Fossil Bone Histology

3 04 2013

9780520273528This is a brand new book by Padian & Lamm, published just last month by University of California Press: Bone Histology of Fossil Tetrapods: Advancing Methods, Analysis, and Interpretation. I have not read it (although it seems like a state-of-the-art book), but thought this would be a good way to introduce a basic post on fossil bone histology.

Histology is a widespread method in biology. At its purest, it’s the practice of slicing structures thin enough that we can shine light through them, making them examinable under a microscope. More advanced histology can involve staining to make certain components stand out. One can also make serial thin sections, scan them digitally, and make 3D reconstructions that can be navigated through.

Histology is also used in geology – making thin sections of rocks is the most surefire way of identifying their mineral components. All three-dimensionally preserved fossils can also be studied histologically – see my post on the Herefordshire locality for examples of fossils that can only be studied by serial histology.

Histology of fossil bones has a long history, dating back at least to the 19th century. See the work of James Bowerbank (1848) for an example using pterosaur bones. Much information can be gleaned from bone histology. For another pterosaur example, de Ricqlès et al. (2000) used histology to find that pterosaurs had a fast metabolism and grew at rates more similar to birds than to reptiles.

Such insights can then lead to more informed hypothesising about the ecology and systematics of extinct animals. For example, histological analyses of theropod bones show that they had bones that they grew very rapidly and with a structure typical of today’s large birds (Erickson et al., 2001); this is one more piece of evidence for the dominant hypothesis of birds being theropods.

The detail that can be received from such analyses is considerable. Varricchio (1993) found that the troodontid dinosaur Troodon formosus reached its adult size in less than five years. The basis for such observations is the fact that bone is a living tissue that records the growth and life of the animal. Bone deposition can occur in seasonal cycles, in which case the histological section shows a tree ring-like pattern, or bone deposition can be continuous. The rapidity of bone deposition results in different bone microstructure, all of it preserved in fossils, allowing easy distinction between fast and slow growth. In essence, you can make a cross section of a bone and read the story of its animal from birth to death, like a timeline. Below you can try it for yourself, using a diagram ripped from Martin’s Introduction to the Study of Dinosaurs (2006, 2nd ed.).

histolog

Starting from the bottom, you have a dark brown line. This is a line of arrested growth (LAG), a line indicating that no growth happened for a certain period. Between the first two LAGs are two closely-packed layers of fibrolamellar bone, characterised by those large white blotches, which are canals. These form when growth rate is high, so fibrolamellar bone is a telltale sign of fast growth.

Between the second and third LAG are two vascularised layers, but there is a distinct space between the layers. This is called an annulus, and the lack of canals tells us that the rate of growth was low.

So, taken all together, what this particular section shows us, generally, is a cyclical growth pattern. LAG, followed by vascularisation, annulus, vascularisation, then another LAG. One could take LAGs to represent yearly lines (as with tree rings), and the alternating vascularisation to represent seasonal cycles of fast/slow growth, and then hypothesise as to how these patterns can emerge. Hypotheses can then be tested somewhat using Recent bones with known growth patterns.

One can then go further and examine differences between growth patterns in adults and juveniles, provided specimens of the same species are around. This allows us to elucidate life history patterns – is there a fast juvenile growth rate then arrest, or did the animal grow at the same rate until death?

I can only offer you this glimpse into this research area, and my aim was not only to introduce it, but to give you an idea of how all the conclusions we come to about dinosaurs, their physiologies, their lifestyles, their ecologies, etc. aren’t baseless speculations, but come from detailed examination and analysis of such things as slices of fossilised bone. As the old palaeontologist adage goes, “every fossil tells a story”.

References:

Bowerbank JS. 1848. Microscopical Observations on the Structure of the Bones of Pterodactylus Giganteus and other Fossil Animals. Quarterly Journal of the Geological Society 4, 2-10.

De Ricqlès AJ, Padian K, Horner JR & Francillon-Vieillot H. 2000. Palaeohistology of the bones of pterosaurs (Reptilia: Archosauria): anatomy, ontogeny, and biomechanical implications. Zoological Journal of the Linnean Society 129, 349-385.

Erickson GM, Rogers KC & Yerby SA. 2001. Dinosaurian growth patterns and rapid avian growth rates. Nature 412, 429-433.

Varricchio DJ. 1993. Bone microstructure of the Upper Cretaceous theropod dinosaur Troodon formosus. Journal of Vertebrate Paleontology 13, 99-104.





Request Fulfilment: Extinct Neopterygii

15 02 2013

I was requested by an anonymous person who is most likely a first year palaeo student preparing for their very first seminar to give an overview of extinct neopterygians. I honestly don’t know much about fishies, but I hope these keywords help you search further, my young Padawan.

The majority of modern fish are teleosts, a clade that arose in the Jurassic. However, the clade that contains the teleosts, the Neopterygii, originated in the Late Permian and has several other clades within it. The gars (Lepisosteidae) and bowfins (Amiiformes) are still alive today, albeit only represented by a handful of species each.

sangiorgio

Of the extinct forms, the most well-studied are the ~30 known species of Triassic-Cretaceous Semionotidae, characterised by large dorsal and ventral fins, and almost symmetrical tails. They had a jaw that jutted forward, bearing many small, sharp teeth. The one pictured above is Sangiorgioichthys sui from the famous Luoping locality in China; the fossil is described by López-Arbarello et al. (2011).

macrosemiid

Macrosemiidae lived contemporaneous to the Semionotidae, and are characterised by unique bones in their eye socket, although their most visible feature was their high dorsal fin. Pictured above is a possible Agoultichthys chattertoni from south-eastern Morocco (source: Martill et al., 2011).

pycnodont

Also living in the same period were the Pycnodontiformes. They had the same body type as sunfish – flattened laterally with long dorsal and anal fins, best suited for lying in the sediment of still waters. The tiny picture above is the only pycnodont I could find among my papers, sorry; it’s from Cavin et al. (2010).

Similar in appearance are the Dapediidae, but they are otherwise rather enigmatic, although they seem to be closely related to the Semionotidae. They lived in the Jurassic and Triassic. I have no papers on them and no pictures of them, only these scribbled sentences from lecture notes. Sorry.

I recommend Benton’s Vertebrate Palaeontology, it should have more info on all of these, or at least references to books or reviews specifically on fish evolution.





My Research: Cyprus’s Marine Palaeoecology

20 01 2013

nicfmThe map above shows the geology around Nicosia, from 5 Ma to the Quaternary. The green boxes are Pliocene fossil localities, with dominant fossils labelled. There are many more localities and many more fossils, I’m just using it as an example for the bulk of my palaeontological work here.

This work is documenting the fossil diversity in these localities in a palaeoecological context. Each locality’s stratigraphy is mapped, and the invertebrate macrofossil contents (identified as much as possible to species level) of each layer documented and put into a GIS-referenced database. The species assemblage for each layer gives an idea of the palaeoenvironment, since the type of ecosystem can be inferred from the species’ ecologies. The layer succession tells us about environmental changes and events that took place in time.

The next, much harder, step is to correlate these fossil localities together, to see when each layer was deposited. When done, this can lead to several interpretations, two of which are of interest to me:

  • If layers are deposited at the same time, then we have the spatial aspect. A layer with shallow water fauna 5 km away from a deep-water layer from the same time means we can trace the continental slope or detect an ancient basin.
  • If layers are deposited at different times, then we have local events affecting the ecosystems, meaning we can get a glimpse at the complexity of the oceanography around Cyprus 5-2 million years ago.

The potential insights gained range from local geology to regional and Mediterranean-wide marine evolution.

On the geological side, it’s known that Troodos, the main mountain of Cyprus, has gone through several pulses of uplift, including one in the Pliocene that continues to now. By having a high-resolution look at the fossil palaeoenvironments, it may be possible to calculate the rates of uplift, by tracing the changing ancient coastline of Cyprus.

But I’m most interested in the evolution of the Mediterranean’s marine biology. The start of the Pliocene in the Mediterranean is marked by a crucial event: the end of the Messinian Salinity Crisis and the restoration of marine conditions. The Messinian Salinity Crisis happened when the Straits of Gibraltar closed the Mediterranean off from the Atlantic, turning it into a gigantic lake that eventually evaporated (kilometer thick gypsum and other evaporite layers attest to this); the Straits opened again at the start of the Pliocene, and the Atlantic flooded back in, complete with a faunal recolonisation.

Studying how animals successively colonised the Mediterranean is a potentially exciting question, needing detailed dating of layers from all over the Mediterranean, to see if the recolonisation was “instant”, or if there was a pattern with some taxa – following circulation patterns, perhaps.

Only the comparison between pre-Messinian and post-Messinian biodiversity is interesting by itself, and Cyprus is perfect for this, since the marine fossil record is continuous from 50+ million years ago, including the macrofossils I study. Of course, this needs similar work done on the older stuff, and that’s the natural extension of this work.

Finally, there are also younger localities, including of archaeological age, and what this allows is a direct comparison of these ancient palaeoenvironments with the environments found off the coast today. For this aspect, I collaborate with marine biologists to explore various ecological aspects, such as predation intensities and species interactions, through time.

There is also the possibility of giving a deep time perspective on the severity of the Lessepsian Migration – the highly-successful migration of Red Sea fauna into the Mediterranean through the Suez Canal – although marine biologists were careful enough to do censuses of marine life on both sides before the canal was opened.





Top Research of 2012: Palaeontology

6 01 2013

Jump to: Arthropods; Botany; Developmental Biology; Ecology; Evolution; Environmental; Geology; Historical Geology; Human Evolution; Zoology.

My top 10 palaeontological research picks of the year, and by far the most difficult listing to complete, because there was a ton of good research this year. Because of that, each item here has a different palaeontological theme, so the list is quite varied. Keep in mind that any arthropod palaeontology is in the arthropod listing. The master list has 62 paper. [OA] indicates open access papers.


10. Selective feeding in an Early Devonian terrestrial ecosystem.

coprolites

The picture shows what this paper describes: coprolites, fossilised pieces of shit, from an ~415 Ma (Early Devonian) locality in Wales. While the study of coprolites is done mostly for the comedic and novelty value of holding million year old feces, it also brings a lot of insights into palaeoecology: match the coprolites to their producers, and you have a summary of what they ate, much like what is done with modern fecal analyses. These coprolites contain bits of nematophytes, an enigmatic group of organisms that are nowadays interpreted as fungi. No plant or animal parts were found, meaning these coprolites are the very first evidence we have of primary fungal feeding, and the producers are the first animals known to be exclusive fungal feeders. The most likely culprits, based on the size and structure of the feces, are millipedes, who nowadays are also fungivores.

