windows of 100 kb across the tomato genomes, clearly giving diverse views of the lineage tree. Lycopersicon are the species under study, while Lycopericoides is an "outgroup" genus used as a control / comparison. 

In the graph above, there is, as they say, rampant discord among genomic segments, versus the overall consensus tree that they arrived at:

"However, these summary support measures conceal rampant phylogenetic complexity that is evident when examining the evolutionary history of more defined genomic partitions."

For one thing, much of the sequence diversity in the ancestor survives in the descendent lineages. The founders were not single plants, by any means. Second, there has been a lot of "introgression", which is to say, breeding / hybridization between lineages after their putative separation. 

Lastly, they find a high rate of novel mutations, often subject to clear positive selection. Ten enyzmes in the carotenoid biosynthesis pathway, which affects fruit color in a group that has evolved red fruits, carry novel mutations. A UV light damage repair gene shows strong signs of positive selection, in high-altitude species. Others show novel mutations in a temperature stress response gene, and selection on genes defending plants against heavy metals in the soil. 

Their conclusion (as that of the previous paper) is that adaptive radiations are characterized by several components that scramble normal phylogenetic analysis, including variably preserved diversity from the originating species, post-divergence gene flow (i.e. mating), and rapid adaptation to new conditions along with strong environmental selection over the pre-existing diversity. All of these mechanisms are happening at the same time, and each position in the genome is being affected at the same time, so this is a massively parallel process that, while slow in human time, can be very rapid in geologic time. They note how tomato speciation compares with some other well-known cases:

"Nonetheless, based on our crude estimates within each analysis, we infer that relatively small yet substantial fractions of the euchromatic genome are implicated in each source of genetic variation. We find little evidence that one of these processes predominates in its contribution, although our estimates suggest that de novo mutation might be relatively more influential and cross-species introgression relatively less so. This latter observation is in interesting contrast with several recent studies of animal adaptive radiations, including in Darwin’s Finches [18], Equids [14], and fish [13], where evidence suggests that hybridization and introgression might be much more pervasive and influential than previously suspected, and more abundant than we detect in Solanum."

Naturally, neither of these studies go back in time to nail down exactly what happened during these evolutionary radiations, nor what caused them. They only give hints about causation. Why the stasis of some species, and the rapid niche-finding and filling by others? Was the motive force natural selection, or god? The latter paper gives some clear hints about possible selective pressures and rationales that were at work in the Andes and Galapagos on the genus of Solanum. But it is always frustratingly a matter of abstract reasoning, in the manner of Darwin, that paints the forces at work, however detailed the genetic and biogeographic analyses and however convincing the analogous laboratory experiments on model, usually microbial, organisms. We have to think carefully, and within the discipline of known forces and mechanisms, to arrive at intellectually honest answers to these questions, insofar as they can be answered at all.

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Ruffling the Feathers of Dinosaurs

The origin of birds remains uncertain, as does the status of feathers on dinosaurs. Review of "Riddle of the Feathered Dragons", by Alan Feduccia. 

As regular readers can surmise, I was raised (scientifically) in an empirical, experimental tradition- that of molecular biology. In that field there is little drama, since any dispute can be taken back to the lab for adjudication. No titanic battles of conflicting interpretations happen, and extremely high standards pervade the field, since any lapse is easily discovered and replicated. Despite the dominant position of molecular biology in the major journals, due to its high productivity, it is thus rarely in the public spotlight. It has been a bit of a culture shock to realize that other areas of science have significantly different standards and epistemology. Many fields (such as astronomy or paleontology) are at heart observational rather than experimental, or have other restrictions or conflicts (medical science, nutrition studies) that impair their ability to find the truth, leading to a great deal more interpretation, drama, and sometimes, rampant speculation.

Paleontology, and the study of the past in general, has an intrinsic lack of data. If the fossils are missing, what can one do but to wonder and speculate what could have happened during that gap? And when fossils do turn up, they still lack alot of information about their unfortunate contributor- they are only the bare bones, after all. They may be in bad condition and particularly hard to interpret. Whole genera or above may be represented by a tooth or single bone. Millions of years may go by with nothing to show for it. No wonder speculation fills the gap- but is that science? Incidentally, I have to thank the Discovery Insitute, with its keen nose for scientific controversy, for pointing me to today's author, who disputes the now-conventional view that birds arose from dinosaurs. While Alan Feduccia has nothing to do with Creationism and its offshoots, and is a perfectly respectable paleontologist, he is, in the course of at least four books on the subject, (of which this is the third), clearly frustrated with the reigning interpretations of his field, which has jumped to what he regards as unwarranted conclusions that have led to a flurry of portrayals of feathered dinosaurs.

The Archaeopteryx fossil, Berlin specimen, which dates to roughly 150 million years ago.

The first bird, more or less, was Archaeopteryx. Its Berlin fossil, found about 1875, and dating to roughly 150 million years ago (mya) is perhaps the most beautiful, and informative, fossil ever found- a complete bird, with fully spread flight feathers on its arms and legs, a long tail, claws on its hands,and teeth in its mouth. It had the precisely the in-between characteristics of both reptiles and birds that gave immediate validation to Charles Darwin's theory of evolution by gradual change and natural selection. But where did it come from? That is the big question. While a great many other fossil birds have been found, none substantially predate Archaeopteryx, (other than perhaps Anchiornis, very similar to Archaeopterix, and dating to roughly 160 mya), and thus we really do not know (as yet) from fossils how birds originated. 