For some more impressive palaeoecology, check out Surprisingly complex community discovered in the mid-Devonian fossil forest at Gilboa, which shows that the Gilboa forest, one of the earliest exceptionally-preserved forest ecosystems, is actually a highly-complex mixed forest wetland with a lot of disturbance, unlike the original depiction of it being a very simple ecosystem.


9. Palaeopathology and fate of Ida (Darwinius masillae, Primates, Mammalia).

ida

Problematic PR aside, Ida has become established as a great fossil with excellent preservation. As the old palaeontological saying goes, every fossil tells a story, and this paper showcases that. Look at the close-up of Ida’s hand above, and notice that the right hand has a giant bump. This isn’t a chemical concretion from its preservation, but actual bone, a callus caused by an obviously large injury – in this case, a broken wrist. In the paper, it all gets explained in a story-like manner. Pretty neat. The tl;dr version is that Ida was mucking around up in the trees, fell and broke her wrist. The injury is obviously very painful for a primate that spends her time in the trees, so she would have been spending an inordinate amount of time in the ground, where one day she inhaled the poisonous gas that was being burped out by the Messel lake, fainted and sank to the bottom where she was preserved along with all the other fauna of Messel. It’s convincing and plausible, it explains why primates are very rare in Messel – they wouldn’t be on the ground to be hit by toxic gas, while Ida was confined to there due to her injury. She has no bite marks, so it wasn’t a predator that got her. Although obviously anyone can come up with another story with the same set of facts.


8. Short-term survival of ammonites in New Jersey after the end-Cretaceous bolide impact. [OA]

Landman_20110068.vp

The above ammonites come from a location in New Jersey directly overlying the K-T event iridium layer. In other words, they show ammonites that survived the K-T event for at least a little while. While the authors note there is still some stratigraphic work that needs to eb done to pinpoint the exact sequence of events, this is still pretty cool, and just goes to show that there is no such thing as an immediate extinction, not even in the geological sense.

The Miocene mammal Necrolestes demonstrates the survival of a Mesozoic nontherian lineage into the late Cenozoic of South America shows a similar situation, again with the K-T event, this time with a Mesozoic mammal – i.e. not a marsupial, placental, or monotreme, the three extant mammal groups – surviving over 40 million years after the extinction event. It’s not the first known, but it is the longest-surviving one.


7. The reconstructed evolutionary process with the fossil record.

This paper goes out to all those who think the fossil record is not a reliable source of information on evolution (yes, such scientists do exist, I have seen them). This paper basically compares extinction and speciation rate estimations from models, fossil record-informed models, and Recent organism only-informed models. Surprise, surprise: using the fossil record gives much better estimates. Maybe it has something to do with, you know, data.

Another paper that shows a great interaction between modelling and fossil data is Robust estimates of extinction time in the geological record, which presents a model for estimating extinction times.

Other papers from this year showing the utility of the fossil record for evolutionary biology include The maximum rate of mammal evolution, which uses a mammoth-sized dataset to set the basis for micro- and macroevolutionary studies in mammal body size evolution and factors affecting it; and Biodiversity tracks temperature over time, which shows that there is a positive relationship between temperature and biodiversity, a correlation that deserves macroevolutionary study.

Detractors of the use of the fossil record cite taphonomical or taxonomical biases – only some types of organisms get preserved, sometimes. While it would be silly to deny these biases exist, it would be even sillier to not quantify them so we know the realism of our data, and all palaeontologists know this: we acknowledge the problems with the fidelity of the fossil record. Case in point: Comparative quality and fidelity of deep-sea and land-based nannofossil records shows that the deep-sea nannofossil record really isn’t so reliable. And, as No gap in the Middle Permian record of terrestrial vertebrates shows with Olson’s Gap in Permian vertebrates, these studies also identify when a perceived fossil record gap is actually illusory.


6. New evidence on the colour and nature of the isolated Archaeopteryx feather.

One of the coolest advances in recent palaeontology has been the study of fossilised pigments in the feathers of the “feathered dinosaurs”. These pigments are identical in microstructure to those of modern birds, so by examining them, we can infer the colour of the feathers. In this case, the famous/iconic isolated Archaeopteryx feather is examined and found to have been black. The feather was a primary covert feather, i.e. a feather on the top layer, not the bottom one. This does not mean that Archaeopteryx was all black – this is just an individual feather, and birds are known to have different-coloured feathers, primarily for sexual communication.


5. Biogenicity of Earth’s earliest fossils: A resolution of the controversy.

The latest strike back in the whole Apex Chert microfossil debate, outlined here. This paper uses Raman spectroscopy and finds that they’re made of kerogen, a strong hint at a biological origin. Expect a riposte next year.

As I stress every time I discuss the Apex Chert, their biogenicity is actually irrelevant – we know that life already existed from biomarkers. Novel molecular fossils of bacteria: Insights into hydrothermal origin of life shows how such biomarkers form using a newly-discovered example.

That said, preservation of the bodies of unicellular organisms does occur, and this year saw several papers describing that: Remarkably preserved prokaryote and eukaryote microfossils within 1 Ga-old lake phosphates of the Torridon Group, NW Scotland; Fossilized bacteria in a Cretaceous pterosaur headcrest; Fossilized fungi in subseafloor Eocene basalts.

Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils shows one way in which we can confirm the biogenicity of an enigmatic fossil: experimental taphonomy, looking at how modern organisms fossilise in the lab and comparing with the rock structure.

Finally, since we’re on the subject of exceptional preservation of tiny organisms, check out Triassic leech cocoon from Antarctica contains fossil bell animal, where a vorticellid is preserved in the cocoon leech.


4. A Marine Stem-Tetrapod from the Devonian of Western North America. [OA]

tinirau

If you were getting used to Tiktaalik as the superawesome oldest transitional tetrapod, you might want to update to Tinirau clackae, described in this paper from a specimen in the late Middle Devonian of Nevada. It’s more basal than Tiktaalik and predates it by 5+ Ma – although keep in mind that we still need to find more basal tetrapods, since we have earlier trackways. The features of Tinirau also make it clear that there was considerable convergence happening, and also emphasises the mosaic pattern of early tetrapod evolution.

For another significant transitional vertebrate, A transitional snake from the Late Cretaceous period of North America fits the bill.

A New Rhynchocephalian from the Late Jurassic of Germany with a Dentition That Is Unique amongst Tetrapods [OA] and A New Eusuchian Crocodyliform with Novel Cranial Integument and Its Significance for the Origin and Evolution of Crocodylia [OA] are other important vertebrate findings.


3. Pikaia gracilens Walcott, a stem-group chordate from the Middle Cambrian of British Columbia.

pikaia

The definitive description of Pikaia, one of the early chordates from the Burgess Shale. If there’s anything you want to know about it, from its morphology to its way of life to its position on the tree of life (note: it was not your n(great)-grandfather) to the history of thought on all of those, this is the paper you’re looking for. You can check out my post on Pikaia for the superdigest version.

This year’s been fairly good for the study of the Cambrian Radiation. Mechanism for Burgess Shale-type preservation [OA] describes how the exceptional preservation in the Burgess Shale and allied Cambrian localities occurred.

Significant new descriptions include: Evidence for gill slits and a pharynx in Cambrian vetulicolians: implications for the early evolution of deuterostomes [OA]; A New Stalked Filter-Feeder from the Middle Cambrian Burgess Shale, British Columbia, Canada [OA]; and Mouthparts of the Burgess Shale fossils Odontogriphus and Wiwaxia: implications for the ancestral molluscan radula.

Some advances on the ecological aspect were done. The biodiversity of Cambrian priapulids has been revised in The disparity of priapulid, archaeopriapulid and palaeoscolecid worms in the light of new data, and a new pripaulid assemblage from the Cambrian of China is described in A new priapulid assemblage from the early Cambrian Guanshan fossil Lagerstätte of SW China.

As for the pre-Cambrian history of animals, some advances have also been made on that front. On the one hand, A merciful death for the “earliest bilaterian,” Vernanimalcula shows how this supposed oldest bilaterian is actually nothing more than geological blah; on the other hand, Bilaterian Burrows and Grazing Behavior at >585 Million Years Ago describes decidedly advanced burrows that were likely produced by bilaterians, giving more evidence for the concept of the Cambrian Radiation being illusory.


2. The architecture of Ediacaran Fronds.

This paper deals with the rangeomorph Ediacarans (see here) and constructs a standardised scheme under which all rangeomorphs can be studied. This is exactly what’s needed, since it allows direct comparisons of the weirdos, and also makes cladistic analyses that much easier to do.

Another significant paper on the Ediacaran period is Distinguishing geology from biology in the Ediacaran Doushantuo biota relaxes constraints on the timing of the origin of bilaterians, which analyses specimens from the famous Doushantuo locality, and identifies how to separate geological muck from actual fossilised remains, something that’s critical in Doushantuo because the potential fossils include embryos and even subcellular details.


1. A new stem-neopterygian fish from the Middle Triassic of China shows the earliest over-water gliding strategy of the vertebrates.

flyingfish

Those who know me might be wondering if I got hit by lightning, putting idiot fish over the Cambrian and Ediacaran stuff I base my interests in palaeontology on. The reason why this gets top spot is simple: it’s an excellent example of how to infer behaviour from function, and function from morphology – and these are key goals in palaeontology. In the case of this one: you have this weird fish from the Middle Triassic of China, which you called Potanichthys (refer to (b) above). It has a big lobe at the front. You analyse it closer and realise it’s the pectoral fin that’s been grossly enlarged. Then you notice that the caudal fin (tail) is also pretty large. This is the same type of morphology seen in modern exocoetid fishes, also known as the flying fishes. They use the tail to generate a lot of thrust, and the large pectoral fin as a “wing” to maintain gliding. In other words, Potanichthys is a flying fish – not an exocoetid, this is a case of convergent evolution, and probably evolved for the same reason in both cases: evading predators. This paper gets top spot for being a good analysis from beginning to end, going from raw morphology through to phylogeny and finally to functional morphology and ecological implications.


Jump to: Arthropods; Botany; Developmental Biology; Ecology; Evolution; Environmental; Geology; Historical Geology; Human Evolution; Zoology.





Top Research of 2012: Historical Geology

4 01 2013

Jump to: Arthropods; Botany; Developmental Biology; Ecology; Evolution; Environmental; Geology; Human Evolution; Palaeontology; Zoology.

My top 10 picks for historical geology research of the year. There is an inevitable overlap with palaeontology, so I’ve included only those papers that can only be considered pure historical geology, so stuff about the origin of life, mass extinctions, the history of climate, that kind of thing. The master list contains 29 papers. [OA] indicates open access papers.

By the way, when you’re done here, check out the 55th Carnival of Evolution, up at Genome Engineering!


10. The Aftermath of Megafaunal Extinction: Ecosystem Transformation in Pleistocene Australia.

Near the end of this post is this diagram showing the relative contributions of climate change and hunting to the megafaunal extinctions of the Pleistocene. Many have asked me how we know that humans could have had such a large impact, especially in Australia. This paper presents the answer, as well as confirmation that it is indeed humans that caused the extinctions there, and not drying of the climate. First of all, there’s the incredible coincidence that the faunas declined and went extinct shortly after human arrival on Australia, 45 ka. But it’s the evidence compiled by Rule et al. that’s the most compelling. They got a core going back 130000 years from a volcanic lake in Queensland, and measured the amounts of Sporomiella spores, charcoal, pollen, and of various plant types. Sporomiella is a fungus that grows in the dung of megaherbivores, and so is indicative of their presence. 130-41 ka, Sporomiella numbers are very high, plants indicate a tropical rainforest setting with little charcoal (no wildfires). Then there was a sudden shift at 41 ka: Sporomiella levels plummet, grassy-type pollen becomes dominant, Eucalyptus forests become the landscape type, and a lot fo charcoal gets deposited. Looking at this in high resolution, Rule et al. observed that the Sporomiella decline was the first change – i.e. it was the megaherbivores that died out first, before the habitat change. This means that climate change was not the cause of their extinction. With the herbivores gone, the habitat changed, and Rule et al. suggest that the change in plant type led to the wildfire-friendly habitats that caused the deposition of lots of charcoal, although it’s just as likely that human-caused fires were the culprit there too. So the case is more or less closed: we did it. Hooray!


9. Spontaneous network formation among cooperative RNA replicators.

I’m not a fan of the RNA world model, but it does have as much evidence, and is as plausible as, the metabolism-first model that I support (see here for summaries of the two models). This paper provides some excellent evidence for the RNA world model. It’s part of a larger research direction these days to create self-replicating RNA systems in the lab. Past studies have managed to make ribozymes (the catalytic components of RNA) that amplify themselves and compete against each other. In this study, Lehmann et al. depart from that and manage to create networks of ribozymes that aren’r selfish, but instead cooperate – they still amplify themselves, but not in a way as to compete with each other. The end result is that these cooperative network are much more efficient than the lone wolves. The implication for the RNA World is that this is what might have been the key trigger: there may have been a soup of competing RNAs, but then a specific set of cooperative ones arose and obliterated the individuals; this research tells us that this is possible, and not just speculation.


8. Hydrogen sulphide poisoning of shallow seas following the end-Triassic extinction.

triassicsulphide

The Hettangian is the first stage of the Jurassic, coming right after the massive end-Triassic extinction. In this paper, Richoz et al. report finding extraordinary amounts of isorenieratane in their German and Luxembourgian shales from the start of the stage, as shown in (e). The significance is that isorenieratane is a biomarker for green sulphur bacteria, and finding such an abundance of it means that the sediments that later became shales were deposited in an anoxic ocean floor with very high hydrogen sulphide concentrations (the environment that green sulphur bacteria thrive in). This then gives us some more insights into the extinction that occurred at the end of the Triassic and the recovery from it – specifically, the strange disconnect between marine and terrestrial recoveries. The first dinosaurs radiated as soon as the earliest Hettangian, but it took 10 million years for the shallow seas to regain their pre-extinction diversities. We now know why.


7. Late Cretaceous restructuring of terrestrial communities facilitated the end-Cretaceous mass extinction in North America.

Even if the Chixculub asteroid hadn’t come, there were several biotic changes happening in the Cretaceous – just look at the wackiness of Cretaceous ammonites. Terrestrial ecosystems were no exception, and this paper provides evidence that the changes occurring there made the extinction more effective. The changes occurred in the Maastrichtian, the last stage of the Cretaceous, and were of varying nature: tectonic changes led to increasing provinciality and isolation; changes in dinosaur species diversity; and functional shifts in ecologies. What they led to was an increased risk of extinction, setting the threshold for secondary extinction lower than in the Campanian (the stage before the Maastrichtian), and thus exacerbated the effect of the extinction event (although, to be fair, they were doomed under the circumstances anyway).


6. Two pulses of extinction during the Permian–Triassic crisis.

The P-T extinction isn’t only the most severe mass extinction to have ever hit the Earth, it’s also a classic example for a delayed recovery from an extinction event. See the last section of this post for details. The results of this study change the anrrative somewhat, since Song et al. find that the brunt of the extinction happened in the early Triassic – when the recovery was supposedly being delayed. There was an earlier extinction pulse 180000 years earlier at the end of the Permian. This just emphasises the need to look at such seemingly sudden events in very high resolution – extinction events are never, ever instantaneous.

That said, the delayed recovery was a true phenomenon, even with this extra extinction pulse. See Delayed recovery of non-marine tetrapods after the end-Permian mass extinction tracks global carbon cycle [OA] for a terrestrial vertebrate example, with the link to the carbon cycle.


5. Vegetation-climate interactions in the warm mid-Cretaceous. [OA]

cretaceousclimate

The mid-Cretaceous is well-known as one of the more severe prolonged greenhouse climate phases the Earth went through. Studying and modelling it provides a useful analog for modern global warming. This paper presents a thorough model of the mid-Cretaceous climate, with a special focus on vegetation responses and feedbacks. The findings are as expected: forests expand towards the poles, leading to lower albedo and thus reinforcing the warming. On the other hand, in temperate and tropical zones, there is a decrease in forest cover, leading to more cooling. There were also some novel results. The ocean surface gets warmer due to more atmospheric vapour leading to more longwave radiation being retained. And there is more precipitation, leading to more freshwater input, leading to a screwing up in the circulation patterns, leading to less heat transfer to the poles. This later stuff isn’t too applicable for us today, since our continental distributions and thus circulation patterns are different, but they do provide an indication of just how complex climate dynamics are.

For more on the mid-Cretaceous greenhouse, see Orbital control on carbon cycle and oceanography in the mid-Cretaceous greenhouse. The oceanographical aspect going to the late Cretaceous is summarised in Evolution of middle to Late Cretaceous oceans—A 55 m.y. record of Earth’s temperature and carbon cycle.

For information on the forests of the Cretaceous, see Cretaceous forest composition and productivity inferred from a global fossil wood database.


4. Ecological ranking of Phanerozoic biodiversity crises: The Serpukhovian (early Carboniferous) crisis had a greater ecological impact than the end-Ordovician.

Mass extinctions are typically ranked by number of extinct species. It works fine, but similar to how metrics other than species richness are used in modern ecology, more insights can be gained from using other indices. For example, phylogenetic diversity, or, as proposed in this paper, resultant ecological changes. The Permian-Triassic and Cretaceous extinctions led to a restructuring of terrestrial and marine ecosystems to accommodate the new dominant organisms. On the other hand, the end-Ordovician extinction resulted in a lot of species going extinct, but the replacements were more or less the same, ecologically. Different actors, same roles – there was very little ecological impact. Hence, by this metric, the end-Ordovician extinction ranks pretty low, and another extinction event comes to take its place: the Serpukhovian extinction (mid-Carboniferous, ~326 Ma), with 31% of species going extinct, mostly ammonites, crinoids, conodonts, and fish. However, the ecological impact was fairly significant, with the glaciation that caused it leading a much decreased recovery rate.


3. Climate warming in the latest Permian and the Permian–Triassic mass extinction.

In #6, I linked to my post containing the summary of the P-T extinction, where it’s made clear that the whole ordeal started with global warming. This paper gives a high-resolution look at the temperature changes, by looking at the isotopes, with the mainr esult being an increase in surface water temperature of 8°C in the low latitudes right before the end of the Permian, so at the start of the first large extinction phase (see commentary to #6).

To see how complex palaeoclimate of the time can be, see Climatic and biotic upheavals following the end-Permian mass extinction.


2. End-Cretaceous marine mass extinction not caused by productivity collapse.

By looking at the foraminifera across the K-T boundary, Alegret et al. find that, like in the terrestrial ecosystems, there wasn’t any drastic ecological collapse in the oceans as a result of the K-T extinction. Of course, there was a drop in productivity at impact time, but ocean primary productivity remained more or less stable. The authors suggest that ocean acidification was the main extinction driver in the oceans, something which doesn’t contradict what we observe from other periods of time nor from today.


1. Origin of first cells at terrestrial, anoxic geothermal fields. [OA]

cellorigin

This one gets first place for being extremely interesting. It’s a typical “where could have the first cells originated?” paper, but it usesd a wide data range to make its case, looking at both phylogenetics and geochemistry. Their argument is basically as follows. All modern cells require large amounts of specific ions. Modern cells have pumps to get these ions from the environment, but the primordial cell-like constructs didn’t have them, so true cells must have originated in a place where these ions are highly-concentrated. Geochemistry tells us that the primordial oceans and geothermal vents in them don’t fulfil the criteria. However, ponds within geothermal fields tick all the right boxes, therefore that’s the more likely place where cells originated. As always with such papers, it’s a war of evidenced speculation. The origin of life/cells near geothermal vents is explained in my origin of life post, where you’ll see the major evidences for it (ancestral hyperthermophily, chemical concentrations) are also fulfiled by this hypothesis. So, basically, believe whatever you want, they’re both as viable as each other at this time :) One very interesting implication of this new hypothesis though is that cells invaded the oceans secondarily. I find it appealing because it provides a convenient explanation (or maybe it’s a dreadful just-so story?) for the origin of genetic repair, mechanisms of which are found all over the kingdoms of life, since a terrestrial origin origin of life and cells means they were exposed to UV and ionising radiation since “birth”, meaning they had to evolve those mechanisms ASAP.

In Open Questions on the Origin of Life at Anoxic Geothermal Fields, the authors deal with all the critiques that have been thrown at them, so read it as an addendum.

The hypothesis hinges on the biogeochemical analysis the authors did. Magnesium didn’t play much of a role, but in The significance of Mg in prebiotic geochemistry [OA], Holm explains how magnesium was important in the origin of life.


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Top Research of 2012: Botany

29 12 2012

Jump to: Arthropods; Developmental Biology; Ecology; Environmental; Evolution; Geology; Historical Geology; Human Evolution; Palaeontology; Zoology.

My top 10 picks for botanical research this year. I’m not a botanist, and although I am fascinated by plant physiology, I’m not intellectually able to keep up with that research. So I only really follow plant evolution, palaeobotany, and plant-arthropod interactions; I have tried to make the list more varied though. Picks and rankings are subjective, based on a master list of 17 papers. [OA] indicates an open-access paper.


10. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. [OA]

charophyta

Land plants (Embryophyta) are highly-specialised streptophyte green algae. Of the other streptophyte groups, three are variably recovered as the sister group to the land plants, the results depending on the genes and methods used, and none ending up with truly rigorous support: the Charales, the Coleochaetales, and the Zygnematales (pond scum). The Charales (stoneworts) are the ones commonly depicted in textbooks and have always gained the most support. This paper may change our view on things: it uses a large dataset of 160 phylogenetically-significant genes, and gets perfect support values for a Zygnematales+Embryophyta clade. This has numerous implications, chief of which is that multicellularity is a convergent land plant innovation rather than a condition inherited from an ancestor (as would be the scenario if Charales are the sister).