Feathers are one diagnostic feature in this lineage. Archaeopterix and many later birds found in China and Mongolia from the Cretaceous have feathers, clearly marking them as birds and as lineally related. But other allied fossils have been found, nominally described as dinosaurs, which are described to have feathers as well. One is shown below. 

Fossil of Sinosauropteryx, which dates roughly to 124 million years ago.

Closeup of the hair-like impressions on the tail of Sinosauropteryx.

Whether these structures are feathers, or related to them, is quite debatable. They look more like hairs, and Feduccia claims that they do not even occur outside the body wall. Some experimentation by others has shown that sub-dermal collagen can form this kind of hair-like fuzz during some forms of decay and fossilization, given proper squashing. Current conventional wisdom, however, describes them as filament-like feathers used for insulation or display. My take, looking closely at these pictures, is that they are not feathers, but are outside the body wall, which, on the tail certainly, would have been very close to the bone. Additionally, as these specimens are all rather late, they could easily be descended from birds, while being large and flightless. Feduccia points out that while land-based animals have never gained/regained flight, flightlessness has evolved many times through the bird lineages. Similarly, extensive lineages of secondarily flightless birds may have developed in the Mesozoic, that conventional paleontologists call dinosaurs, (often with feathers), and posit as evidence that the reverse happened- that birds evolved from dinosaurs. For example, the conventional view of dinosaurs and birds draws on many later fossils from the Cretaceous (such as Deinonychus), which had both bird-like and dinosaur-like features: the "raptors". 

Another character at issue is flight itself. If birds are basal- that is, they arose prior to or separately from the other dinosaurs- then they could easily have developed from small arboreal lizards that learned to glide from place to place. On the other hand, dinosaurs are all relatively large and bipedal. So conventional paleontologists have labored to come up with ways that flight could have developed "from the ground up". Such theories as insect trapping by nascent small wings, or occasional tree climbing with tiny wings, to escape predators, have been invoked as rationales for feathers and wings to develop in terrestraial bipedal dinosaurs. Feduccia counters that in the whole history of flight, all animals (birds, bats, squirrels, others) have developed flight from gliding, not from the ground up. Indeed, there are countless flightless birds, and none of them have resumed flight, despite presumably having much of the genetic wherewithal to do so.

Given patchy data, the leading method to make sense of it and organize organisms from the fossil record into a phylogenetic story is the cladistic method. Practitioners choose a wide range of "characters", (such as the lengths, angles, holes, and other morphologies in the available bones) and tabluate their values from all the proposed species. Then they can mathematically just total up who is more distant from whom. Feducci emphasizes that this is an excellent method for ordering closely related genera and species. But over the long run, evolution repeats itself alot, making numerous flightless birds, for example, or similarly shaped swimming animals, not all of which are as closely related as they might look morphologically. Cladistics is a classic case of garbage-in-garbage-out analysis, and has routinely been overturned by molecular evidence when, among extant species, genomic data is available. Sadly, genomic data is not available for the fossils from the Mesozoic (the age of the dinosaurs, which encompasses, in order, the Triassic (245 mya to 208 mya), the Jurassic (208 to 144 mya) and the Cretaceous (144 to 65 mya) periods), nor from any living descendants of the dinosaurs... other than their putative decendants, birds.

As an aside, molecular phylogenies are also at heart cladistic in their theory and method. They just have a lot more "characters"- i.e. the letters of the DNA sequences in homologous / aligned sequences. But even more importantly, since a large proportion of these characters are neutral, (to natural selection), and thus vary (in sort-of clock-like fashion) no matter what convergent evolution might happen morphologically, molecular phylogenies can easily resolve difficult questions of phylogeny on the short to medium geologic terms. When it comes to the deepest phylogenies, however, going over a billion years, neutral characters become wholly useless due to homogenization by the vast times that have passed, so for such time periods these methods become less incisive.

Crude cladogram illustrating the alternative hypotheses- that birds are descended from theropod dinosaurs, or that birds arise from a basal lineage of their own, directly from the common stem of archosaurs. In the latter hypothesis, numerous bird-like lineages currently construed as dinosaurs might be secondarily flightless birds.

It is cladistics (along with other evidence) that has enshrined birds within the dinosaur lineage, finding that theropods came first, and the avians came later on. (With a contrasting view, and a critique of the contrasting view.) Theropods and birds are certainly similar, compared to their crocodilian / archosaur antecedents. They are bipedal, with similar hip structures, neck structures, and hands/feet reduced from five to three toes. But if much of what we take to be the dinosaurs (those with feathers and the whole so-called "raptor" class), are actually secondarily flightless birds, then one can make a lot of sense of some of these similarities, while casting the origin of birds quite a bit father back in time, more or less co-incident with the origin of true dinosaurs. Such as in the diagram above.

The problem with all this is again time. The early Jurassic and Triassic, amounting to almost one hundred million years before Archaeopterix, provide a lot of evidence for dinosaurs. They first appear roughly 240 mya, and flourish after the major exinction event that ended the Triassic, at 201 mya. The stark lack of evidence for birds, and widespread evidence for dinosaurs, including the lineage (theropods) that are most related to birds, suggests strongly that birds did not originate back in the Triassic, in parallel with the core dinosaur lineages. It suggests, rather, that among the many theropod dinosaurs during the ten or twenty million years before Archaeopterix were some small enough to take to the trees, grow longer arms, and be in position for flight. There were doubtless plenty of insects up there, at least until just about this time of the late-Jurassic, when birds started to eat them! Fossil record gaps are treacherous things, but this one indicates strongly that birds evolved in the middle Jurassic, along with (and within) the wider adaptive radiation of dinosaurs.