9. Plant UVR8 Photoreceptor Senses UV-B by Tryptophan-Mediated Disruption of Cross-Dimer Salt Bridges.

This paper studies the molecular basis for UV light detection (280-320 nm) in plants, by looking at the reactions of UVR8, a photoreceptor known to react to UV light. Christie et al. went classical in this paper: they used crystallographic methods to elucidate UVR8′s structure, best summarised as a doughnut; then they used targeted mutations to find out how the protein works. When inert, it’s found as a dimer: two doughnuts connected by bridges. When UV light shines on the plant, these bridges break due to electrons getting excited. The single doughnut then binds to another protein, COP1, to complete the reaction.


8. Phylogenetic niche conservatism in C4 grasses.

c4

I’ve written an overview of C4 photosynthesis, so refer to that post for necessary background. This paper analyses various traits in grasses of the Chloridoideae and Panicoideae, grasses in which C4 photosynthesis is dominant (in the phylogeny above, yellow indicates C3, all other colours are types of C4). It finds that the evolution of these traits, as well as ecological preferences, are determined not by the evolution of C4 photosynthesis, but by phylogeny. In other words, it’s the ancestry that counts. This in turn has implications about how we should treat C4 photosynthesis: there is a tendency to lump C4 plants together as one functional group, regardless of phylogeny. This finding says we are better off sticking to phylogenetic lumping, since there is clear niche conservatism: C4 photosynthesis doesn’t determine the ecology of these plants. Ancestry does, and C4 photosynthesis just tags along.


7. A critical transition in leaf evolution facilitated the Cretaceous angiosperm revolution. [OA]

veins

This paper presents a cool hypothesis for a contributing factor to the great angiosperm radiation of the Cretaceous: leaf vein density (Dv in the above diagram) as a key feature. This is an observation in the fossil record, that the density of the veins increases in two bursts, once in the initial angiosperm radiation (100 Ma) and another time at 65 Ma to reach today’s levels. The greater vein density leads to vastly improved gas exchange rates, which would have provided them with a distinct advantage as the CO2 levels decreased in the Cretaceous, allowing them to more easily outcompete the conifers and other land plants.


6. Widespread impact of horizontal gene transfer on plant colonization of land. [OA]

hgt

This genomic analysis of a moss, Physcomitrella patens, finds that it has 57 nuclear gene families by horizontal gene transfer from bacteria, fungi, or viruses. 18 of them are inherited ancestrally; 18 of them are recent acquisitions; and 15 of them are also found in more derived land plants, passed on from the last common ancestor with mosses. To put these numbers into perspective, the functions of the acquired genes are essential, involved in defence and stress tolerance, hormone biosynthesis, and even DNA repair. The picture painted by these facts is one of a harsh environment that early land plants had to colonise, in which UV radiation was rampant and the ground was inhospitable; these genes enabled the early mosses to survive by helping DNA stability in early mosses (later plants got yellow pollen, the yellow pigment serving as a UV shield), and numerous stress tolerance mechanisms and development helpers to keep them surviving in the harsh environment.


5. Arabidopsis synchronizes jasmonate-mediated defense with insect circadian behavior.

This is some pretty cool research from an ecological and from a plant-insect interaction perspective. The study finds that plant defence systems can be synchronised with insect feeding times; at least it is so in the case of the caterpillar of Trichoplusia ni and the Arabidopsis weed this experiment was done on. The synchronisation is achieved not by detecting the caterpillar, but by circadian rhythms – when raised on the same day/night cycle, the plant’s defence system will adjust to be active at the same time as the caterpillar is active. When circadian mechanisms are interrupted or the hormone jasmonate’s production is deficient, then the synchronisation gets thrown off and the plant experiences much higher herbivory levels and are thus at a physiological disadvantage. I’m interested in seeing how this plays out in nature with day-active vs. night-active insects.


4. Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants.

This paper reports the draft nuclear genome of the basal glaucophyte alga Cyanophora paradoxa. The most significant result is evidence for the monophyly of the Plantae, as even the untypical plastid of the glaucophytes appears to be homologous with that of the rhodophytes and green algae (together, these three groups make up the Plantae). The data gathered from the genome says that 274 of the alga’s proteins were transferred from endosymbiotic cyanobacteria, and that 444 gene families were transferred by horizontal gene transfer from other bacteria. Many of these proteins and genes are involved in photosynthesis and associated processes, as well as plastid integration, meaning that we now have more light shone on how built-in photosynthesis in plants first evolved.


3. Oldest known mosses discovered in Mississippian (late Visean) strata of Germany.

Mosses are expected to be one of the earliest plants to have evolved on land, but their early fossil record has been severely lacking because of their very low preservation potential. This paper describes the oldest mosses to date, which grew in the tropical forests of the German Carboniferous. Older ones are still to be expected, but their lack is merely an example of an expected inadequacy in the fossil record.


2. Underground leaves of Philcoxia trap and digest nematodes.

I admittedly include this so high up because of the coolness factor, but it does bring up deeper issues. But first, the cool stuff: the plant has sticky leaves that grow underground. Nematodes stick to them, and the plant digests them. In other words, this is a carnivorous plant, and it uses a completely novel way to capture its food. The deeper ecological and evolutionary issue to be brought up is about how such a unique strategy can evolve.The plant grows in a region with one of the poorest soils of the world, the Brazilian Cerrado. So it could be that the evolution of carnivory is instigated by soil nutrient deficiencies, and so they eat animals in order to get those critical nutrients.


1. Rise to dominance of angiosperm pioneers in European Cretaceous environments.

This paper reviews the early record of angiosperm fossils from Europe to propose a temporal framework for their megadiversification in the Cretaceous in which they outcompeted the conifers and other land plants. The scenario Coiffard et al. synchs up with the view from the North American record, so it can be viewed as reliable. The scenario has three bursts of diversification into new habitats. From the abstract: “(i) Barremian (ca. 130–125 Ma) freshwater lake-related wetlands; (ii) Aptian–Albian (ca. 125–100 Ma) understory floodplains (excluding levees and back swamps); and (iii) Cenomanian–Campanian (ca. 100–84 Ma) natural levees, back swamps, and coastal swamps.”


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Zoology





Top Research of 2012: Arthropods

26 12 2012

Jump to: Botany; Developmental Biology; Ecology; Environmental; Evolution; Geology; Historical Geology; Human Evolution; Palaeontology; Zoology.

Now that we’re done with the top books of the year, let’s look at the top research of the year. I re-examined a total of 412 papers published this year, sorted in the following categories: Arthropods; Botany; Developmental Biology; Ecology; Environmental; Evolution; Geology; Historical Geology; Human Evolution; Palaeontology; and Zoology. As with the books, every day, I will do a top 10 research for each category. The top 10s will be inverted like a proper countdown. As with any top 10 lists, your mileage may vary; these picks and the rankings are all subjective and prone to my own biases.

Let’s start off with the arthropods. The top 10 papers were chosen from a master list of 74 papers. [OA] indicates open access papers. The topic listing, from 10 to 1: spider intelligence; spider silk; fossil insect behaviour; fossil pupation chambers; caste-specific neuroanatomy; early arthropod evolution; evolutionary dynamics; early fossil insect; earliest amber arthropods; treehopper helmet.


10. The discerning predator: decision rules underlying prey classification by a mosquito-eating jumping spider.

culi-oph

Jumping spiders’ excellent eyesight has led to their also having high intelligence, being able to observe and filter what they see to the point that the African jumping spider Evarcha culicivora can differentiate their prey, female Anopheles mosquitoes, from all other insects flying around just by looking at their antennae. This is what Nelson & Jackson showed with this elegant experiment.

By combining parts from male and female mosquitoes and using the resultant Frankenmosquitoes as lures for the spiders to attack, they identified the two clues that led to the most attacks: a red, blood-engorged abdomen, and slender antennae. Both of these are female mosquito features: male mosquitoes don’t feed on blood (they’re nectar feeders), and males have bushy antennae. As for the specificity for Anopheles mosquitoes, that’s explained by their posture – other mosquitoes rest with their body parallel to the ground, while Anopheles rest with a 45° angle.

For showing that such a tiny spider is capable of such complex prey-distinction and thus giving even more credence to the notion that intelligence is not a function of brain size, as well as for having a great experimental design, Nelson & Jackson get the #10 place.


9. Post-secretion processing influences spider silk performance.

Spider silk is not a simple strand that’s the same in every species. There’s many different types of silk that come out of different glands, and the silk is also modified after it’s secreted. The study focuses on major ampullate silk, the type of silk that makes up the framework of an orb web and whose stiffness is responsible for the strength of the webs. The researchers examined natural silk, and silk that they supercontracted to remove any post-secretion modifications. What they found was that these supercontracted silks lost the stiff properties of their natural counterparts, meaning that their properties come from whatever modification is made to them, not from the actual structure and composition of the silk. I find this discovery significant because it adds a new dimension to the study of spider silk, a field that has quite a lot of technological and biomimetic research ahead of it.

Other significant spider silk and web-related research this year include:

The role of capture spiral silk properties in the diversification of orb webs: how various silk types affect the web’s properties.

Nonlinear material behaviour of spider silk yields robust webs: This research provides more insight into the factors mentioned above, finding that it isn’t just the type of and modification of silks that affect the web’s properties, but that the geometry of the web is as important in determining its strength and behaviour.

Early Events in the Evolution of Spider Silk Genes [OA]: A phylogeny of genes from the silk-producing glands reveals gene duplications associated with more diverse ecological use of silk and webs.

Functional values of stabilimenta in a wasp spider, Argiope bruennichi: support for the prey-attraction hypothesis: research into the use of stabilimenta, UV-reflective strands of silk that orb-weavers have.


8. Jurassic mimicry between a hangingfly and a ginkgo from China. [OA]

gingko

This is cool more than anything else, and the mimicry is shown in the picture above, from the original paper: A, B, E, and F are gingko leaves; C and H are the described specimen and its wing, D and I are a closely-related species which also exhibits mimesis with gingkos; J and K are gingko leaf closeups. As you can see, the similarities are striking, and the artist’s conception in G shows how well the hangingfly would have blended in. The paper has more details on the coevolution of mimesis between this group of hangingflies and gingkos. In all, a neat piece of work with evolutionary insights as well as cool fossil preservation.

Another paper this year has preserved evidence of insect behaviour: Wing stridulation in a Jurassic katydid (Insecta, Orthoptera) produced low-pitched musical calls to attract females. The mating call of a katydid has been reconstructed based on the preservation of its stridulatory apparatus, a hard file that the wings strike against to make the music. Related, this paper from this year shows how sensitive the hearing of katydids is: Auditory change detection by a single neuron in an insect.


7. The Earliest Evidence of Holometabolan Insect Pupation in Conifer Wood. [OA]

xylokrypta

This paper describes U-shaped burrows in 210 Ma wood from Utah, USA. These were previously assumed to be bee or wasp borings, but the detailed analysis presented in the paper shows that these borings are actually pupation chambers made by a small organism that ate its way into the wood, then emerged from the other side, as presented in the diagram above. From the size of the borings, the authors propose that the organism is a cupedid beetle, showing that these beetles were dominant before the other beetles radiated later.


6. Division of Labor in the Hyperdiverse Ant Genus Pheidole Is Associated with Distinct Subcaste- and Age-Related Patterns of Worker Brain Organization. [OA]

pheidole_brain

That different castes will have a different brain organisation is expected and has been shown in many papers (e.g. 1, 2, 3). This paper is significant because it’s so thorough: it examines castes of three species of Pheidole ants and their brain anatomy. The diagram above summarises the pattern observed: the colours are species, the shapes are castes; the axes are two variables that together make up 87% of the brain variation seen. The pattern is clear: neuroanatomy is determined by caste, not by species. This is just underlines the incredible amount of plasticity in ants (and other eusocial insects), where the environment can dictate how an individual will function and develop to allow the colony to adapt to changing needs and conditions.


5. A Carboniferous Non-Onychophoran Lobopodian Reveals Long-Term Survival of a Cambrian Morphotype.

carbotubulus

This paper has equal relevance to palaeontology as it does to arthropods: like several other papers of the past few years (e.g.), it reinforces the idea that the Cambrian freaks didn’t go extinct, but that the nature of the fossil record changes since the Cambrian to make their preservation much rare (the advent of burrowing made it much harder for such soft-bodied forms to be preserved). This one is the most stirking example yet: a long-legged lobopod, 200 million years after the Cambrian (it comes from the famous Mazon Creek locality in Illinois, USA, 296 Ma)! Lobopods are a wastebasket taxon in which soft-bodied arthropods with stubby legs are dumped, including many fossil-only taxa, tardigrades, and onychophorans. There are two groups: short-legged forms (includes the last two) and long-legged ones, up until this paper known only from the Cambrian.

It was a good year for arthropod evolution, with many excellent studies into the biology and diversity of early arthropods:

Exceptionally preserved crustaceans from western Canada reveal a cryptic Cambrian radiation: These Canadian fossils bring the earliest fossil records of branchiopods, copepods, and ostracods back to the mid-Cambrian.

Silurian horseshoe crab illuminates the evolution of arthropod limbs: A horseshoe crab from Herefordshire, showing a very exciting biramous limb, the significance of which would need an entire post to explain.

A Silurian myodocope with preserved soft-parts: cautioning the interpretation of the shell-based ostracod record is another Herefordshire find that finds that ostracod shells, very abundant fossils with significant stratigraphic and other practical use, are not quite as informative taxonomically as previously thought.

Cambrian lobopodians and extant onychophorans provide new insights into early cephalization in Panarthropoda [OA]: A complete redescription of Onychodictyon‘s head, showing that the arthropod mouth may have originated multiple times.

Cambrian bivalved arthropod reveals origin of arthrodization: A new Burgess Shale arthropod suggests that the key feature of arthropods, the exoskeletal segmentation, was a feature that evolved for swimming.

Morphology of Cambrian lobopodian eyes from the Chengjiang Lagerstätte and their evolutionary significance shows that Cambrian lobopods had pretty sophisticated eyesight.

Complex brain and optic lobes in an early Cambrian arthropod: Eyes are nice and all, but how about preserved brains and nervous tissue?

Internal Soft-Tissue Anatomy of Cambrian ‘Orsten’ Arthropods as Revealed by Synchrotron X-Ray Tomographic Microscopy [OA] shows more spectacular internal details of long-extinct arthropods.

Exceptionally Preserved Cambrian Trilobite Digestive System Revealed in 3D by Synchrotron-Radiation X-Ray Tomographic Microscopy [OA]: As above.


4. Loss of flight promotes beetle diversification. [OA]

flightloss

In this study, a molecular phylogeny of Japanese carrion beetles was done, and the result found was that flight loss promotes speciation. Flightless populations have more genetic differences between themselves than do flight-enabled populations. This is to be expected: flight enables greater geographic dispersal, allowing distant populations to reproduce and keep gene flow between them; with flight loss, this doesn’t happen, resulting in more isolation and thus more speciation, as shown in the above bar chart. The authors went further and did a short meta-analysis for other beetle groups and found a similar effect. I look forward to deeper studies examining the precise interplay between diversification and flight loss – does flight loss really directly cause speciation, or is it an indirect knock-on effect. Loss of flight must be related to other factors such as habitat requirements, life history, or feeding preferences, as the authors note; maybe it’s those other factors that actually promote the speciation. The authors checked for this in their carrion beetle dataset, but it’s worth looking into with other taxa.


3. A complete insect from the Late Devonian period.

strudiella

The fossil doesn’t quite look like an insect until you examine it closely – when I first saw the picture, I thought it was some notostracan. But then it becomes clear that there’s a pair of antennae, then you see the head, then the rest of the body – this is an insect. It’s not the oldest – that honour remains with Rhyniognatha hirsti – but it does come from a time when the fossil record of insects is completely lacking, the Late Devonian, and it’s by far the earliest complete insect – this really is a landmark find.


2. Arthropods in amber from the Triassic Period.

triassicambermite

This is not the oldest amber (that’s from the Carboniferous), but it is the oldest fossiliferous amber. Microorganisms have been reported from it before, but this paper records the oldest arthropod inclusions in amber, beating the previous records from the Middle East by some 100 million years. The arthropods are one fly and two mites (one of which is pictured above), with more still to come in future papers.

Some more cool insect preservation papers published this year include:

The original colours of fossil beetles details how preservation of beetle cuticle allows us to reconstruct the colour of fossil beetles – after all, the metallic sheen that some beetles have isn’t due to pigments, but due to the nanostructure of the cuticle playing tricks with the light. THE CONTROLS ON THE PRESERVATION OF STRUCTURAL COLOR IN FOSSIL INSECTS outlines the details of how cuticle preservation affects recovered colour.

WIDESPREAD PYRITIZATION OF INSECTS IN THE EARLY CRETACEOUS JEHOL BIOTA shows that the insects from Jehol – the famous lacustrine fossil locality that has yielded many feathered dinosaurs – are pyritised with the help of bacterial acitvity.


1. On Dorsal Prothoracic Appendages in Treehoppers (Hemiptera: Membracidae) and the Nature of Morphological Evidence. [OA]

helmet

In 2011, Prud’homme et al. published an intriguing paper with developmental and some morphological evidence that the helmet of treehoppers, pictured above, is actually a cooption of an ancestral wing-like structure. This is obviously a very extraordinary claim, and this paper reviews all the evidence and comes up with alternative scenarios that show flaws in the Prud’homme et al. paper. It gets the top spot not only for the subject matter, but also for being a prime example of the scientific method in action.

A morphology-only critique of the Prud’homme et al. paper was done very early in the year by Yoshizawa [OA].


Jump to: Botany; Developmental Biology; Ecology; Environmental; Evolution; Geology; Historical Geology; Human Evolution; Palaeontology; Zoology.





Top Books of 2012: Palaeontology

24 12 2012

Jump to another list: Environmental and Climate Change; Evolution; Historical Geology; History of ScienceHuman Evolution and Anthropology; Zoology

These are my top 10 palaeontology books of the year, running the gamut from historically-oriented books detailing the histories of palaeontological discoveries and of the science of palaeontology to books about now-extinct animals (e.g. dinosaurs). There is one children’s book (about dinosaurs, of course; #10), with most of the books aimed at educated laymen or working biologists; a couple of purely academic books are mixed in too.

  1. Long. The Dawn of the Deed: The Prehistoric Origins of Sex. (University of Chicago Press)
9780226492544_p0_v1_s260x420 I had to debate myself about whether to put this awesome book in the zoology or the palaeontology section, because it is part overview of weird ways animals have sex, and part scientific memoir of Long’s palaeontological research and findings. In the end, the palaeontological stuff wins out, because Long uses his research to illuminate the evolution of sex. In any case, I recommend anyone to read this book just for the quirkiness described in it, and also to see how exceptional finds in palaeontology can give us insights into things we wouldn’t think palaeontology would have a say about.

  1. Falk. The Fossil Chronicles: How Two Controversial Discoveries Changed Our View of Human Evolution. (University of Chicago Press)
full-cover-Falk_Fossil-206x300 A 2012 paperback release of a 2011 hardback, this book is an insider’s account of the scientific and popular controversies of the varying interpretations of the Taung child and of Homo floresiensis. I have a thing for these kinds of books that don’t just talk about the facts, but also give the perspective of the scientist who is working on them, because it gives the best view on how real science evolves and progresses, away from the idealised conceptions of philosophers. This book is an excellent showcase of that, using two prominent fossil cases and described by Falk, whose illustrious career in part revolved around them.

  1. Fastovsky & Weishampel. Dinosaurs: A Concise Natural History. (Cambridge University Press)
dinosaurs-a-concise-natural-history This is the ultimate book for someone who’s not a dinosaur palaeontologist, but is nonetheless interested in the biology and study of dinosaurs. It’s not a textbook, but it’s not some picture guide. It’s a comprehensive overview of what we currently know about dinosaurs, without the niggly anatomical details that a proper textbook like The Dinosauria would have. It also discusses the open questions that we have. In all, a great resource for anyone from the serious amateur to the professor stuck teaching about dinosaurs even though they’re not his/her specialty (it’s happened to me several times).

  1. Sánchez. Embryos in Deep Time: The Rock Record of Biological Development. (University of California Press)
9780520271937 Non-palaeontologists are often surprised at the fact that we have preserved life history stages of various animals – from vertebrates of different ages to the moult stages of trilobites (the majority of trilobite fossils are in fact exoskeletons discarded after moulting). This book exposes them all to show the utility of palaeontology in studying the evolution of development. I was impressed by the phylogenetic breadth it covers, including examples I had no idea about.

  1. Sepkoski. Rereading the Fossil Record: The Growth of Paleobiology as an Evolutionary Discipline. (University of Chicago Press)
rereading-the-fossil-record-the-growth-of-paleobiology-as-an-evolutionary-discipline This book arguably belongs in the history of science list, but I’ll put it here because it’s more relevant to palaeontology as a science. It’s an outline of the history of palaeobiology, the field that combines palaeontology and evolutionary biology, using fossils to study evolution and evolutionary patterns. For a long time, palaeontologists were regarded as irrelevant stamp collectors (it’s a view that still persists among idiotic scientists); palaeobiology turned that over on its head. The book overall is excellent, going from the 19th century to the present; if I had one qualm, it’s what I perceive as a bit of US-centrism, but that may be due to my education in Germany exposing me to palaeontologists who presaged palaeobiology’s development as a field.