"Yet Archaeopteryx is still the classic urvogel- the oldest well-studied bird yet discovered, perhaps some 25 or more million years older than most of the Early Cretaceous Chinese fossils. As we saw in chapter 3, the Solnhofen urvogel is a mosaic of reptilian and avian features, a true bird, and the more it is studied, the more and more birdlike it is revealed to be. Ignoring the element of geologic time, however, many paleontologists have proposed that the Liaoning fossils provide evidence for all the stages of the evolution not only of birds and bird flight but also of feathers, from fiberlike protofeathers to pennaceous, asymmetrical flight remiges. Such a claim is remarkable and would be astounding in any fauna, but is especially so for a fauna so temporally removed from the time of avian origins, presumably before the Middle Jurassic and perhaps well back into the Triassic. 

University of Pennsylvania paleontologist Peter Dodson, remarking on the inadequacies of cladistic methodology, tells us: 'To maintain that the problem of the origin of birds has been solved when the fossil record of the Middle or Late Jurassic bird ancestors is nearly a complete blank is completely absurd. The contemporary obsession with readily available computer-assisted algorithms that yield seemingly precise results that obviate the need for clear-headed analysis diverts attention away fron the effort that is needed to discover the very fossils that may be the true ancestors of birds. When such fossils are found, will cladistics be able to recognize them? Probably not.'"

Feducci makes a lot of insightful points and hits some sensitive marks, in addition to all the trash-talk. Cladistics has problems, hairs are not feathers, and Cretaceous birds don't tell us much about the evolution of bird flight, which doubtless began as gliding between trees tens of millions of years earlier. And he is right that the hunt for clear antecedents of Archaeopterix, whether far in the past or near, should be the focus of this field. But overall, it is hard to fully credit the "birds early" story. 

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Empty Skepticism at the Discovery Institute

What makes a hypothesis scientific, vs a just-so story, or a religious fixation?

"Intelligent" design has fallen on hard times, after a series of court cases determined that it was, after all, a religious idea and could not be foisted on unsuspecting schoolchildren, at least in state schools and under state curricula. But the very fact of religious motivation leads to its persistence in the face of derision, evidence, and apathy. The Discovery Institute, (which, paranthetically, does not make any discoveries), remains the vanguard of intelligent design, promoting "skepticism", god, alternative evolutionary theories, and, due to the paucity of ways to attack evolution, tangential right-wingery such as anti-vaccine agitation. By far their most interesting author is Günter Bechly, who delves into the paleontological record to heap scorn on other paleontologists and thereby make room for the unmentioned alternative hypothesis ... which is god.

A recent post discussed the twists and turns of ichthyosaur evolution. Or should we say biological change through time, with unknown causes? Ichthyosaurs flourished from about 250 million years ago (mya) to 100 mya, with the last representatives dated to 90 mya. They were the reptile analogs of whales and dophins, functioning as apex predators in the ocean. They were done in by various climate crises well-prior to the cometary impact that ended the Cretaceous and the reign of dinosaurs in general.

Bechly raises two significant points. First is the uncertain origins of Ichthyosaurs. As is typical with dramatic evolutionary transitions like that from land to water in whales, the time line is compressed, since there are a lot of adaptations that are desirable for the new environment that might have been partially pre-figured, but get fleshed out extensively with the new ecological role and lifestyle. Selection is presumably intense and transitional fossils are hard to find. This was true for whales, though beautiful transitional fossils have been found more recently. And apparently this is true for the Ichthyosaurs as well, where none have been found, yet. There is added drama stemming from the time of origin, which is right after the Permian exinction, perhaps the greatest known extinction event in the history of the biosphere. Radiations after significant extinction events tend to be rapid, with few transitional fossils, for the same reason of new niches opening and selection operating rapidly.

Ichthyosaur

Bechly and colleagues frequently make hay out of gaps in the fossil record, arguing that something (we decline to be more specific!) else needs to be invoked to explain such lack of evidence. It is a classic god of the gaps argument. But since the fossils are never out of sequence, and we are always looking at millions of years of time going by with even the slimmest layers of rock, this is hardly a compelling argument. One thing that we learned from Darwin's finches, and the whole argument around punctuated equilibrium, is that evolution is typically slow because selection is typically not directional but conservative. But when selection is directional, evolution by natural selection can be startlingly fast. This is an argument made very explicitly by Darwin through his lengthy discussions of domestic species, whose changes are, in geological terms, instant. 

But Bechly makes an additional interesting argument- that a specific hypothesis made about ichthyosaurs is a just-so story, a sort of hypothesis that evolutionary biologists are very prone to make. Quite a few fossils have been found of ichthyosaurs giving birth, and many of them find that the baby comes out not only live (not as an egg, as is usual with reptiles), but tail-first. Thus some scientists have made the argument that each are adaptations to aquatic birth, allowing the baby to be fully borne before starting to breathe. Yet Bechly cites a more recent scientific review of the fossil record that observes that tail-first birth is far from universal, and does not follow any particular phylogenetic pattern, suggesting that it is far from necessary for aquatic birth, and thus is unlikely to be, to any significant extent, an adaptation. 

Ha! Just another story of scientists making up fairy tales and passing them off as "science" and "evolutionary hypotheses", right?  