  1. Maxwell. Piltdown Man and Other Hoaxes: A book about Lies, Legends, and the Search for the Missing Link. (American Book Publishing)
piltdown-man-other-hoaxes-book-about-lies-legends-jonathan-maxwell-paperback-cover-art A book on scientific hoaxes. It’s not an academic text, just a breeze through some prominent ones, especially those involving palaeontology and cryptozoology. I include it here because of the large section on Piltdown Man.

  1. Berta. Return to the Sea: The Life and Evolutionary Times of Marine Mammals. (University of California Press)
return-to-the-sea-the-life-and-evolutionary-times-of-marine-mammals Arguably a book that should be in the zoology list, I put it here because it discusses the fossil history of cetaceans and pinnipeds and takes a deep time view of everything. Despite its somewhat high price, it’s actually easy-reading and I easily recommend it to the interested layman.

  1. Reynolds & Gallagher. African Genesis: Perspectives on Hominin Evolution. (Cambridge University Press)
african-genesis-perspectives-on-hominin-evolution Please note that there’s a strange screwup with Amazon link above: the title is some weird quantum stuff, but the rest of the page is on this book. This is an academic text containing a comprehensive review of all known hominin fossils and what they tell us about human evolution, as well as current open questions and unknowns. Not easy reading, but if you’re a palaeontologist or palaeoanthropologist looking for the most up-to-date human palaeontology compendium, this is it.

  1. Meredith. Born in Africa: The Quest for the Origins of Human Life. (PublicAffairs)
born-in-africa-the-quest-for-the-origins-of-human-life A 2012 paperback of a 2011 hardback, this is a book bridging history of science with human palaeontology, explaining the history of the major findings in human palaeontology and their implications, and how our views on hominin evolution have evolved in the light of new discoveries. Highly recommended if you’re into human evolution (I’m not, hence the low placing).

  1. Gee & Rey (ill.). A Field Guide to Dinosaurs: The Essential Handbook for Travelers in the Mesozoic. (Chartwell Books)
9780785829027 This is by far the current best dinosaur book for children. It’s got gorgeous illustrations by Luis Rey, one of the top palaeoartists today, it’s as accurate as can be for the intended audience, and the descriptions and information are even usable for middle and high school students. So, in all, if you’re looking for a book to give to a child or teen who’s fascinated by dinosaurs, this is the ultimate one.

Jump to another list: Environmental and Climate Change; Evolution; Historical Geology; History of ScienceHuman Evolution and Anthropology; Zoology





Pikaia: One of the Earliest Chordates

16 10 2012

Pikaiais one of the most celebrated of the Burgess Shale fossils due to its status as one of the earliest chordate (or close to chordate) animals. Originally described as an annelid, it was then reinterpreted as a (stem) cephalochordate by Simon Conway Morris when interest in the Burgess Shale rebounded in the 1970s. Alternative, not highly-supported, interpretations include that it’s more basal than cephalochordates (Simonetta et al., 1999), a protostome (Butterfield, 1990), or a hagfish (Janvier, 1997). Take a look for yourself with the fossils above, from Conway Morris & Caron (2012), by far the most comprehensive review of Pikaia. Read it for any information you want (PDF available on request); I didn’t make this post a full profile of Pikaia for fear of inadvertently plagiarising it! Once you’re done considering, read on.

Pikaia‘s general appearance resembles that of modern-day lancelets, as drawn above (Conway Morris & Caron, 2012), a resemblance reinforced by its small size and fins. Pikaia was ~5cm long and had a collagenous body wall, preserved in the Burgess Shale fossils as a silvery film. A dorsal thread can be seen running along the body, flanked by putative V-shaped muscle blocks; this is interpreted as a notochord or even a combination nerve- and notochord. This notochord and the muscles are key to Pikaia‘s positioning as an early chordate. A pharynx (i.e. a mouth) has been suggested at the anterior end of the animal, based on concentrations of sediment at the interior of the animals there (Shu et al., 1996); if accepted, this further solidifies a chordate interpretation. No eyes have been discovered in any specimen.

Two features separate it from known modern chordates, though. It has a strange organ running down the dorsal trunk, shaped like a sausage and with a possible stabilisatory function (Conway Morris & Caron, 2012). Chordates use the notochord for this, but Pikaia‘s notochord may not have been up to the task yet. It also has a so-called dorsal unit, a sort of head shield. It also has a couple of tentacles on its head, although these can be interpreted as gills. These features are probably apomorphic for Pikaia – after all, just because it’s in the “stem group”, it doesn’t mean it can’t have its own evolutionary quirks (this is a point that needs to be stressed to any beginners in phylogenetics!).

In summary, Pikaia is considered to be a stem-group chordate, probably a derived cephalochordate, based on the presence of a notochord, mytomes (muscles) flanking it, gill slits, and the pharynx. Note: unlike what is written in most popular science articles, Pikaia is not a direct vertebrate ancestor.

It was most probably a suspension or deposit feeder swimming like a blind eel near the benthos, although a burrowing lifestyle can’t be discounted (Holland & Chen, 2001).

If you’re interested in other Cambrian chordates and chordate-likes, check out Yunnanozoon, Cathaymyrus, Haikouichthys, Metaspriggina, and mylokunmingiids.

References:

Butterfield NJ. 1990. Organic preservation of non-mineralizing organisms and the taphonomy of the Burgess Shale. Paleobiology 16, 272-286.

Conway Morris S & Caron J-B. 2012. Pikaia gracilens Walcott, a stem-group chordate from the Middle Cambrian of British Columbia. Biological Reviews 87, 480-512.

Holland ND & Chen JY. 2001. Origin and early evolution of the vertebrates: new insights from advances in molecular biology, anatomy, and palaeontology. Bioessays 23, 142-151.

Janvier P. 1997. The vertebrates before the Silurian. Geobios 30, 931-950.

Shu D-G, Conway Morris S & Zhang X-L. 1996. A Pikaia-like chordate from the Lower Cambrian of China. Nature 384, 157-158.

Simonetta AM, Pucci A & Dzik J. 1999. Hypotheses on the origin and early evolution of chordates in the light of recent zoological and palaeontological evidence. Italian Journal of Zoology 66, 99-119.





The Scientific Method, Exemplified By Palaeontology

30 06 2012

Note: You can read this post over on Cyprus FreeThinkers.

This talk is aimed at the basic, general public level, and is about how science is done through the scientific method, and how to differentiate ideas that belong in the yellow circle downwards from the ideas that are in the nebulous circles outside. To save it from being a very dry, boring, philosophical talk, all introduced concepts will be exemplified using my own science, that of palaeontology.

The talk was organised by the two organisations I’m affiliated with, Cyprus FreeThinkers and Enalia Physis Environmental Research Center, and took place in an impossible-to-find building at the University of Cyprus. Here is the original announcement.

The talk is very simple with only four parts. First is a definition of what science’s aims are. Then we will look at what makes an idea a proper scientific hypothesis, then we’ll see how hypotheses are tested to confirm or reject them. Finally, all we’ve seen will be summarised in order to demonstrate why science has been so successful since its inception.

I took this definition of science’s goals from Carl Hempel‘s excellent 1965 book, Aspects of Scientific Explanation. Science has two goals: to describe and to understand. In other words, the scientist gathers observations (description) and tries to find hypotheses (theoretical understanding) to explain those observations.

Basically, all of science can then be boiled down to why questions. “Why do I observe this, and not that? Because of this hypothesis.” For example: Why do we observe humans alive today, and not Neandertals? Because humans managed to survive the climate changes; or humans killed all the Neandertals; or whatever other hypothesis comes to mind.

As an example of the interplay between observation and hypothesis, consider cetaceans. If you dissect any cetaceans from any species, any gender, and any life cycle stage, you will notice that they all have these tiny bones in their abdomen that don’t have any conceivable function. So as a scientist, you have to ask yourself why they’re there.

So you start hypothesising. Maybe the first hypothesis that comes to your mind is that these bones are just pieces that, for some reason, break off from the spine or the rib. But additional observations don’t match up with that hypothesis: the bones don’t look like spine or rib bones, and they don’t develop that way anyway.

Then you notice the position of the bones and think to yourself that they’re in precisely the spot that hindlimbs would be. So you hypothesise that they’re pubic and femoral bones. The problem with that hypothesis is that they don’t have the proper attachments: they’re not attached to themselves or to the rest of the skeleton, as pubic and femoral bones should be.

But then you notice the size of the bones, and another hypothesis pops into your mind. However, biology using modern organisms will only take you this far. To test your new hypothesis, you need to look at palaeontology.

This hypothesis is that they’re vestigial pubic and femoral bones, i.e. that they got reduced through evolution because they no longer had any use (think of cave fish and how they become blind over evolutionary time). In order to test this hypothesis though, you need to look at the evolutionary history of your taxon, and the only line of evidence that directly preserves the evolutionary history of any taxon is, of course, the fossil record.

The slide summarises the major points of the fossil record; look at this post for some more information. At the beginning, 52 Ma, cetaceans were completely terrestrial dog-like animals. Gradually, they became more and more amphibious and eventually became fully aquatic, as demonstrated by the last common ancestor of the whales, Basilosaurus.

If you look at the hindlimbs, you’ll also notice their evolution: as soon as the animal became aquatic and no longer used the hindlimbs for locomotion, they immediately became small (no doubt because having useless legs flopping around would also be an impediment to the aerodynamics of the animal).

In summary, your hypothesis is now supported by your observations of the fossil record.

Diagram Source: Uhen MD. 2010. The Origin(s) of Whales. Annual Review of Earth and Planetary Sciences 38, 189-219.

Hypotheses can’t just be any idea that plop into your head. They have to fulfil certain criteria. The four most essential ones will be introduced here.

The first criterion is rationality. Your hypothesis has to make sense. I couldn’t think up of an example from real palaeontology that was irrational (creationist poppycock doesn’t count), so I made one up: the hypothesis that trilobites are made of cheese.

This hypothesis makes no sense at all. Cheese is mostly-edible rotten milk. Trilobites are now-extinct arthropods that, when alive, had a calcitic exoskeleton, and are now known only as rocks. Rock that are not made of cheese. The hypothesis simply does not compute. And even if you had to test it, a quick geochemical analysis shows you the chemical composition of your fossilised trilobites. Heck, a taste test could confirm that they’re not made of cheese.

Picture and Analysis Source: Klug C, Schulz H & de Baets K. 2009. Red Devonian Trilobites with Green Eyes from Morocco and the Silicification of the Trilobite Exoskeleton. APP 54, 117-123.

The next criterion for a hypothesis is truth. I don’t want to get into any philosophical wankery about truth is and what truth means; what’s meant here is that your hypothesis has to conform to the most basic factual standards that we have. As an example, I chose a monumental screw-up from Cyprus’s own Ministry of Education.

The pictured page is taken from the new school year’s 7th grade (12-13 year olds) biology textbooks for the public schools, and it brings forward a hypothesis for the origin of modern biodiversity: some dude called Noah built a big boat and brought all organisms on it, to save them from a global flood that lasted 40 days. He then released them. This is, of course, the myth of Noah’s Ark from the Book of Genesis, part of the Christian mythological canon.

This does not conform to the truth criterion for way too many reasons to list. We know that this is nothing more than a fable, plagiarised from earlier fables from the Babylonians and Sumerians (see here). We know that the story is logistically impossible. Building the boat is one story, gathering up all biodiversity is another, and both are as impossible as each other (how did he plan on making sure he got every single bacterium without a microscope?). We know that there was no global flood at any relevant time (there was one large local flood, which was probably the original inspirations for the story). And, most importantly, we have the entire fossil record telling us that the origin of modern biodiversity did not involve a boat, either literal or metaphorical (there was no single center of origin for modern biodiversity).

In other words, the story is complete bunkum and fails as a hypothesis because it completely ignores established fact. If, like any reasonable person, you feel a sense of outrage at such bullshit being taught to 12-13 year olds, feel free to send an e-mail to our ministry of education. Here is my own letter, with personal intro and without personal intro. You can also sign this petition (Greek) that we at Cyprus FreeThinkers set up.

The next criterion is objectivity. What’s meant here is that your hypothesis has to be based on lines of evidence that don’t just come from the subjective melting pot that is your brain. It’s a big problem in palaeontology, given the nature of fossils.

The example shown is that of the Apex Chert “microfossils”. The validity or not of their interpretation is not what’s underscrutiny here, just the strength of this one piece of evidence, taken from one of the original papers where they were presented. See this post for more about them; basically, the Apex Chert comes from a 3.465 Ga locality in Australia with these strange structures preserved in it, and these have been postulated as being the earliest body fossils of microorganisms (they have a mention in every relevant textbook or popular book).

Consider this one piece of evidence for this hypothesis presented up there: pictures (objective evidence) and drawings (subjective). The pictures are fine, even if not very informative. The drawings, however, are not very solid – they are too subjective and show only what Professor Schopf saw in these structures. If I were to draw them, I probably wouldn’t see the same things. As I said, this is a problem in a lot of palaeontology, especially when dealing with such old and enigmatic stuff. The surefire way of supporting your drawings is finding intruments that support your interpretations – pictures, 3D models, geochemicals analyses. But drawings alone are not sufficient, at least not without copious amounts of justification.

Paper: Schopf JW. 1993. Microfossils of the Early Archean Apex Chert: New Evidence of the Antiquity of Life. Science 260, 640-646.

The last criterion is realism. A hypothesis has to be realistic. I couldn’t think of a real palaeontological hypothesis that’s not realistic, so I turned to a notorious lunatic from the internet, Wretch Fossil. I knew him from lurking around Usenet, and he also has a website (the one on the slide is his old domain, doesn’t work anymore).

His MO is rather simple. He looks at thin sections of meteorites and moon rocks, and misinterprets what are basic mineralogical and petrological structures as animal parts (look at the captions in the screenshot up there: neurons, brain tissue, blood vessels, meat).

If Wretch Fossil was smart – a rather difficult thought experiment to go with, but bear with me – then he would have misinterpreted these structures as “microorganisms”, or something similarly vague. That would have fulfilled the minimal standard of realism, since it is not entirely unplausible for biology at a microscopic scale to have happened somewhere else in the universe (I would still call him a crackpot, but someone with an investment in astrobiology might give him some benefit of the doubt).

However, his critical error is saying these structures are animalian – and brain tissue, blood vessels, neurons, and meat are distinctly, autapomorphically animalian structures, not found in any other taxon. The reason is that animals, the Metazoa, are just a single branch of evolution, one of over 50, and it undoubtably originated right here on Earth, as all sources of evidence tell us. Heck, we even have good glimpses of their early fossil record (with major gaps, of course). In other words, postulating that this one single branch of evolution can be found in space is quite simply insane, even if convergent evolution is brought into play.

One thing that you will never see is any sort of minimal boundary for how realistic a hypothesis has to be to be acceptable. The reason is that in science, you never deal with absolutes of certainty, just levels of certainty. This is in contrast to maths, where you do have a concept of proof; in science, all you have are probabilities and likelihoods.

To demonstrate this, look at the four fossils on the slide. The ones on the left and in the middle are very obviously snails, as you can tell from the coiled calcitic shell. In colloquial terms, anyone would say these are “definitely” snails. In purely scientific semantic terms, one would say these are 99.999999% snails, leaving a 0.000001% opening in case future systematic changes disrupt what we currently characterise as “snails” (it happens to even the most iconic groups; think “Reptilia“).

Now look at the two on the right. Above is Acaenoplax from the Silurian Herefordshire locality, described by Sutton et al. (2004) as a relative of the Aplacophora, wormish molluscs without a shell. However, it’s not so hard to reinterpret it as a polychaete worm (Steiner & Salwini-Plawen, 2001). What this means is that you can only say that this is “probably” a mollusc, but not with any higher level of certainty; if you’re confident in your analsis, you would say it’s “likely to be” a mollusc.

The fossil below is pretty much the same story: the Ediacaran Kimberella. Current concensus places it as a bilaterian animal due to the bilateral symmetry of the body fossil. Trace fossils associated with it have allowed a further consensus to form that Kimberella is a stem-group mollusc. However, nobody will say that “Kimberella is definitely a mollusc”, because that wouldn’t be intellectually honest.

Pictures:

Platyceras: Sutton MD, Briggs DEG, Siveter DJ & Siveter DJ. 2006. Fossilized soft tissues in a Silurian platyceratid gastropod. Proc. R. Soc. B 273, 1039-1044.

Acaenoplax: Sutton MD, Briggs DEG, Siveter DJ & Siveter DJ. 2004. Computer reconstruction and analysis of the vermiform mollusc Acaenoplax hayae from the Herefordshire Lagerstätte (Silurian, England), and implications for molluscan phylogeny. Palaeontology 47, 293-318.

Kimberella: Xiao S & Laflamme M. 2009. On the eve of animal radiation: phylogeny, ecology and evolution of the Ediacara biota. TrEE 24, 31-40.

The fact that science only deals with levels of certainty and not in absolute proof underlies what is one of the most powerful concepts of the scientific method: that of falsifiability. For a hypothesis to be considered scientific, it has to be falsifiable, i.e. you must be able to show it to be wrong. By definition, every single hypothesis fulfils this criterion.

To demonstrate it, we’ll look at the anomalocarids, stem-group arthropods characterised by their large eyes, pineapple mouths, and great appendages. They were the very first apex predators back in the Cambrian, and reached a reasonable diversity – we know of three complete body fossils and a dozen or so isolated appendages.

Anyway, up until five years ago, anomalocarids were known only from the usual Cambrian Lagerstätten – Burges, Chengjiang, Sirius Passet. In addition to the fact that a small mass extinction apparently occurred at the end of the Cambrian, it was most reasonable to hypothesise that anomalocarids died out at the end of the Cambrian.

But then this fossil was discovered from the Hunsrück Slates: Schinderhannes bartelsi. The Hunsrück Slates are Devonian in age, having been dopsited 405 Ma – that’s 100 million years after the last anomalocarids of the Burgess Shale. And Schinderhannes is a clear-cut anomalocarid.

Therefore, the hypothesis that anomalocarids died out at the end of the Cambrian has been falsified.

Schinderhannes paper: Kühl G, Briggs DEG & Rust J. 2009. A Great-Appendage Arthropod with a Radial Mouth from the Lower Devonian Hunsrück Slate, Germany. Science 323, 771-773.

The key to falsifying a hypothesis is to always test it. Hypothesis testing is just about what a scientist does all day when working. As an example, imagine you’re digging around in Carboniferous sediments and you find this spectacular insect fossil, which you immediately recognise as a protodonate.

You measure it and notice it’s 70 cm big – the largest insect to have ever lived,a s far as we know. This is a far cry from the largest insects nowadays, which are 16 cm big beetles. So as a scientist, you have to hypothesise about what made these insects grow so large. You know from geochemistry that that the oxygen levels back in the Carboniferous were much higher than today, so you hypothesise that the oxygen levels had something to do with the large size, knowing full well that insects breathe mostly through diffusion because of their tracheal system.

You then have to test this hypothesis, and there are two ways. The first is to look at the fossil record of insects and see if their general size changes correlate with oxygen level changes (they do, roughly). The other way is to apply the uniformitarian principle, that processes happening today are also happening in the past (the laws of physics haven’t changed, etc.). In this case, you can raise insects in artificially oxygen-enhanced atmospheres in the lab (and you notice that theydo get bigger).

From there, you can then hypothesise about how these enormous animals lived. They have strongly-supported veins, so you hypothesise that they were agile predators. Testing this hypothesis can be through modeling (CFD on your computer, scale model, a robot), or by looking for modern analogues and comparing (dragonflies).

For more on gigantism in insects: This post.

Once your hypothesis is tested with positive results, you can the go to a conclusion by inference. There are three types of inference used in science, all of them known since Aristotle and probably from before: deducation, induction, and abduction.

Deduction is when you have a set of statements, and your inference is a logical follow-up to those statements. “Humans are mortals. I’m a human. Therefore I’m mortal,” is the classic example. As long as your statements are true, your deduction will also always be true.

Phacopid source: Fortey RA. 2001. TRILOBITE SYSTEMATICS: THE LAST 75 YEARS. Journal of Paleontology 75, 1141-1151.

Induction is basically prediction based on previously-known facts. The classic example is from the periodic table in chemistry: if you know the properties of calcium and magnesium, you can derive the properties of barium or strontium, for example. Palaeontological examples come a dime a dozen. For example, all known sauropods are enormous (with the exception of island sauropods), so by induction, you can predict that any sauropod you find in the future will also be enormous, and you then infer that gigantism is therefore a sauropod trait.

Size diagram: Sander PM, Christian A, Clauss M, Fechner R, Gee CT, Griebler E-M, Gunga H-C, Hummel J, Mallison H, Perry SF, Preuschoft H, Rauhut OWM, Remes K, Tütken T, Wings O & Witzel U. 2011. Biology of the sauropod dinosaurs: the evolution of gigantism. Biological Reviews 86, 117-155.

Abduction, while also known for a long time, was formalised only at the start of the 20th century by Charles Sanders Peirce. The way it works is if you have an observation that can only be explained by a certain hypothesis, then that hypothesis must be valid by virtue of that observation existing.