"Evolutionary biology again and again proves to be an enterprise in imaginative story-telling rather than hard science. But when intelligent design theorists question the Darwinist paradigm based on empirical data and a rational inference to the best explanation, they are accused of being science deniers. Which science?" ... "And we will not let Darwinists get away with a dishonest appeal to the progress of science when they simply rewrite their stories every time conflicting evidence can no longer be denied."

Well, that certainly is a damning indictment. Trial and sentencing to follow! But let's think a little more about what makes an explanation and a hypothesis, on the scientific, that is to say, empirical, level. Hypotheses are always speculative. That is the whole point. They try to connect observations with some rational or empirically supported underlying mechanism / process to account for (that is, explain) what is observed. Thus the idea that aquatic birth presents a problem for mammals who have to breathe represents a reasonable subject for an hypothesis. Whether headfirst or tailfirst, the baby needs to get to the surface post haste, as soon as its breathing reflex kicks in. While the direction of birth doesn't seem to the uninitiated (and now, apparently to experts with further data at hand) to make much difference, thinking it does is a reasonable hypothesis, based on obvious geometric arguments and biological assumptions, that it is possible that the breathing reflex is tied to emergence of the head during birth, in which case coming out tailfirst might delay slightly the time it takes between needing to breathe and being able to breathe. 

This argument combines a lot of known factors- the geometry of birth, the necessity of breathing, the phenomenon of the breathing reflex initiating in all mammals very soon after birth, by mechanisms that doubtless are not entirely known, but at the same time clearly the subject of evolutionary tuning. And also the paleontological record. Good or bad, the hypothesis is based on empirical data. What characterizes science is that it follows a disciplined road from one empirically supported milestone to the next, using hypotheses about underlying mechanisms, whether visible or not, which abide by all the known/empirical mechanisms. Magic is only allowed if you know what is going on behind the curtain. Unknown mechanisms can be invoked, but then immediately become subjects of further investigation, not of protective adulation and blind worship.

In contrast, the intelligent design hypothesis, implicit here but clear enough, is singularly lacking in any data at all. It is not founded on anything other than the sentiment that what has clearly happened over the long course of the fossil record operates by unknown mechanisms, by god operating pervasively to carry out the entire program of biological evolution, not by natural selection (a visible and documented natural process) but by something else, which its proponents have never been able to demonstrate in the least degree, on short time scales or long. Faith does not, on its own, warrant novel empirical mechanisms, and nor does skeptical disbelief warrant them. Nor does one poor, but properly founded, hypothesis that is later superceded by more careful analysis of the data impugn the process of science generally or the style of evolutionary thinking specifically.

Imagine, for example, if our justice system operated at this intellectual level. When investigating crimes, police could say that, if the causes were not immediately obvious, an unnamed intelligent designer was responsible, and leave it there. No cold cases, no presumption of usual natural causality, no dogged pursuit of "the truth" by telegenic detectives. Faith alone would furnish the knowledge that the author of all has (inscrutibly) rendered "his" judgement. It would surely be a convenient out for an over-burdened and under-educated police force!

Evolution by natural selection requires a huge amount of extrapolation from what we know about short time scales and existing biology to the billions of years of life that preceeded us. On the other hand, intelligent design requires extrapolation from nothing at all- from the incredibly persistent belief in god, religion, and the rest of the theological ball of wax not one element of which has ever been pinned down to an empirical fact. Believers take the opposite view solely because religious propaganda has ceaselessly drilled the idea that god is real and "omnipotent" and all-good, and whatever else wonderful, as a matter of faith. With this kind of training, then yes, "intelligent" design makes all kinds of sense. Otherwise not. Charles Darwin's original hypothesis was so brilliant because it drew on known facts and mechanisms to account (with suitable imagination and extrapolation) for the heretofore mysterious history of biology, with its painfully slow yet inexorable evolution from one species to another, one epoch to another. Denying that one has that imagination is a statement about one's intelligence, no matter how it was designed.

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Hand-Waving to God

A decade on, the Discovery Institute is still cranking out skepticism, diversion, and obfuscation.

A post a couple of weeks ago mentioned that the Discovery Institute offered a knowledgeable critique of the lineages of the Ediacaran fauna. They have raised their scientific game significantly, and so I wanted to review what they are doing these days, focusing on two of their most recent papers. The Discovery Institute has a lineage of its own, from creationism. It has adapted to the derision that entailed, by retreating to "intelligent design", which is creationism without naming the creators, nailing down the schedule of creation, or providing any detail of how and from where creation operates. Their review of the Ediacaran fauna raised some highly skeptical points about whether these organisms were animals or not. Particularly, they suggested that cholesterol is not really restricted to animals, so the chemical traces of cholesterol that were so clearly found in the Dickinsonia fossil layers might not really mean that these were animals- they might also be unusual protists of gigantic size, or odd plant forms, etc. While the critique is not unreasonable, it does not alter the balance of the evidence which does indeed point to an animal affinity. These fauna are so primitive and distant that it is fair to say that we can not be sure, and particularly we can not be sure that they had any direct ancestral relationship to any later organisms of the ensuing Cambrian period, when recognizable animals emerged.