The classic example comes from the discovery of the cause of the K-T mass extinction, the one that killed off the non-avian dinosaurs. The picture shows a picture of the Fish Clay layer from Stevns Klint, Denmark. Stevns Klint is a cliff that preserves Cretaceous layers at the bottom and Tertiary layers at the top, with the Fish Clay in between. If you were to do a geochemical analysis of this Fish Clay layer, you’d notice an enormous spike in iridium. Iridium is an element not produced on Earth, only found in space.

The Alvarez father and son team, back in the 1980s, discovered this iridium anomaly in Italian rocks from the K-T boundary and, by abduction, came to the only logical conclusion: that the iridium must have gotten there from space, probably by asteroid impact. A huge controversy ensued, but the abductive inference was solid – and later vindicated with the discovery of the Chicxulub Crater.

While nobody can generalise how science is done with every person and in every lab, what can be done is tracing the ideal way a research project would go through, from the inference standpoint. The first step is to look at what it is you’re researching and, by abduction, think up of all the hypotheses that could possibly explain your observations. You then distill your research observations to the most basic facts and, by deduction, think of what logical conclusions those facts lead you to. This will tell you how to test your hypotheses. Finally, you do the science and test your hypotheses, which will allow you to come to conclusions about whether your hypotheses are right or wrong, by induction.

For example, imagine you’re digging around the Messel pit, and you find a fossil of two turtles arranged in this peculiar position.

You have to think of hypotheses to explain this position, by abduction. Your null hypothesis would be that this is coincidental – they happened to be like this and they died. But then you notice the size difference, and you can hypothesise that maybe this is some kind of social clue: maybe parent-offspring or maybe sexual dimorphism.

By deduction, you distil everything down to statistics, in this case measurements. You find more similar fossils and measure them all. You notice a consistent dimorphism in the tails.

Such dimorphism is a classic, tell-tale sign of sexual dimorphism. And so, by induction, you come to the conclusion that your turtles are representatives of male-female pairs; the one pictured first was probably in the act of copulation, given the position.

Paper: Joyce WG, Micklich N, Schaal SFK & Scheyer TM. in press. Caught in the act: the first record of copulating fossil vertebrates. Biology Letters.

The final point about inferences that one must keep in mind is the nature of the evidence on which inferences are based. The evidence must be relevant. This may be an obvious statement, but it’s an important aspect to keep in mind at all time, especially in palaeontology, where every single fossil has many stories to tell. I don’t mean to be poetic, but it’s true that any palaeontologist worth his salt will be able to tell you amazing narratives based only on a single fossil.

Consider that random ammonite I pulled off the internet, and think of just how much disparate evidence there is in that single shell.

Here’s a small selection. One can get stratigraphical evidence from it – where it was found, and use it to date other layers where it’s present. One can stick it in a synchrotron or µCT and get the detailed structure of the mouthparts. One can place it in the grand scheme of ammonite evolution, or use it to reconstruct the life cycle of its species (in combination with other conspecific fossils), or it can be used to place more detail in the phylogeny of the ammonoids. Finally, its ecological position can be inferred.

But consider what evidence is used to get each of that information. The structure of the mouthparts will inform you about the ecology. The ecology will give you information to enable you to better interpret the stratigraphy. But the stratigraphy will not help you at all with reconstructing the life cycle (stratigraphy deals with geological time, life cycles with biological time). Many life cycles might inform you about evolutionary trends, but the evolutionary trends would never, ever be able to be reconstructed without a solid phylogenetic framework. This framework might use mouthpart information, but it will not help you in interpreting your stratigraphy.

In other words, there is an entire web of evidence, and while there are tentative strings connecting them all, some of these strings are nearly invisible and way too fragile to be used. The very best scientists are the ones who can combine disparate types of evidence in novel ways to come up with innovative concepts.

Diagram sources:

Stratigraphy: Ifrim C & Stinnesbeck W. 2007. Early Turonian ammonites from Vallecillo, north-eastern Mexico: taxonomy, biostratigraphy and palaeobiogeographical significance. Cretaceous Research 28, 642-664.

Ecology: Klug C, Kröger B, Kiessling W, Mullins GL, Servais T, Frýda J, Korn D & Turner S. 2010. The Devonian nekton revolution. Lethaia 43, 465-477.

Mouthparts: Kruta I, Landman N, Rouget I, Cecca F & Tafforeau P. 2011. The role of ammonites in the Mesozoic marine food web revealed by jaw preservation. Science 331, 70-72.

Evolutionary trends: Monnet C, de Baets K & Klug C. 2011. Parallel evolution controlled by adaptation and covariation in ammonoid cephalopods. BMC Evolutionary Biology 11, 115.

Life cycle: Klug C. 2001. Life-cycles of some Devonian ammonoids. Lethaia 34, 215-233.

Phylogeny: Bilotta M. 2010. Aequiloboidea: A new Early Jurassic ammonite superfamily of the Mediterranean Tethys. Geobios 43, 581-604.

What has been said so far are the basic generalities of how the scientific method works in practice. We will now see why those generalities have combined to make such a powerful tool.

The first reason, harkening back to the slide about the goal of science, is that science doesn’t allow for miracles. Everything in science can be explained – that’s the goal of science. Consider this painting of the Baltic Amber forest up there. Nothing there is made up by the artist. The mantophasmatodean in the foreground is known to have lived in the Baltic Amber forest. We know that praying mantises could have been caught in amber resin. We have a fairly good idea that those painted trees could have produced this resin. We know that the Baltic Amber forest was this kind of environment. That lemur whatever animal on the tree, and the emu-like animal in the background, both are known to have existed there.

The existence of these freaky animals in the Baltic Amber forest wasn’t miraculously divined by Richard Bizley, nor did he make them up. We know they were there, due to the application of the scientific method.

Painting: Richard Bizley; to be released in David Penney’s 2013 book, Fossil Insects.

The second reason why science is so successful is because science is self-correcting. Hypotheses and inferences have to be, by definition, falsifiable, so anything in science can potentially be wrong. But the only process that will uncover and correct these “mistakes” is more science.

Consider the stylophorans, a bunch of extinct echinoderms. For a logn time, three hypotheses for their functional morphology and systematic position have been around. The first one (C and b in the diagrams) is that it’s some form of stem-group echnoderm. The second one (B and d) is that it’s a relative of the crinoids. The third (A and c) is that they’re calcichordates, a hypothesised grouping of the Chordata and Echinodermata as sister clades, with the stylophorans being the last common ancestor. This obviously would have an enormous impact on how we view deuterostomian evolution.

The view was tenable and supportable – a notochord in the stalk, and area at the front was occupied by a brain and organs. However, recent fossil finds and associated trace fossils have shown that the proposed morphology and behaviour of the stylophorans isn’t compatible with the fossil record, and so the calcichordate is discarded. Science has corrected itself.

Diagram sources:

Behaviour: Sutcliffe OE, Südkamp WH & Jefferies RPS. 2000. Ichnological evidence on the behaviour of mitrates: two trails associated with the Devonian mitrate Rhenocystis. Lethaia 33, 1-12.

Anatomy: Clausen S & Smith AB. 2005. Palaeoanatomy and biological affinities of a Cambrian deuterostome (Stylophora). Nature 438, 351-354.

Stylophoran: Smith AB. 2005. The pre-radial history of echinoderms. Geological Journal 40, 255-280.

A natural consequence of the self-correcting property of science is that science is always evolving by discovering new things or reworking old knowledge. Science will never, ever be static, by definition.

For example, consider the origin of birds. It’s something that biology with extant organisms could never, ever throw light on. But the discovery of Archaeopteryx (and other theropods) and its correct interpretation provided a huge revolution in the study of both birds and dinosaurs.

In the past couple of decades, China has proven itself to be the most exciting place for palaeontology, in no small part due to the amazingly-preserved feathered dinosaurs found there (many more unpublished fossils still lie in archives or undiscovered).

Zhongjianornis source: Zhou Z & Li FZZ. 2010. A new Lower Cretaceous bird from China and tooth reduction in early avian evolution. Proc. R. Soc. B 277, 219-227.

Eoconfuciusornis source: Zhang F, Zhou Z & Benton MJ. 2008. A primitive confuciusornithid bird from China and its implications for early avian flight. Science in China D 51, 625-639.

Confuciusornis source: Benton MJ, Zhongzhe Z, Orr PJ, Fucheng Z & Kearns SL. 2008. The remarkable fossils from the Early Cretaceous Jehol Biota of China and how they have changed our knowledge of Mesozoic life: Presidential Address, delivered 2nd May 2008. Proceedings of the Geologists’ Association 119, 209-228.

These new, spectacular fossils give us unprecendented insights into the early evolution of birds, not only among themselves (as in the phylogeny above), but also their evolution from their theropodan ancestors. This is how science always advances – the individual steps are incremental (individual fossil finds), but gathered together, you get an ever-shifting landscape of discoveries.

Phylogeny source: Padian K & de Ricqlès A. 2009. L’origine et l’évolution des oiseaux: 35 années de progrès. Comptes Rendus Palévol 8, 257-280.

And finally, the final reason why science has been so successful is precisely because it’s been successful. A tautology, but it’s true. Think of every single advancement in the history of human culture. Now I challenge you to name one that wasn’t the result of science (even before the scientific method was formalised, science existed on the intuitive scale).

That’s right. You can’t name one. The agriculture revolution, from the Middle Ages to today – all the work of science. The medical revolutions, all the work of science (and the wrong ones, all corrected by science). The technological revolutions, again, all brought forward by science. The fact that you can read this post is purely because of science, nothing else.

And I’ll take this one step further. Any modern scientific revolutions would not have been possible without the application of the scientific method in palaeontology. The reason is oil. No matter what your stance on environmentalism is, the there’s no use denying that our entire world runs on oil. If you want to deny that, shun the use of plastics (including medicinal products and apparatus). Don’t live in a building, since buildings are all built with oil-run machines. Just go into a cave and live as a hermit.

Oil is all micropalaeontology, not just in its composition, but in prospecting for oil. Long gone are the days when you can dig an oil well with a shovel – we’ve exhausted all of those. Now, all the oil is wither buried deep, or well-hidden. And the only way to get to it is by trusting a micropalaeontologist to use the inferential methods outlined earlier to properly get the layout of the underground, and guide the drill straight into the oil reservoir. Otherwise, he’s cost the oil company millions of dollars, and is doomed to a future of selling hot dogs.

Foraminifera: Husinec A & Sokač B. 2006. Early Cretaceous benthic associations (foraminifera and calcareous algae) of a shallow tropical-water platform environment (Mljet Island, southern Croatia). Cretaceous Research 27, 418-441.

That does it for the talk. Just a bit of advertising for me – you can help me in applying the scientific method, by helping support my research project on Petridish.org. Share it around your social networks, and consider donating if you can! See here for more scientific background info.








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