Fair enough. But what of their larger point? The Discovery Institute is trying to make the point, I believe, about the sudden-ness of early Cambrian evolution of animals, and thus its implausibility under conventional evolutionary theory. But we are traversing tens of millions of years through these intervals, which is a long time, even in evolutionary terms. Secondly, the Ediacaran period, though now represented by several exquisite fossil beds, spanned a hundred million years and is still far from completely characterized paleontologically, even supposing that early true animals would have fossilized, rather than being infinitesimal and very soft-bodied. So the Cambrian biota could easily have predecessors in the Ediacaran that have or have not yet been observed- it is as yet not easy to say. But what we can not claim is the negative, that no predecessors existed before some time X- say the 540 MYA point at the base of the Cambrian. So the implication that the Discovery Institute is attempting to suggest has very little merit, particularly since everything that they themselves cite about the molecular and paleontological sequence is so clearly progressive and in proper time sequence, in complete accord with the overall theory of evolution.

For we should always keep in mind that an intelligent designer has a free hand, and can make all of life in a day (or in six, if absolutely needed). The fact that this designer works in the shadows of slightly altered mutation rates, or in a few million years rather than twenty million, and never puts fossils out of sequence in the sedimentary record, is an acknowledgement that this designer is a bit dull, and bears a strong resemblence to evolution by natural selection. To put it in psychological terms, the institute is in the "negotiation" stage of grief- over the death of god.

The Pillow Creatures That Time Forgot

Did the Ediacaran fauna lead to anything else, or was it a dead end?

While to a molecular biologist, the evolution of the eukaryotic cell is probably the greatest watershed event after the advent of life itself, most others would probably go with the rise of animals and plants, after about three billion years of exclusively microbial life. This event is commonly located at the base of the Cambrian, (i.e. the Cambrian explosion), which is where the fossils that Darwin and his contemporaries were familiar with began, about 540 million years ago. Darwin was puzzled by this sudden start of the fossil record, from apparently nothing, and presciently held (as he did in the case of the apparent age of the sun) that the data were faulty, and that the ancient character of life on earth would leave other traces much farther back in time.

That has indeed proved to be the case. There are signs of microbial life going back over three billion years, and whole geologies in the subsequent time dependent on its activity, such as the banded iron formations prevalent around two billion years ago that testify to the slow oxygenation of the oceans by photosynthesizing microbes. And there are also signs of animal life prior to the Cambrian, going back roughly to 600 million years ago that have turned up, after much deeper investigations of the fossil record. This immediately pre-Cambrian period is labeled the Ediacaran, for one of its fossil-bearing sites in Australia. A recent paper looked over this whole period to ask whether the evolution of proto-animals during this time was a steady process, or punctuated by mass extinction event(s). They conclude that, despite the patchy record, there is enough to say that there was a steady (if extremely slow) march of ecological diversification and specialization through the time, until the evolution of true animals in the Cambrian literally ate up all the Ediacaran fauna. 

Fossil impression of Dickinsonia, with trailing impressions that some think might be a trail from movement. Or perhaps just friends in the neighborhood.

 
For the difference between the Ediacaran fauna and that of the Cambrian is stark. The Ediacaran fauna is beautiful, but simple. There are no backbones, no sensory organs. No mouth, no limbs, no head. In developmental terms, they seem to have had only two embryological cell layers, rather than our three, which makes all the difference in terms of complexity. How they ate remains a mystery, but they are assumed to have simply osmosed nutrients from their environment, thanks to their apparently flat forms. A bit like sponges today. As they were the most complex animals at the time, (and some were large, up to 2 meters long), they may have had an easy time of it, simply plopping themselves on top of rich microbial mats, oozing with biofilms and other nutrients.

The paper provides a schematic view of the ecology at single locations, and also of longer-term evolution, from a sequence of views (i.e. fossils) obtained from different locations around the world of roughly ten million year intervals through the Ediacaran. One noticeable trend is the increasing development or prevalence of taller fern-like forms that stick up into the water over time, versus the flatter bottom-dwelling forms. This may reflect some degree of competition, perhaps after the bottom microbial mats have been over-"grazed". A second trend is towards slightly more complexity at the end of the period, with one very small form (form C (a) in the image below) even marked by shell remains, though what its animal inhabitant looked like is unknown. 

Schematic representation of putative animals observed during the Ediacaran epoch, from early, (A, ~570 MYA, Avalon assemblage), middle, (B, ~554 MYA, White River and other assemblages), and late (C, ~545 MYA, Nama assemblage). The A panel is also differentiated by successional forms from early to mature ecosystems, while the C panel is differentiated by ocean depth, from shallow to deep. The persistence of these forms is quite impressive overall, as is their common simplicity. But lurking somewhere among them are the makings of far more complicated animals.

Very few of these organisms have been linked to actual animals of later epochs, so virtually all of them seem to have been superceded by the wholly different Cambrian fauna- much of which itself remains perplexing. One remarkable study used mass-spec chemical analysis on some Dickinsonia fossils from the late Ediacaran to determine that they bore specific traces of cholesterol, marking them as probable animals, rather than overgrown protists or seaweed. But beyond that, there is little that can be said. (Note a very critical and informed review of all this from the Discovery Institute, of all places.) Their preservation is often remarkable, considering the age involved, and they clearly form the sole fauna known from pre-Cambrian times. 

But the core question of how the Cambrian (and later) animals came to be remains uncertain, at least as far as the fossil record is concerned. One relevant observation is that there is no sign of burrowing through the sediments of the Ediacaran epoch. So the appearance of more complex animals, while it surely had some kind of precedent deep in the Ediacaran, or even before, did not make itself felt in any macroscopic way then. It is evident that once the triploblastic developmental paradigm arose, out of the various geologic upheavals that occurred at the bases of both the Ediacaran and the Cambrian, its new design including mouths, eyes, spines, bones, plates, limbs, guts, and all the rest that we are now so very familiar with, utterly over-ran everything that had gone before.

Some more fine fossils from Canada, ~ 580 MYA.

• A video tour of some of the Avalon fauna.
• An excellent BBC podcast on the Ediacaran.
• We need to measure the economy differently.
• Deep dive on the costs of foreign debt.
• Now I know why chemotherapy is so horrible.
• Waste on an epic scale.
• The problem was not the raids, but the terrible intelligence... by our intelligence agency.

Supergroups in Search of Their Roots

The early stages of eukaryotic evolution are proving hard to reconstruct.

There is normal evolution, and then there are great evolutionary transitions. Not to say that the latter don't obey the principles of normal evolution, but they go by so fast, and render so many transitional forms obsolete along the way, that there is little record left of what happened. Among those great transitions are the origin of life itself, the origin of humans, and the origin of eukaryotes. We are slowly piecing together human evolution, from the exceedingly rare fossils of intermediate forms and branch off-shoots. But looking at the current world, we are the lone hominin, having displaced or killed off all competitors and predecessors to stand alone atop the lineage of primates, and over the biosphere generally. Human evolution didn't violate any natural laws, but it seems to have operated under uniquely directional selection, especially for intelligence and social sophistication, which led to a sort of arms race of rapid evolution that laid the groundwork for an exponential rate in the invention of technologies and collective social forms over the last million years.

Similarly, it is clear that however the origin of life started out, it was a very humble affair, with each innovation quickly displacing its progenitors, just as the early cell phones came out in quick succession, until a technological plateau was reached from which further development was / is less obvious. While the origin and success of eukaryotes did not erase the prokaryotic kingdoms from which they sprang, it does seem to have erased the early stages of its own development, to the point that those stages are very hard to reconstruct, especially given the revolutionary and multifarious nature of their innovations.

Eukaryotes differ from prokaryotes in possessing: nuclei and a nuclear membrane with specialized pores; mitochondria descended from a separate bacterial ancestor (and photosynthetic plastids descended from yet other bacterial ancestors in some cases); sex and meiosis; greater size by several orders of magnitude; phagocytosis by amoeboid cells; internal membrane organelles like golgi, peroxisomes, lysosomes, endocytic and exocytic vesicles; cyclins that run the cell cycle; microtubules that participate in the cell cycle, cytoskeleton, and cilia; cilia, as distinct from flagella; an active actin-based cytoskeleton, with novel motor proteins; a greatly elaborated transcriptional apparatus with modular enhancers and novel classes of transcription regulators; histones; mRNA splicing and introns; nucleolus and small nucleolar RNAs; telomeres on linear chromosomes; a significant increment in the size of both ribosomal subunits. Indeed, the closer one looks at the molecular landscape, the more differences accumulate. This was quite simply a quantum leap in cellular organization, which happened sometime between 1.8 and 3 billion years ago. Indeed, eukaryotes are not just the McMansions of the microbial world, but the Downton Abbeys- with dutiful servants and complex and luxurious internal economies that prokaryotic cells couldn't conceive of.

Major lineages of eukaryotes are traced back to their origins in a molecular-based phylogeny. Animals (and fungi!) are in the Opisthokonta, plants in the Chloroplastida. So many groups connect right to the "root" of this tree that there is little way to figure out which came first. Also, the dashed lines indicate uncertainty about those orderings/rootings as well, which leaves a great deal of early eukaryotic evolution obscure. Some abbreviations / links are- CRuMs: collodictyonids (syn. diphylleids) + rigifilida + mantamonas; excavates, hemimastigophora, haptista, TSAR:  telonemids, stramenopiles, alveolates, and rhizaria.

A recent paper recounts the current phylogenetic state of affairs, and a variety of other papers over the last decade delve into the many questions surrounding eukaryotic origins. While molecular phylogenies have improved tremendously with the advent of faster, whole-genome sequencing and the continued collection of obscure single-celled eukaryotes, (aka protists), the latest phylogeny, as shown above, remains inconclusive. The deepest root is both uncertain with regard to its bacterial progenitor, and to which current eukaryotes bear the closest relation. There are occasional fossil kelps, algae, and other biochemical traces back to 2.0 to 2.7 billion years, (though some do not put the origin earlier than 1.8 billion years) but these have not been able to shed any light on the order of events either.

Nevertheless, the field can agree on a few ideas. One is that the assimilation of mitochondria (whether willing or unwilling) is perhaps the dominant event in the sequence. That doesn't mean it was necessarily the first event, but means that it created a variety of conditions that led to a cascade of other consequences and features. The energy mitochondria provided enabled large cell sizes and the accumulation of a whole new household full of junk, like lipids in several new membrane compartments. The genome that they contributed brought in thousands of new genes, including introns. 

Secondly, the loss of cell walls and the adoption of amoeboid carnivory is likely one of the first events in the evolutionary sequence. Shedding the obligatory cell wall that all bacteria have necessitates a cytoskeleton of some kind, and it is also conducive to the engulfment of the proto-mitochondrion. For while complicated co-symbiotic metabolic arguments have been devised to explain why these two cells may have engaged in a long-term mutual relationship long before their ultimate consumation, the most convenient hypothesis for assimilation remains the simplest- that one engulfed the other, in a meal that lasted well over a billion years.

Thirdly, the question of what the progenitor cell was has been refined somewhat. One of the most intriguing findings of the last half-century of biology was the discovery of archaebacteria (also called archaea)- a whole new kingdom of bacteria characterized by their tendency to occupy extreme habitats, their clear separation from bacteria by chemical and genetic criteria, and also their close relationship to eukaryotes, especially what is presumed to be the original host genome. Many proposals have been made, (including that archaea are the original cell, preceding other bacteria), but the best one currently is that archaea split from the rest of bacteria rather late, after which eukaryotes split off from archaea, thus making the latter two sister groups. This explains the many common traits they share, while allowing significant divergence, plus the incorporation of many bacterial features into eukaryotes, either through the original lineage, or by later transfer from the proto-mitochondrion. So here at last is one lineage that survived out of the gradual development of eukaryotes- the archaea, though one wouldn't guess it from looking at them. It took analysis at the molecular level to even know that archaea existed, let alone that they are the last extant eukaryotic sister group.

A comically overstuffed figure from an argument for the late development of archaebacteria out of pre-existing bacteria (prokaryotes), with subsequent split and diversification of eukaryotes out of a proto-archaeal lineage. Many key molecular and physiological characters are mentioned.

Lastly, surveying the various outlying protist lineages for clues about which might hearken back to primitive eukaryotic forms, one research group suggests that the collodictyonids might fit the bill. Being an ancient lineage means that it is lonesome, without a large family of evolutionary development to show diversification and change. It also means that in molecular terms, it is highly distinct, branching deeply from all other groups. Whether that all means that it resembles an ancient / early form of the eukaryotic cell, or went its own way on a unique evolutionary trajectory, is difficult to say. For each trait, (including sequence traits), a phylogenetic analysis is done to figure out whether it is differential- shared with some other lineages but not all- whether those without the trait lost it at some later point, or whether it was gained by a sub-group. After analyzing enough such traits, one can make a statement about the overall picture, and thus the "ancient-ness", of an organism.

Is anything special about collodictyon? Not really. It is predatory, and has four flagella and a feeding groove, which functions as a sort of mouth. It can make pseudopods, has normal microtubule organizing centers for its flagella, and generally all the accoutrements of a eukaryotic cell. It lacks nothing, and thus may be an early branching eukaryote, but is not in any way a transitional form.

An unassuming protist (collodictyon) as possible representative of early eukaryotes. Its cilia are numbered.

At this point, we are left still peering darkly into the past, though obscure living protists and their molecular fossils, trying to figure out what happened when they split from the bacteria and archaea. A tremendous amount happened, but little record survives of the path along the way. That tends to be characteristic of the most momentous evolutionary events, which cause internal and external cataclysms, (including the opening of whole new lifestyles to exploit), that necessitate a rapid dynamic of further adaptation before their descendents achieve a stable and successful state sufficient to ride out the ensuing billion or more years ... before we come on the scene with the ability and interest to contemplate what went before.

• Red regions have three times the death rates from Covid as blue regions. Will that change electoral math?
• Annals of secession, cont.
• Sad spectacle at the court.
• Analysis of how the energy transition might go. Again, a carbon tax would help.

Native Americans and Genetics

A fraught story.

The recent profusion of DNA studies of human lineages have clarified a lot about human history- where we came from and where we have travelled over the millennia. All this depends on samples from native populations- the ones we came from. It is only apparent that we came out of Africa if there are stable African populations that constitute the source and retain the vast diversity of our oldest homeland. But what if the natives do not want to be sampled? What if they are woke to the colonialist and genocidal legacy of the science / scientists doing the sampling, and want no part of it?

That is what happened, in part, in the recent flap over Elizabeth Warren's announcement of Native American heritage. Native South or Central American, that is. As told by a couple of experts, the lab that performed the analysis could not get permission to use North American samples, so used DNA from populations elsewhere in the Americas. Since Warren is herself from North America, indeed Oklahoma, and since the history of native peoples throughout the Americas is known to be relatively recent, expanding over last 15,000 years at the outside, the method is clearly valid in inferring, indirectly, some North American native ancestry for Warren.

So why the guff she caught from the Native American community? It was quite puzzling to hear their representatives trying their hardest to pour cold water on her claim, as though they were getting talking points from the FOX propaganda channel. Despite her not claiming to be a tribal member or wanting to be, they trotted out their arcane rules for membership, which certainly wouldn't accept anything so white as DNA testing. But lo and behold the tribe- the Cherokee in this case- use fractional blood relations determined from a list compiled by white people of the US government back in 1902. There are no good answers here, after half a millenium of disposession, destruction and abuse, but denying the obvious is not one of them.

The deeper issue is the appropriation and objectification of Native Americans and their culture by others, from here to Germany and beyond. Playing cowboys and indians, putting on Karl May dramas, naming sports franchises ... we have a very fraught relationship of romanticization and trivialization, little of which has anything to do with real Native Americans, particularly those living today who wish to be custodians of their own culture even while still suffering under the various debilities of their treatment by the dominant culture. I was part of this myself, in the Boy Scouts, which still play at being Indians, mortifyingly enough. Then the history of eugenics, and the plundering of native treasures, archeology, and burials, etc. has put so-called scientists in a particularly bad light.

This forms the backdrop of the notorious fate of the Kennewick man, an archeological find that led to bitter, drawn-out controversy. The almost complete skeleton, found in Washington state at the Columbia river, was 9,000 years old, and by morphology was more similar to other peoples such as the Jomon aboriginal people of Japan than native Americans. Ironically, it was DNA testing that confirmed affinity with Native Americans after all, after which the remains were given to the local Native American nations, including the Umatilla, which buried them at an unpublished location. From the native perspective, this fed into the narrative that their history is eternal and static, meaning that any pre-Columbian artifacts or remains found on what is currently their land is associated with their culture in some way, despite the thousands of years that may have passed and migrations that may have happened, and thus presents the right of possession and cultural use. One gets the distinct impression that Native Americans do not really want to know their own deep history, preferring a religious narrative of having been forever in the Americas, instead of having wandered in a few thousand years before the Europeans did.

From a scientific perspective, the episode was a travesty of political correctness, as a 9,000 year old skeleton could have no imaginable cultural connection to the current inhabitants of the area, while being an inestimably rich source of knowlege about this early post-glacial time of North American settlement. This antiscience attitude is perhaps a fair harvest for all the harms and hurts inflicted over the last few centuries, science being one of the most domineering and distinctive expressions of Western culture. Still, the loss to general knowledge rankles.

One Cherokee representative spoke of how irritating it is to repeatedly meet people who claimed to be part Cherokee, expecting some positive pat on the head. But those people wouldn't dream of moving back to the reservation, or taking part in Cherokee culture, as is undoubtedly true of Elizabeth Warren as well. It is a "heritage" without practice and of dubious significance. Nor may they be alive to the sense of loss and injury this represents, as such blood mixing may not have been voluntary, but the result of rape and rapine of various sorts.

Nevertheless, it would seem advisable for Native Americans to get off their metaphorical high horses and be more welcoming to the diversity that exists in the US. Even if the pride that Warren feels in her minuscule Native American ancestry is somewhat false, romaticized, and lacking in practice/practical effect, it is still pride, unmistakably, rather than its opposite. Citizens of the US generally take pride in vibrant Native American cultures and take steps through the government to help them, via direct aid, educational assistance, gambling concessions, and other benefits, after and in compensation for, the deeper history of genocide, reservation confinement, ethnic cleansing, and cultural extermination. The relationship is surely a difficult, guilty one. No one wants to alter the definitions that American Indian nations have developed for their formal membership. But their wider membership of genetic descendants is also a positive asset, in pursuit, not of assimilation, but of friendly relations with the wider, shared culture.

• Stiglitz on inequality.
• Meanwhile, the Taliban may not be popular, but they are persistent.
• Class action? Good luck.
• What are you if you enjoy lying? 
• Homelessness is a growing crisis of inequality and government sclerosis.
• Now for some nice piano.
• And some nice paintings.

Pterosaurs

Yes, they really did fly- the amazing world of pterosaurs.

National Geographic recently had a beautiful spread on pterosaurs- those ungainly creatures that nobody thought could fly, until, apparently, we realized they really did fly. Indeed, they ruled the skies for over 160 million years- far longer than birds have. They operated a good deal like bats, with wings of membrane spread between modified fingers, which also stretched back to their legs. But a crucial difference is that, unlike bats, pterosaurs used only a modified fifth finger to carry the outside of the wing. The other fingers made up a strong hand about mid-wing that could be used for walking and lifting off. Thus pterosaurs were much better walkers than bats, and could also lift off from a standstill more effectively.

Reconstruction of the largest known pterosaur, Quetzalcoatlus, as tall as a giraffe, from the late Cretaceous.

What remains astonishing is how much apparent weight these animals carried, especially in front. The largest known pterosaur, Quetzalcoatlus, weighed about 440 pounds and had an enormous head. The head may have been quite thin, but, with neck, takes up roughly half its length. All pterosaurs tended to have large heads, and frequently added remarkable crests or horns, as if snubbing their beaks at aerodynamics. But looks are deceiving, since, like the toucan's bill, pterosaur crests and bones are hollow, very thin (1 mm), and thus were very light. The classic Pteranodon, with a crest almost as long as its enormous bill, is estimated to have weighed only 25 pounds, easily carried by a wingspan of 25 feet. Whether they could have carried off the hapless Zara Young is another matter.

Beautiful specimen of Rhamphorhynchus, from the Jurassic, with impressions of wing and tail membranes.

What is almost as compelling as the fossils of pterosaur bones are fossilized trackways, which show them in action. Over thirty walking tracks have been found, and one paper even describes what the authors interpret as a landing track. Typical pterosaur walking tracks show the heavier hind feet on the inside, and the wing/hands much more lightly on the outside. At each stride, the rear feet pull up roughly parallel to where the wing/hands have just left (b, in the figure). In these novel tracks, which begin abruptly, there are only hind feet for two strides, before the wing/hands appear. Secondly, the first hind feet tracks have elongated claw marks. Thirdly, the first two or three hind foot track sets are parallel and show a very short stride, different from typical walking gaits, of which the rest of this track is an example. These characteristics all lead to the idea that this pterosaur was landing, and hopped a couple of times with both feet before transitioning to a walking gait.

150 million year-old tracks from France. Top is an interpretation of the middle tracks, as evidence of landing. Below is a typical walking sequence and interpretation from the same location / source. The scale bar at bottom is 10 cm, so this pterosaur was relatively small.

This is not new work, dating from 2009, but the message is still a little hard to wrap one's head around- that tens of millions of years went by with these incredible creatures carrying on the battle for survival, with great success, and high style as well.

Nyctosaurus gracilis, reconstructed, from the late Cretaceous.

• A dumber nation- Thanks, Scott Pruitt!
• Xmas notes on another flying life form.